---
# System prepended metadata

title: Spot check duplicated regions
tags: [OMM]

---

---
title: Spot check duplicated regions
tags: OMM
description: Personal hackmd notes
image: https://partechshaker.com/wp-content/uploads/2018/10/logo_square.png
robots: noindex, nofollow
GA: UA-165598729-1
---

---

[TOC]

---

Spot check duplicated regions
===

Extract coordinates of one region
---

Region 1 (transposase)
----

Duplicated region is on 1411179 to 1413329. Exported bed file of this region to `/net/sgi/oligomm_ab/OligoMM-report/IGV_files/`. Exported using [bedtools getfasta](https://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html)

`region.bed` (tab delim)
```
B_caecimuris	1411179	1413329
```

```bash!
bedtools getfasta -fi ../databases/omm_new/joined_reference_curated.fasta -bed region.bed > duplicated_sequence.fasta
```

```!
>B_caecimuris:1411179-1413329
aaatagtacccattttttactctgtttgcttttgtatgtcattggattttagtatatttacattgttggaaaatttaaagtcgattgacccactattatactctaaattgacccatcaaaaaaatattagatttaaataaagaaaaatgcattttaacccgggtcattttcaattataataatctacaatatatactatttctttttagcattaatctttcttacagaatccccggtaagttcaatcttgtgtgctgtatgtacaattctgtccaggattgcgtcagctactgtaggatcaccaattgcatcataccggctttcgacaggaagttgtgatgttattatgattgattttaatccgtgtctgtcttctattatttccataaggattgacctttccctggcatccagtcctataagaaacagatcgtcaagaatcagcagttgacacttttctatttttttcatctcagattctatagtgcccttgtttttggcaattttaagctgtcccataagctttgacgcatttgaatacaaagtctttattccattcttacatgcctcatatcctatggctgaagctatatagcttttacctgtaccggagcttcccgtgatgaaaacattctgtccgtctcttataaaatcaagagatgcaagtctctcaagctggttacggtcaaggttacgttttatggtatagtctattttttccatatatgccttatatctgaagtttgcagactttatcagtctctcaatgcttacattgcgtctgtaatcatattcgctttcaagaagccatttaagaaactcatcgtttgtcataccatcagaggatgtggtcctgcagtcatttctatatgtttcaagcataccgtaaaaacgtaacttggagagtagttccattattctgtccatattttttccgacagttctgcttgttttattattacttgtcatttttatccatgtttttagagttaaaataatccttgcctctgagatttctgtgtttgggggtaagttctggagcctgtccctccatctgtacatgatacttctcatcttccctgtttaccagaatactttcaagttcgttgtatccgaacataccgaattccattgccacctgacatgaaagaaccaccctgtcatgtccgaaacgctccacaagacttaatatgccatcggctgaacgtacggcctggaccggatatttcttggcaacggccacacgctttatgtactcttccaataccggatcaattccacatgccttgcggtatatatcatccattctgattctgtattcatgtggcactcccgaaagtttgtgggacggtttttctgaataagtgaaaggtgtatcatcctttcgatgtgtcgttatgtgtctgaacttatgatatatctccactgtgtccccatcatacagtaattctacagtatcgccgatatactctttaggaacactgtaatagtgattgttaagcgatacataactgtttctcatgacagttgccgttttccggctttttgatataaattttgttgccggcaatgtatgcagcctgtctttctcgacttcgaggaaacgttcccgacggctgtagttgcgattgtacatctttcggctgttcaacgcatccgtatgcttcattatttctatgttcaaggcttcaagatcattgaatttcaatcccgtcatctttgaatacacctccctgtagagcagtcttacagcattctcaaccagagctttgtctttaggctttcgtactcttgccgggaagacaacacatccataatggtctgcaaatgcagcaaagtcgtcattgattacaggttcaacacctccaggctttgttacggctgatctcaggttgtctggaactatggcattggggacacctccaaaataatggaaagcattttcacatgcctggataaggtgttctttcttttgtgatggtacagcctcgtaataggtaatctggctgcatggaagtatggcggcaaatacttctacgggaaccttattgcctgttctttcgtatgagagataaagtttgtcaccggcaaaatccacatacatctgatcaccggctatatgatctatgcgtccaacaggactctttact
```

Align this region to reference `databases/omm_new/joined_reference_curated.fasta`

```bash!
bowtie2 -x /net/sgi/oligomm_ab/OligoMM-report/databases/omm_new/joined_reference_curated -f IGV_files/duplicated_sequence.fasta -S IGV_files/region1.sam
```

```
1 reads; of these:
  1 (100.00%) were unpaired; of these:
    0 (0.00%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    1 (100.00%) aligned >1 times
100.00% overall alignment rate
```

> By default, bowtie2 searches for distinct, valid alignments for each read. When it finds a valid alignment, it continues looking for alignments that are nearly as good or better. The best alignment found is reported (randomly selected from among best if tied).

so we run it with `--no-contain -a --no-mixed` to obtain more than one mapping region

```bash!
bowtie2 -x /net/sgi/oligomm_ab/OligoMM-report/databases/omm_new/joined_reference_curated -f IGV_files/duplicated_sequence.fasta -S IGV_files/region1.sam --no-contain -a --no-mixed
```

And the `IGV_files/region1.sam` show 7 valid mapping locations all on the same contig:

![](https://i.imgur.com/NusV5uG.png)

## Mauve on all genomes in OMM set

![](https://i.imgur.com/CmeyPR9.png)

However, export of Mauve seems not working, testing out other approaches.

## Mummer

```bash
cd /home/aime/projects/oligomm-claudia
mkdir mummer && cd mummer
wget https://github.com/mummer4/mummer/releases/download/v4.0.0beta2/mummer-4.0.0beta2.tar.gz
tar xvzf mummer-4.0.0beta2.tar.gz
cd mummer-4.0.0beta2

./configure
make
sudo make install
mummer -h
```

Manual at https://github.com/mummer4/mummer/blob/master/MANUAL.md

```bash!

nucmer ../../databases/omm_new/joined_reference_curated.fasta ../../databases/omm_new/C_innocuum_I46.fasta -p C_innocuum_I46    
show-coords C_innocuum_I46.delta -w -o

show-diff C_innocuum_I46.delta
```

example output of `show-diff C_innocuum_I46.delta`


>  Outputs a list of structural differences for each sequence in
the reference and query, sorted by position. For a reference
sequence R, and its matching query sequence Q, differences are
categorized as GAP (gap between two mutually consistent alignments),
DUP (inserted duplication), BRK (other inserted sequence), JMP
(rearrangement), INV (rearrangement with inversion), SEQ
(rearrangement with another sequence). The first five columns of
the output are seq ID, feature type, feature start, feature end,
and feature length. Additional columns are added depending on the
feature type. Negative feature lengths indicate overlapping adjacent
alignment blocks.

> This program classifies alignment breakpoints for the quantification of macroscopic differences between two genomes. It takes a standard, unfiltered delta file as input, determines the best mapping between the two sequence sets, and reports on the breaks in that mapping.

```
IDR GAP gap-start gap-end gap-length-R gap-length-Q gap-diff
IDR DUP dup-start dup-end dup-length
IDR BRK gap-start gap-end gap-length
IDR JMP gap-start gap-end gap-length
IDR INV gap-start gap-end gap-length
IDR SEQ gap-start gap-end gap-length prev-sequence next-sequence
```

From meeting with Eric: `BRK` seems to be the sequence before/after the break and unintersting for us (since the use case for Mummer is for strain comparison). So only column `DUP` is interesting for us.

```
$show-diff test/Cin.delta | xclip -i -selection clipboard
/home/aime/projects/oligomm-claudia/databases/omm_new/joined_reference_curated.fasta /home/aime/projects/oligomm-claudia/databases/omm_new/C_innocuum_I46.fasta
NUCMER

[SEQ]	[TYPE]	[S1]	[E1]	[LEN 1]
Acutalibacter_muris	BRK	1	3406851	3406851
Acutalibacter_muris	DUP	3406852	3407744	893
Acutalibacter_muris	BRK	3407745	3802913	395169
Blautia_coccoides	BRK	1	1237502	1237502
Blautia_coccoides	DUP	1237503	1239438	1936
Blautia_coccoides	BRK	1239439	1410980	171542
Blautia_coccoides	DUP	1410981	1411521	541
Blautia_coccoides	BRK	1411522	5128582	3717061
Clostridioforme	BRK	1	3951294	3951294
Clostridioforme	DUP	3951295	3951472	178
Clostridioforme	DUP	3951296	3953537	2242
Clostridioforme	BRK	3953538	3958272	4735
Clostridioforme	DUP	3958273	3958492	220
Clostridioforme	BRK	3958493	5416939	1458447
Clostridioforme	DUP	5416940	5421324	4385
Clostridioforme	BRK	5421325	6123472	702148
Clostridioforme	DUP	6123473	6123642	170
Clostridioforme	BRK	6123643	7157610	1033968
Muribaculum_intestinale	BRK	1	3306967	3306967
Muribaculum_intestinale	DUP	3306968	3307069	102
```


However, `show-coords` output seem to be similar, not sure what are the differnces exaclty?

```
$  show-coords test/Cin.delta | xclip -i -selection clipboard 
```

Open _details_ to see large file
:::spoiler

```
    [S1]     [E1]  |     [S2]     [E2]  |  [LEN 1]  [LEN 2]  |  [% IDY]  | [TAGS]
=====================================================================================
       1  4469084  |        1  4469084  |  4469084  4469084  |   100.00  | Clostridium_innocuum	Clostridium_innocuum
   37000    37732  |  3640005  3639271  |      733      735  |    89.52  | Clostridium_innocuum	Clostridium_innocuum
   39423    41073  |  3637673  3636020  |     1651     1654  |    92.26  | Clostridium_innocuum	Clostridium_innocuum
   39423    41061  |  1487976  1486335  |     1639     1642  |    93.61  | Clostridium_innocuum	Clostridium_innocuum
   39423    41053  |  3248872  3247242  |     1631     1631  |    90.32  | Clostridium_innocuum	Clostridium_innocuum
   79146    79568  |  1252622  1252201  |      423      422  |    99.05  | Clostridium_innocuum	Clostridium_innocuum
  104939   105753  |   650018   649205  |      815      814  |    85.12  | Clostridium_innocuum	Clostridium_innocuum
  104941   105740  |  2146199  2145398  |      800      802  |    83.83  | Clostridium_innocuum	Clostridium_innocuum
  129616   129979  |  2036278  2035915  |      364      364  |    99.45  | Clostridium_innocuum	Clostridium_innocuum
  236448   236616  |  2639811  2639643  |      169      169  |    94.08  | Clostridium_innocuum	Clostridium_innocuum
  236785   236887  |   584147   584045  |      103      103  |   100.00  | Clostridium_innocuum	Clostridium_innocuum
  236886   238278  |  2412253  2410861  |     1393     1393  |    99.86  | Clostridium_innocuum	Clostridium_innocuum
  236886   238278  |  2639373  2637981  |     1393     1393  |    99.28  | Clostridium_innocuum	Clostridium_innocuum
  241359   241713  |  2407916  2407586  |      355      331  |    92.68  | Clostridium_innocuum	Clostridium_innocuum
  343208   343568  |  3266878  3266522  |      361      357  |    96.95  | Clostridium_innocuum	Clostridium_innocuum
  352727   352898  |  3375830  3375659  |      172      172  |    88.95  | Clostridium_innocuum	Clostridium_innocuum
  370683   371495  |   383901   383089  |      813      813  |    99.38  | Clostridium_innocuum	Clostridium_innocuum
  370687   371475  |  2146179  2145391  |      789      789  |    85.17  | Clostridium_innocuum	Clostridium_innocuum
  370688   371574  |   649995   649111  |      887      885  |    83.60  | Clostridium_innocuum	Clostridium_innocuum
  370687   371486  |  1613773  1612974  |      800      800  |    85.27  | Clostridium_innocuum	Clostridium_innocuum
  371368   371504  |   383079   382943  |      137      137  |    98.54  | Clostridium_innocuum	Clostridium_innocuum
  383089   383901  |   371495   370683  |      813      813  |    99.38  | Clostridium_innocuum	Clostridium_innocuum
  383769   383924  |   370677   370522  |      156      156  |    98.09  | Clostridium_innocuum	Clostridium_innocuum
  432119   433906  |  2887872  2886085  |     1788     1788  |    99.83  | Clostridium_innocuum	Clostridium_innocuum
  432121   433907  |  1939454  1937668  |     1787     1787  |    99.89  | Clostridium_innocuum	Clostridium_innocuum
  443901   445698  |  1903722  1901924  |     1798     1799  |    99.83  | Clostridium_innocuum	Clostridium_innocuum
  443906   445693  |  3165444  3163656  |     1788     1789  |    99.94  | Clostridium_innocuum	Clostridium_innocuum
  562366   564120  |  2412615  2410861  |     1755     1755  |    99.77  | Clostridium_innocuum	Clostridium_innocuum
  574892   575057  |  4202779  4202614  |      166      166  |   100.00  | Clostridium_innocuum	Clostridium_innocuum
  584045   584147  |   236887   236785  |      103      103  |   100.00  | Clostridium_innocuum	Clostridium_innocuum
  649205   650018  |   105753   104939  |      814      815  |    85.12  | Clostridium_innocuum	Clostridium_innocuum
  702391   702844  |  2578323  2577846  |      454      478  |    87.03  | Clostridium_innocuum	Clostridium_innocuum
  735357   737142  |  1939454  1937669  |     1786     1786  |    99.94  | Clostridium_innocuum	Clostridium_innocuum
  735355   737142  |  2887872  2886085  |     1788     1788  |    99.78  | Clostridium_innocuum	Clostridium_innocuum
  743331   745085  |  1746527  1744772  |     1755     1756  |    99.49  | Clostridium_innocuum	Clostridium_innocuum
  743334   745085  |  1024096  1022345  |     1752     1752  |    99.77  | Clostridium_innocuum	Clostridium_innocuum
  747132   747404  |   851433   851160  |      273      274  |    95.99  | Clostridium_innocuum	Clostridium_innocuum
  841624   842073  |  2578313  2577846  |      450      468  |    87.23  | Clostridium_innocuum	Clostridium_innocuum
  851160   851433  |   747404   747132  |      274      273  |    95.99  | Clostridium_innocuum	Clostridium_innocuum
 1022343  1024096  |  3044228  3042474  |     1754     1755  |    99.54  | Clostridium_innocuum	Clostridium_innocuum
 1022345  1024096  |   745085   743334  |     1752     1752  |    99.77  | Clostridium_innocuum	Clostridium_innocuum
 1023857  1024096  |   584046   583807  |      240      240  |   100.00  | Clostridium_innocuum	Clostridium_innocuum
 1023858  1024098  |   573406   573166  |      241      241  |    99.59  | Clostridium_innocuum	Clostridium_innocuum
 1022345  1024098  |  1802632  1800878  |     1754     1755  |    99.60  | Clostridium_innocuum	Clostridium_innocuum
 1231365  1231504  |  2034465  2034326  |      140      140  |    97.14  | Clostridium_innocuum	Clostridium_innocuum
 1237205  1239156  |  1675607  1673656  |     1952     1952  |    98.00  | Clostridium_innocuum	Clostridium_innocuum
 1239015  1239154  |  1231504  1231365  |      140      140  |    97.14  | Clostridium_innocuum	Clostridium_innocuum
 1251152  1252621  |  2472388  2470940  |     1470     1449  |    97.55  | Clostridium_innocuum	Clostridium_innocuum
 1251153  1252621  |  3947639  3946191  |     1469     1449  |    92.85  | Clostridium_innocuum	Clostridium_innocuum
 1251153  1252622  |  3951009  3949560  |     1470     1450  |    97.48  | Clostridium_innocuum	Clostridium_innocuum
 1251154  1252624  |  1264719  1263250  |     1471     1470  |    92.67  | Clostridium_innocuum	Clostridium_innocuum
 1251154  1252621  |  2328923  2327476  |     1468     1448  |    92.92  | Clostridium_innocuum	Clostridium_innocuum
 1251851  1252621  |  4468984  4468214  |      771      771  |    97.15  | Clostridium_innocuum	Clostridium_innocuum
 1252201  1252622  |    79568    79146  |      422      423  |    99.05  | Clostridium_innocuum	Clostridium_innocuum
 1263250  1264719  |  1252624  1251154  |     1470     1471  |    92.67  | Clostridium_innocuum	Clostridium_innocuum
 1293617  1297262  |  3597352  3593708  |     3646     3645  |    90.45  | Clostridium_innocuum	Clostridium_innocuum
 1298550  1299860  |  3592331  3591021  |     1311     1311  |    90.78  | Clostridium_innocuum	Clostridium_innocuum
 1301902  1304875  |  3589426  3586453  |     2974     2974  |    98.72  | Clostridium_innocuum	Clostridium_innocuum
 1307136  1312128  |  3585210  3580230  |     4993     4981  |    82.52  | Clostridium_innocuum	Clostridium_innocuum
 1312975  1313835  |  3579404  3578544  |      861      861  |    83.33  | Clostridium_innocuum	Clostridium_innocuum
 1323918  1324105  |  3570362  3570178  |      188      185  |    84.13  | Clostridium_innocuum	Clostridium_innocuum
 1324785  1326773  |  3569496  3567507  |     1989     1990  |    92.38  | Clostridium_innocuum	Clostridium_innocuum
 1436799  1436902  |  4212099  4211996  |      104      104  |    99.04  | Clostridium_innocuum	Clostridium_innocuum
 1436799  1436909  |  1899631  1899521  |      111      111  |    95.50  | Clostridium_innocuum	Clostridium_innocuum
 1463710  1464016  |  3551157  3550860  |      307      298  |    86.17  | Clostridium_innocuum	Clostridium_innocuum
 1463710  1464016  |  4286109  4285812  |      307      298  |    87.62  | Clostridium_innocuum	Clostridium_innocuum
 1486344  1487976  |  3075989  3074357  |     1633     1633  |    92.11  | Clostridium_innocuum	Clostridium_innocuum
 1486335  1487976  |    41061    39423  |     1642     1639  |    93.61  | Clostridium_innocuum	Clostridium_innocuum
 1486345  1489503  |  2372099  2368940  |     3159     3160  |    93.83  | Clostridium_innocuum	Clostridium_innocuum
 1486333  1487976  |  1771751  1770107  |     1644     1645  |    93.86  | Clostridium_innocuum	Clostridium_innocuum
 1673656  1675607  |  1239156  1237205  |     1952     1952  |    98.00  | Clostridium_innocuum	Clostridium_innocuum
 1673657  1675610  |  2034466  2032521  |     1954     1946  |    97.45  | Clostridium_innocuum	Clostridium_innocuum
 1673652  1675610  |  2137134  2135153  |     1959     1982  |    96.42  | Clostridium_innocuum	Clostridium_innocuum
 1675609  1677057  |  2328924  2327476  |     1449     1449  |    93.93  | Clostridium_innocuum	Clostridium_innocuum
 1675609  1677060  |  4291981  4290530  |     1452     1452  |    99.93  | Clostridium_innocuum	Clostridium_innocuum
 1675610  1677058  |  2472386  2470939  |     1449     1448  |    99.86  | Clostridium_innocuum	Clostridium_innocuum
 1675610  1677057  |  3951008  3949561  |     1448     1448  |    99.93  | Clostridium_innocuum	Clostridium_innocuum
 1675610  1677057  |  3947638  3946191  |     1448     1448  |    93.86  | Clostridium_innocuum	Clostridium_innocuum
 1675715  1676529  |    80490    79676  |      815      815  |    91.66  | Clostridium_innocuum	Clostridium_innocuum
 1676287  1677057  |  4468984  4468214  |      771      771  |    96.37  | Clostridium_innocuum	Clostridium_innocuum
 1676637  1677057  |    79568    79147  |      421      422  |    98.82  | Clostridium_innocuum	Clostridium_innocuum
 1677058  1677132  |  2032529  2032455  |       75       75  |    98.67  | Clostridium_innocuum	Clostridium_innocuum
 1680693  1681030  |  3244881  3244544  |      338      338  |    93.79  | Clostridium_innocuum	Clostridium_innocuum
 1722532  1722808  |  3530140  3529865  |      277      276  |    94.58  | Clostridium_innocuum	Clostridium_innocuum
 1744770  1746526  |  3942290  3940535  |     1757     1756  |    99.54  | Clostridium_innocuum	Clostridium_innocuum
 1744757  1744939  |   333046   332867  |      183      180  |    98.36  | Clostridium_innocuum	Clostridium_innocuum
 1744771  1746525  |  3475307  3473554  |     1755     1754  |    99.72  | Clostridium_innocuum	Clostridium_innocuum
 1744771  1744937  |   585696   585530  |      167      167  |   100.00  | Clostridium_innocuum	Clostridium_innocuum
 1744771  1746528  |  1802633  1800875  |     1758     1759  |    99.94  | Clostridium_innocuum	Clostridium_innocuum
 1744810  1746182  |   574881   573509  |     1373     1373  |   100.00  | Clostridium_innocuum	Clostridium_innocuum
 1744772  1746524  |  3044226  3042474  |     1753     1753  |    99.94  | Clostridium_innocuum	Clostridium_innocuum
 1744772  1746524  |  4219583  4217831  |     1753     1753  |    99.32  | Clostridium_innocuum	Clostridium_innocuum
 1746286  1746526  |   331384   331144  |      241      241  |   100.00  | Clostridium_innocuum	Clostridium_innocuum
 1744772  1746527  |   745085   743331  |     1756     1755  |    99.49  | Clostridium_innocuum	Clostridium_innocuum
 1748276  1750029  |  4120763  4119010  |     1754     1754  |    99.83  | Clostridium_innocuum	Clostridium_innocuum
 1767803  1768415  |  3251076  3250464  |      613      613  |    85.67  | Clostridium_innocuum	Clostridium_innocuum
 1770107  1771740  |  3248872  3247240  |     1634     1633  |    91.06  | Clostridium_innocuum	Clostridium_innocuum
 1770107  1771751  |  1487976  1486333  |     1645     1644  |    93.86  | Clostridium_innocuum	Clostridium_innocuum
 1770107  1771743  |  3637673  3636038  |     1637     1636  |    92.85  | Clostridium_innocuum	Clostridium_innocuum
 1772787  1772864  |  1795872  1795795  |       78       78  |   100.00  | Clostridium_innocuum	Clostridium_innocuum
 1795795  1795872  |  1772864  1772787  |       78       78  |   100.00  | Clostridium_innocuum	Clostridium_innocuum
 1800875  1802633  |  1746528  1744771  |     1759     1758  |    99.94  | Clostridium_innocuum	Clostridium_innocuum
 1872687  1874666  |   616002   614023  |     1980     1980  |    99.34  | Clostridium_innocuum	Clostridium_innocuum
 1872687  1874666  |  4003662  4001683  |     1980     1980  |    99.34  | Clostridium_innocuum	Clostridium_innocuum
 1872687  1872813  |   616139   616013  |      127      127  |   100.00  | Clostridium_innocuum	Clostridium_innocuum
 1937668  1939454  |   433907   432121  |     1787     1787  |    99.89  | Clostridium_innocuum	Clostridium_innocuum
 1937669  1939454  |   737142   735357  |     1786     1786  |    99.94  | Clostridium_innocuum	Clostridium_innocuum
 2032455  2032529  |  1677132  1677058  |       75       75  |    98.67  | Clostridium_innocuum	Clostridium_innocuum
 2032521  2034466  |  1675610  1673657  |     1946     1954  |    97.45  | Clostridium_innocuum	Clostridium_innocuum
 2034326  2034465  |  1231504  1231365  |      140      140  |    97.14  | Clostridium_innocuum	Clostridium_innocuum
 2035915  2036278  |   129979   129616  |      364      364  |    99.45  | Clostridium_innocuum	Clostridium_innocuum
 2061085  2061195  |  2223479  2223369  |      111      111  |    93.69  | Clostridium_innocuum	Clostridium_innocuum
 2099398  2100271  |  2243385  2242512  |      874      874  |    97.60  | Clostridium_innocuum	Clostridium_innocuum
 2099427  2100251  |  3467729  3466905  |      825      825  |    90.31  | Clostridium_innocuum	Clostridium_innocuum
 2099410  2100271  |  3276602  3275741  |      862      862  |    89.48  | Clostridium_innocuum	Clostridium_innocuum
 2135153  2137134  |  1675610  1673652  |     1982     1959  |    96.42  | Clostridium_innocuum	Clostridium_innocuum
 2217821  2217916  |  3746130  3746035  |       96       96  |    95.83  | Clostridium_innocuum	Clostridium_innocuum
 2217821  2217983  |  4113548  4113386  |      163      163  |    98.77  | Clostridium_innocuum	Clostridium_innocuum
 2217816  2217983  |   343573   343406  |      168      168  |    97.62  | Clostridium_innocuum	Clostridium_innocuum
 2217821  2217983  |  4235599  4235437  |      163      163  |    97.55  | Clostridium_innocuum	Clostridium_innocuum
 2242380  2243414  |  2799280  2798221  |     1035     1060  |    90.85  | Clostridium_innocuum	Clostridium_innocuum
 2242512  2242760  |  2100868  2100621  |      249      248  |    93.60  | Clostridium_innocuum	Clostridium_innocuum
 2242512  2243385  |  2100271  2099398  |      874      874  |    97.60  | Clostridium_innocuum	Clostridium_innocuum
 2242536  2243353  |  4384925  4384108  |      818      818  |    91.69  | Clostridium_innocuum	Clostridium_innocuum
 2253484  2253683  |  4411320  4411121  |      200      200  |    95.50  | Clostridium_innocuum	Clostridium_innocuum
 2295618  2297379  |  4120773  4119010  |     1762     1764  |    99.72  | Clostridium_innocuum	Clostridium_innocuum
 2295628  2297380  |  3475306  3473553  |     1753     1754  |    99.94  | Clostridium_innocuum	Clostridium_innocuum
 2327476  2328924  |  1677057  1675609  |     1449     1449  |    93.93  | Clostridium_innocuum	Clostridium_innocuum
 2368940  2372099  |  3250392  3247242  |     3160     3151  |    91.31  | Clostridium_innocuum	Clostridium_innocuum
 2368940  2372099  |  1489503  1486345  |     3160     3159  |    93.83  | Clostridium_innocuum	Clostridium_innocuum
 2368940  2372099  |  3639200  3636043  |     3160     3158  |    93.35  | Clostridium_innocuum	Clostridium_innocuum
 2369213  2369507  |  3212063  3211769  |      295      295  |    99.32  | Clostridium_innocuum	Clostridium_innocuum
 2407586  2407916  |   241713   241359  |      331      355  |    92.68  | Clostridium_innocuum	Clostridium_innocuum
 2407790  2410720  |   567190   564260  |     2931     2931  |    99.97  | Clostridium_innocuum	Clostridium_innocuum
 2407790  2410720  |   241348   238418  |     2931     2931  |    99.97  | Clostridium_innocuum	Clostridium_innocuum
 2407585  2412618  |  4103577  4098545  |     5034     5033  |    99.62  | Clostridium_innocuum	Clostridium_innocuum
 2410861  2412253  |   238278   236886  |     1393     1393  |    99.86  | Clostridium_innocuum	Clostridium_innocuum
 2410861  2412615  |   564120   562366  |     1755     1755  |    99.77  | Clostridium_innocuum	Clostridium_innocuum
 2412521  2412618  |   236618   236521  |       98       98  |    96.94  | Clostridium_innocuum	Clostridium_innocuum
 2446342  2446605  |  3641083  3640820  |      264      264  |    96.59  | Clostridium_innocuum	Clostridium_innocuum
 2470939  2472386  |  1677058  1675610  |     1448     1449  |    99.86  | Clostridium_innocuum	Clostridium_innocuum
 2470940  2472388  |  1252621  1251152  |     1449     1470  |    97.55  | Clostridium_innocuum	Clostridium_innocuum
 2509085  2510854  |  4120773  4119004  |     1770     1770  |    99.60  | Clostridium_innocuum	Clostridium_innocuum
 2510609  2510848  |   573406   573167  |      240      240  |   100.00  | Clostridium_innocuum	Clostridium_innocuum
 2509084  2510858  |  1802646  1800871  |     1775     1776  |    99.38  | Clostridium_innocuum	Clostridium_innocuum
 2577846  2578313  |   842073   841624  |      468      450  |    87.23  | Clostridium_innocuum	Clostridium_innocuum
 2577846  2578323  |   702844   702391  |      478      454  |    87.03  | Clostridium_innocuum	Clostridium_innocuum
 2634649  2635036  |   567590   567200  |      388      391  |    98.47  | Clostridium_innocuum	Clostridium_innocuum
 2634703  2639764  |  4103578  4098519  |     5062     5060  |    99.41  | Clostridium_innocuum	Clostridium_innocuum
 2634705  2635035  |   241713   241359  |      331      355  |    92.39  | Clostridium_innocuum	Clostridium_innocuum
 2635036  2637839  |   567063   564260  |     2804     2804  |    99.96  | Clostridium_innocuum	Clostridium_innocuum
 2635035  2637839  |   241222   238418  |     2805     2805  |    99.96  | Clostridium_innocuum	Clostridium_innocuum
 2637981  2639764  |   564120   562338  |     1784     1783  |    98.65  | Clostridium_innocuum	Clostridium_innocuum
 2637981  2639373  |   238278   236886  |     1393     1393  |    99.28  | Clostridium_innocuum	Clostridium_innocuum
 2639643  2639811  |   236616   236448  |      169      169  |    94.08  | Clostridium_innocuum	Clostridium_innocuum
 2698252  2700225  |  3318245  3316272  |     1974     1974  |    99.95  | Clostridium_innocuum	Clostridium_innocuum
 2698252  2700221  |  3954040  3952071  |     1970     1970  |    99.95  | Clostridium_innocuum	Clostridium_innocuum
 2798221  2799280  |  2243414  2242380  |     1060     1035  |    90.85  | Clostridium_innocuum	Clostridium_innocuum
 2798283  2799104  |  3467726  3466905  |      822      822  |    90.88  | Clostridium_innocuum	Clostridium_innocuum
 2798295  2799124  |  3276570  3275741  |      830      830  |    90.60  | Clostridium_innocuum	Clostridium_innocuum
 2886085  2887872  |   433906   432119  |     1788     1788  |    99.83  | Clostridium_innocuum	Clostridium_innocuum
 2916757  2917173  |  2939721  2939365  |      417      357  |    83.45  | Clostridium_innocuum	Clostridium_innocuum
 2916956  2917826  |  3036175  3035305  |      871      871  |    95.06  | Clostridium_innocuum	Clostridium_innocuum
 2917364  2917827  |  2939364  2938901  |      464      464  |    95.26  | Clostridium_innocuum	Clostridium_innocuum
 2938901  2939364  |  2917827  2917364  |      464      464  |    95.26  | Clostridium_innocuum	Clostridium_innocuum
 2939368  2939555  |  3467084  3466897  |      188      188  |    93.62  | Clostridium_innocuum	Clostridium_innocuum
 2939365  2939721  |  2917173  2916757  |      357      417  |    83.45  | Clostridium_innocuum	Clostridium_innocuum
 2949804  2950673  |  3329924  3329055  |      870      870  |    97.82  | Clostridium_innocuum	Clostridium_innocuum
 2957610  2958473  |  3329924  3329061  |      864      864  |    98.50  | Clostridium_innocuum	Clostridium_innocuum
 3022506  3023237  |  4320497  4319766  |      732      732  |   100.00  | Clostridium_innocuum	Clostridium_innocuum
 3035305  3036175  |  2917826  2916956  |      871      871  |    95.06  | Clostridium_innocuum	Clostridium_innocuum
 3042474  3044228  |  1024096  1022343  |     1755     1754  |    99.54  | Clostridium_innocuum	Clostridium_innocuum
 3071933  3072678  |  3640005  3639258  |      746      748  |    88.52  | Clostridium_innocuum	Clostridium_innocuum
 3074357  3075989  |  1487976  1486344  |     1633     1633  |    92.11  | Clostridium_innocuum	Clostridium_innocuum
 3074357  3075989  |  3637673  3636042  |     1633     1632  |    91.86  | Clostridium_innocuum	Clostridium_innocuum
 3074357  3075989  |  3248872  3247241  |     1633     1632  |    92.11  | Clostridium_innocuum	Clostridium_innocuum
 3163656  3165444  |   445693   443906  |     1789     1788  |    99.94  | Clostridium_innocuum	Clostridium_innocuum
 3173589  3173821  |    80732    80500  |      233      233  |    98.28  | Clostridium_innocuum	Clostridium_innocuum
 3173589  3175075  |  2328923  2327476  |     1487     1448  |    94.49  | Clostridium_innocuum	Clostridium_innocuum
 3173694  3174528  |    80490    79676  |      835      815  |    93.77  | Clostridium_innocuum	Clostridium_innocuum
 3173588  3175075  |  3947639  3946191  |     1488     1449  |    94.43  | Clostridium_innocuum	Clostridium_innocuum
 3174286  3175075  |  4468984  4468214  |      790      771  |    95.58  | Clostridium_innocuum	Clostridium_innocuum
 3173589  3175076  |  1264719  1263252  |     1488     1468  |    89.67  | Clostridium_innocuum	Clostridium_innocuum
 3211769  3212063  |  2369507  2369213  |      295      295  |    99.32  | Clostridium_innocuum	Clostridium_innocuum
 3244544  3244881  |  1681030  1680693  |      338      338  |    93.79  | Clostridium_innocuum	Clostridium_innocuum
 3247242  3247696  |    41053    40599  |      455      455  |    92.11  | Clostridium_innocuum	Clostridium_innocuum
 3247242  3250128  |  2372099  2369213  |     2887     2887  |    92.67  | Clostridium_innocuum	Clostridium_innocuum
 3247241  3248872  |  3075989  3074357  |     1632     1633  |    92.11  | Clostridium_innocuum	Clostridium_innocuum
 3247240  3248872  |  1771740  1770107  |     1633     1634  |    91.06  | Clostridium_innocuum	Clostridium_innocuum
 3250433  3251076  |    37763    37120  |      644      644  |    84.81  | Clostridium_innocuum	Clostridium_innocuum
 3266521  3266878  |  4113549  4113188  |      358      362  |    95.59  | Clostridium_innocuum	Clostridium_innocuum
 3266522  3266878  |   343568   343208  |      357      361  |    96.95  | Clostridium_innocuum	Clostridium_innocuum
 3266522  3266878  |  3512283  3511924  |      357      360  |    96.12  | Clostridium_innocuum	Clostridium_innocuum
 3266522  3266878  |  4235599  4235239  |      357      361  |    95.57  | Clostridium_innocuum	Clostridium_innocuum
 3275733  3276585  |  4384958  4384105  |      853      854  |    93.21  | Clostridium_innocuum	Clostridium_innocuum
 3275741  3276570  |  2799124  2798295  |      830      830  |    90.60  | Clostridium_innocuum	Clostridium_innocuum
 3276059  3276456  |  3035842  3035445  |      398      398  |    84.92  | Clostridium_innocuum	Clostridium_innocuum
 3276134  3276456  |  2939364  2939042  |      323      323  |    85.76  | Clostridium_innocuum	Clostridium_innocuum
 3316272  3318245  |  2700225  2698252  |     1974     1974  |    99.95  | Clostridium_innocuum	Clostridium_innocuum
 3316271  3318246  |  4151450  4149475  |     1976     1976  |    99.90  | Clostridium_innocuum	Clostridium_innocuum
 3328977  3329924  |  2950755  2949804  |      948      952  |    95.39  | Clostridium_innocuum	Clostridium_innocuum
 3329061  3329924  |  2958473  2957610  |      864      864  |    98.50  | Clostridium_innocuum	Clostridium_innocuum
 3375659  3375830  |   352898   352727  |      172      172  |    88.95  | Clostridium_innocuum	Clostridium_innocuum
 3466897  3467084  |  2939555  2939368  |      188      188  |    93.62  | Clostridium_innocuum	Clostridium_innocuum
 3466912  3467740  |  4384922  4384094  |      829      829  |    93.97  | Clostridium_innocuum	Clostridium_innocuum
 3466905  3467726  |  2799104  2798283  |      822      822  |    90.88  | Clostridium_innocuum	Clostridium_innocuum
 3473553  3475306  |  2297380  2295628  |     1754     1753  |    99.94  | Clostridium_innocuum	Clostridium_innocuum
 3473554  3475306  |  1750029  1748277  |     1753     1753  |    99.94  | Clostridium_innocuum	Clostridium_innocuum
 3473555  3475306  |  1024096  1022345  |     1752     1752  |    99.89  | Clostridium_innocuum	Clostridium_innocuum
 3511924  3512283  |  3266878  3266522  |      360      357  |    96.12  | Clostridium_innocuum	Clostridium_innocuum
 3529865  3530140  |  1722808  1722532  |      276      277  |    94.58  | Clostridium_innocuum	Clostridium_innocuum
 3550860  3551157  |  1464016  1463710  |      298      307  |    86.17  | Clostridium_innocuum	Clostridium_innocuum
 3567507  3569496  |  1326773  1324785  |     1990     1989  |    92.38  | Clostridium_innocuum	Clostridium_innocuum
 3570178  3570362  |  1324105  1323918  |      185      188  |    84.13  | Clostridium_innocuum	Clostridium_innocuum
 3578544  3579404  |  1313835  1312975  |      861      861  |    83.33  | Clostridium_innocuum	Clostridium_innocuum
 3580230  3585210  |  1312128  1307136  |     4981     4993  |    82.52  | Clostridium_innocuum	Clostridium_innocuum
 3586453  3589426  |  1304875  1301902  |     2974     2974  |    98.72  | Clostridium_innocuum	Clostridium_innocuum
 3591021  3592331  |  1299860  1298550  |     1311     1311  |    90.78  | Clostridium_innocuum	Clostridium_innocuum
 3593708  3597352  |  1297262  1293617  |     3645     3646  |    90.45  | Clostridium_innocuum	Clostridium_innocuum
 3632259  3634044  |  1903717  1901932  |     1786     1786  |   100.00  | Clostridium_innocuum	Clostridium_innocuum
 3632259  3634044  |  3165444  3163659  |     1786     1786  |   100.00  | Clostridium_innocuum	Clostridium_innocuum
 3636020  3637673  |    41073    39423  |     1654     1651  |    92.26  | Clostridium_innocuum	Clostridium_innocuum
 3636038  3637673  |  1771743  1770107  |     1636     1637  |    92.85  | Clostridium_innocuum	Clostridium_innocuum
 3636043  3639200  |  2372099  2368940  |     3158     3160  |    93.35  | Clostridium_innocuum	Clostridium_innocuum
 3639258  3640005  |  3072678  3071933  |      748      746  |    88.52  | Clostridium_innocuum	Clostridium_innocuum
 3639271  3640005  |  1768415  1767683  |      735      733  |    88.57  | Clostridium_innocuum	Clostridium_innocuum
 3639271  3640005  |    37732    37000  |      735      733  |    89.52  | Clostridium_innocuum	Clostridium_innocuum
 3640820  3641083  |  2446605  2446342  |      264      264  |    96.59  | Clostridium_innocuum	Clostridium_innocuum
 3756417  3757639  |  3761967  3760745  |     1223     1223  |    84.38  | Clostridium_innocuum	Clostridium_innocuum
 3760745  3761967  |  3757639  3756417  |     1223     1223  |    84.38  | Clostridium_innocuum	Clostridium_innocuum
 3855196  3855819  |  4430334  4429731  |      624      604  |    92.47  | Clostridium_innocuum	Clostridium_innocuum
 3856032  3856747  |  4429535  4428820  |      716      716  |    97.35  | Clostridium_innocuum	Clostridium_innocuum
 3940537  3942288  |  1024096  1022345  |     1752     1752  |    99.83  | Clostridium_innocuum	Clostridium_innocuum
 3940536  3942288  |  1750029  1748277  |     1753     1753  |    99.89  | Clostridium_innocuum	Clostridium_innocuum
 3940535  3942290  |  1746526  1744770  |     1756     1757  |    99.54  | Clostridium_innocuum	Clostridium_innocuum
 3952046  3954044  |  4165203  4163206  |     1999     1998  |    99.60  | Clostridium_innocuum	Clostridium_innocuum
 3952068  3954043  |  3937706  3935733  |     1976     1974  |    99.80  | Clostridium_innocuum	Clostridium_innocuum
 3990989  3991071  |  4292168  4292086  |       83       83  |   100.00  | Clostridium_innocuum	Clostridium_innocuum
 4098545  4103577  |  2412618  2407585  |     5033     5034  |    99.62  | Clostridium_innocuum	Clostridium_innocuum
 4098519  4103578  |  2639764  2634703  |     5060     5062  |    99.41  | Clostridium_innocuum	Clostridium_innocuum
 4119005  4120762  |  4204373  4202615  |     1758     1759  |    99.77  | Clostridium_innocuum	Clostridium_innocuum
 4119004  4120773  |  2510854  2509085  |     1770     1770  |    99.60  | Clostridium_innocuum	Clostridium_innocuum
 4119010  4120763  |  1750029  1748276  |     1754     1754  |    99.83  | Clostridium_innocuum	Clostridium_innocuum
 4119010  4120773  |  2297379  2295618  |     1764     1762  |    99.72  | Clostridium_innocuum	Clostridium_innocuum
 4149475  4151450  |  3318246  3316271  |     1976     1976  |    99.90  | Clostridium_innocuum	Clostridium_innocuum
 4149476  4151445  |  3954040  3952071  |     1970     1970  |    99.95  | Clostridium_innocuum	Clostridium_innocuum
 4163206  4165203  |  3954044  3952046  |     1998     1999  |    99.60  | Clostridium_innocuum	Clostridium_innocuum
 4202614  4202779  |   575057   574892  |      166      166  |   100.00  | Clostridium_innocuum	Clostridium_innocuum
 4202615  4204373  |  4120762  4119005  |     1759     1758  |    99.77  | Clostridium_innocuum	Clostridium_innocuum
 4211996  4212099  |  1436902  1436799  |      104      104  |    99.04  | Clostridium_innocuum	Clostridium_innocuum
 4235437  4235599  |  2217983  2217821  |      163      163  |    97.55  | Clostridium_innocuum	Clostridium_innocuum
 4285812  4286109  |  1464016  1463710  |      298      307  |    87.62  | Clostridium_innocuum	Clostridium_innocuum
 4290530  4291981  |  1677060  1675609  |     1452     1452  |    99.93  | Clostridium_innocuum	Clostridium_innocuum
 4290533  4291980  |  1252621  1251154  |     1448     1468  |    97.48  | Clostridium_innocuum	Clostridium_innocuum
 4292086  4292168  |  3991071  3990989  |       83       83  |   100.00  | Clostridium_innocuum	Clostridium_innocuum
 4292090  4292168  |  3988823  3988745  |       79       79  |    98.73  | Clostridium_innocuum	Clostridium_innocuum
 4319766  4320497  |  3023237  3022506  |      732      732  |   100.00  | Clostridium_innocuum	Clostridium_innocuum
 4319763  4320497  |  1772752  1772018  |      735      735  |    99.86  | Clostridium_innocuum	Clostridium_innocuum
 4384108  4384925  |  2243353  2242536  |      818      818  |    91.69  | Clostridium_innocuum	Clostridium_innocuum
 4384105  4384958  |  3276585  3275733  |      854      853  |    93.21  | Clostridium_innocuum	Clostridium_innocuum
 4384094  4384922  |  3467740  3466912  |      829      829  |    93.97  | Clostridium_innocuum	Clostridium_innocuum
 4411121  4411320  |  2253683  2253484  |      200      200  |    95.50  | Clostridium_innocuum	Clostridium_innocuum
 4428820  4429535  |  3856747  3856032  |      716      716  |    97.35  | Clostridium_innocuum	Clostridium_innocuum
 4429731  4430334  |  3855819  3855196  |      604      624  |    92.47  | Clostridium_innocuum	Clostridium_innocuum
 3951295  3951472  |  3074534  3074357  |      178      178  |    97.19  | Clostridioforme	Clostridium_innocuum
 3951295  3951472  |  1770284  1770107  |      178      178  |    94.94  | Clostridioforme	Clostridium_innocuum
 3951296  3953537  |  2370644  2368404  |     2242     2241  |    91.27  | Clostridioforme	Clostridium_innocuum
 3958273  3958492  |  3067381  3067163  |      220      219  |    85.52  | Clostridioforme	Clostridium_innocuum
 3958273  3958492  |  1762678  1762460  |      220      219  |    85.52  | Clostridioforme	Clostridium_innocuum
 5416940  5421324  |  3597351  3592961  |     4385     4391  |    90.08  | Clostridioforme	Clostridium_innocuum
 6123473  6123642  |    74263    74094  |      170      170  |    83.04  | Clostridioforme	Clostridium_innocuum
 1237503  1239438  |  1314865  1312919  |     1936     1947  |    83.10  | Blautia_coccoides	Clostridium_innocuum
 1410981  1411521  |  1322232  1321692  |      541      541  |    86.53  | Blautia_coccoides	Clostridium_innocuum
 3306968  3307069  |   720839   720738  |      102      102  |   100.00  | Muribaculum_intestinale	Clostridium_innocuum
 3406852  3407744  |    69318    68426  |      893      893  |    78.24  | Acutalibacter_muris	Clostridium_innocuum
```
:::

:::danger
There are many intra-sample duplications. Is this real or a artifact of alignment or due to a bad-reference genome?
:::

--- 

### Generate Mummer output for all _new_ OMM~12~ ref sequences

- Added snakemake pipeline for analysis [commit](https://github.com/philippmuench/OligoMM-report/commit/f443ef8ccb4be68a2dc6b255b45b30ff8827ccc5)
- start on new genomes `snakemake -s Snakefile_reference --jobs 40`
- start on old genomes `snakemake -s Snakefile_reference_old --jobs 40`

### Generate duplication statistics

```bash
cd /home/aime/projects/oligomm-claudia/databases/omm_new/duplication_coords
cat *.tsv > merged.tsv
# manually remove all lines that have _identity_ at last column
rds_all_genomes.tsv
```


- 2903 duplications new ref set (2904 in old)
	- of which 2618 (90%) are in same genome
	- 285 between species
	- have same size (mean = 1123.511; sd = 1187.204)

Counts of same-genome similarities

```
Clostridioforme                                               738
B_caecimuris                                                  437
Clostridium_innocuum                                          263
Muribaculum_intestinale                                       255
Acutalibacter_muris                                           244
T_muris                                                       166
Lactobacillus_reuteri_I49_1                                   142
F_plautii_1                                                   113
Enterococcus_faecalis                                         111
Blautia_coccoides                                              66
Akkermansia_muciniphila                                        61
Bifidobacterium_animalis_YL2_1                                 15
Bifidobacterium_animalis_YL2_2                                  7
```

Counts of between-genome similarities

```
Clostridioforme                                                           83
F_plautii_1                                                               62
Acutalibacter_muris                                                       37
Blautia_coccoides                                                         35
Muribaculum_intestinale                                                   30
B_caecimuris                                                              20
Clostridium_innocuum                                                      10
Bifidobacterium_animalis_YL2_1                                             3
Bifidobacterium_animalis_YL2_2                                             3
Enterococcus_faecalis                                                      1
Lactobacillus_reuteri_I49_1                                                1
```

Duplicated nucleotides
- between: 320,672
- same genome: 2,941,351


Genome sizes new
```
Akkermansia_muciniphila	2737357
Acutalibacter_muris	3802913
Bifidobacterium_animalis_YL2_1	1133782
Bifidobacterium_animalis_YL2_2	888144
B_caecimuris	4800606
Blautia_coccoides	5128582
Clostridium_innocuum	4469084
Clostridioforme	7157610
Enterococcus_faecalis	3025655
F_plautii_1	3743035
F_plautii_2	70670
Lactobacillus_reuteri_I49_1	2045096
Lactobacillus_reuteri_I49_2	14338
Lactobacillus_reuteri_I49_3	4170
Muribaculum_intestinale	3307069
T_muris	2887949
```

Genome sizes old 45,215,430
Genome sizes new :45,216,060

:::success
- 7.2 % of total reference is duplicated (new and old reference set similar)
:::

```
genome var_in_dup var_total %
CP021420.1 0 11 0
CP021421.1 13 56 23
CP022713.1 10 24 42
NHMU01000001.1 32 34 94
NHMU01000002.1 1 3 33
NHMU01000003.1 11 18 61
NHMU01000004.1 56 66 85
NHMU01000005.1 5 10 50
NHMU01000008.1 14 14 100
NHMU01000009.1 12 45 27
NHMU01000012.1 0 3 0
NHMU01000018.1 7 7 100
NHTR01000001.1 18 68 26
NHTR01000002.1 27 36 75
NHTR01000003.1 0 5 0
NHTR01000004.1 21 30 70
NHTR01000006.1 29 29 100
NHTR01000007.1 6 6 100
NHTR01000008.1 7 8 88
NHTR01000009.1 26 28 93
NHTR01000011.1 10 45 22
CP022722.1 9 28 32
NHMP01000002.1 0 7 0
NHMP01000003.1 0 2 0
NHMP01000004.1 2 9 22
NHMQ01000001.1 14 38 37
NHMQ01000002.1 1 15 7
NHMQ01000003.1 0 2 0
NHMU01000013.1 0 5 0
NHMP01000005.1 0 18 0
NHMP01000007.1 0 10 0
NHMR02000001.1 0 2 0
NHMR02000002.1 0 4 0
NHMT01000001.1 9 19 47
NHMP01000012.1 11 11 100
NHTR01000010.1 0 2 0
CP021422.1 0 1 0
CP022712.1 3 3 100
NHMP01000009.1 0 5 0
```

variants iun duplicated regions: 48.69326%
