---
# System prepended metadata

title: Quality assessment of rDerCor1_cur20201106
tags: [' Genome', VGP]

---

---
title: Quality assessment of rDerCor1_cur20201106
tags:  VGP, Genome 
description: Exploration of quality in the curated version of rDerCor1 date 2020.11.06
--- 
## General Stats
Stats from Sanger pipeline from [Sanger Team](https://github.com/sanger-pathogens/assembly-stats)

|Stats|rDerCor1.pri.cur.20201106.fasta|		[N]|
|---|---:|---|
|Sum|	2,164,762,090|	40
|N50|	137,568,771	|5
|N60|	127,644,590	|7
|N70|	105,213,316|	9
|N80|	79,995,514	|11
|N90	|25,428,285	|17
|N100	|4,772	|40
|Average|	54,119,052	
|Largest|	354,478,938	
|N_count|	5,594,612	
|Gaps|	667|	


## DotPlot
We compare the genome with pri.curation.20200406; rCheMyd1.curation20200811 & rCheMyd1_DNAZoo using [Dgenies](http://dgenies.toulouse.inra.fr/).
<i>Cabanettes F, Klopp C. (2018) D-GENIES: dot plot large genomes in an interactive, efficient and simple way. PeerJ 6:e4958 https://doi.org/10.7717/peerj.4958</i>

<center>

![HiC_DNAZoo](https://i.imgur.com/DOL5MUc.jpg)
*rDerCor1_cur_VS_DNAZoorCheMyd1*

![rCheMyd1_cur](https://i.imgur.com/NEH3M60.jpg)
*rCheMyd1_cur_VS_rDercor1_cur*

![rDerCor1_previous.cur](https://i.imgur.com/3o1hnGh.jpg)
*rDerCor1_cur20201106VS20200406*


##### Comparing with rCheMyd1_pri_cur_20200811

![](https://i.imgur.com/kR06zbf.png)
*Region low identity*

![](https://i.imgur.com/XObxurp.png)
*Region low identity*

![](https://i.imgur.com/yKGpS1p.png)
*Break and reorder*

![](https://i.imgur.com/kay1LGF.png)
*Break and low identity*

![](https://i.imgur.com/FvOQif0.png)
*Last Scaffolds*

![](https://i.imgur.com/j9lVXaB.jpg)
*Last Scaffolds*

![](https://i.imgur.com/7m1z7gk.png)
*Scaffolds 9;10;11;14 in rDerCor1 to check shift*


![](https://i.imgur.com/i4MJJt5.png)
*Scaffolds 9;10;11;14 in rDerCor1 to check shift, shifted*

</center>

### Busco3

||rDerCor1.pri.cur.20200406.fasta|| rDerCor1.pri.cur.20200406.fasta	|
|---|---:|---:|---|:---:|
|Complete BUSCOs (C)	|2,426	|  93.80%|	2,464| 95.20%|
|Complete and single-copy BUSCOs (S)|	2,410|	93.20%|	2,455|	94.90%
|Complete and duplicated BUSCOs (D)	|16|	0.60%|	9|	0.30%
|Fragmented BUSCOs (F)|	104|	4.00%|	77|	3.00%|
|Missing BUSCOs (M)|	56|	2.20%|	45|	1.80%
|Total BUSCO groups searched|	2,586|	--|	2,586|	--|






### Merqury


|Assembly | K-mers asm | Kmers asm & reads | QV | Error rate|
|---|---:|---:|---|---|
|rDerCor1.pri.cur.20201106	|5,705,907	|2,159,153,338|	38.9963|	0.000126|
|rDerCor1_merfin_pri_SortedSize|	5,727,562	|2,159,914,818	|38.9814|	0.000126434
|rDerCor1_t3_primary|	18,168,030|	2,159,644,793|	33.9555|	0.000402209

#### Copy-number spectrum analysis for rDerCor1.20201106
<center>

![](https://i.imgur.com/v8lqxC4.png)
![](https://i.imgur.com/YnR0mjE.png)

</center>

Table XX. Length %GC and %N for curated 2020.11.06 version of rDerCor1

|Name_Scaffold|	Leng|	%GC|	%N|
|---|---|---|---|
|SUPER_1|	354,478,938	|0.4227926371|	0.003112108737
|SUPER_2|	272,704,568	|0.4195716223|	0.004507460249
|SUPER_3|	212,168,110	|0.4223197303|	0.0005436726566
|SUPER_4|	146,520,673	|0.4173785224|	0.004935453716
|SUPER_5|	137,568,771	|0.4204562168|	2.66E-05
|SUPER_6|	131,128,815	|0.4310519621|	0.001805987494
|SUPER_7|	127,644,590	|0.4308359876|	0.002006070136
|SUPER_8|	109,294,577	|0.4311128996|	0.000574840964
|SUPER_9|	105,213,316	|0.4297130508|	0.003656371785
|SUPER_10|	86,472,384	|0.4376877478|	0.002140105216
|SUPER_11|	79,995,514	|0.4221339462|	0.003428929777
|SUPER_12|	44,241,090	|0.4329135652|	0.002098320814
|SUPER_13|	41,159,716	|0.4523335632|	0.001191067499
|SUPER_14|	40,021,378	|0.4640961888|	0.005266810153
|SUPER_15|	33,199,653	|0.4470593413|	8.92E-06
|SUPER_16|	26,401,370	|0.4544061918|	0.003022987065
|SUPER_17|	25,428,285	|0.4483935507|	1.16E-05
|SUPER_18|	23,665,181	|0.4614426148|	3.74E-05
|SUPER_19|	20,023,515	|0.4719584449|	0.002042049061
|SUPER_20|	19,206,509	|0.5205470187|	0.002162339861
|SUPER_21|	18,859,425	|0.4695203592|	5.78E-05
|SUPER_22|	18,746,278	|0.4604031264|	5.80E-05
|SUPER_23|	17,228,317	|0.5341474736|	9.16E-05
|SUPER_24|	16,950,461	|0.5114341138|	0.01037181231
|SUPER_25|	16,479,532	|0.4913683835|	4.19E-05
|SUPER_26|	16,472,168	|0.4625251515|	0.006196634226
|SUPER_27|	16,294,212	|0.4895787535|	3.03E-05
|SUPER_28|	6,736,449	|0.5116992647|	0.03263588873
|SUPER_11_unloc_1|	161,456	|0.5007494302|	0.003084431672
|SUPER_11_unloc_2|	88,916	|0.5123262405|	0
|SUPER_11_unloc_3|	62,672	|0.4594555782|	0.009557697217
|SUPER_11_unloc_4|	30,635	|0.5188836298|	0
|SUPER_11_unloc_5|	27,714	|0.522046619	|0
|SUPER_11_unloc_6|	24,225	|0.5138493292|	0
|SUPER_11_unloc_7|	21,914	|0.4550515652|	0
|SUPER_11_unloc_8|	12,220	|0.4931260229|	0
|SUPER_11_unloc_9|	9,024	|0.4655363475|	0.01108156028
|SUPER_11_unloc_10|	8,721	|0.4346978558|	0.01146657493
|SUPER_11_unloc_11|	6,026	|0.4412545636|	0
|SUPER_11_unloc_12|	4,772	|0.4377619447|	0


Table XX. Length %GC and %N for curated 2020.11.06 version of rCheMyd1

|Name_Scaffold|	leng|	%GC|	%N |
|---|---|---|---|
|SUPER_1|	348,265,484|	0.426608139|	0.005
|SUPER_2|	262,513,884|	0.4258510457|	0.000
|SUPER_3|	204,120,564|	0.426853215|	0.000
|SUPER_4|	142,324,156|	0.4234725622|	0.002
|SUPER_5|	134,428,053|	0.4273345758|	0.027
|SUPER_6|	133,272,604|	0.4243452315|	0.001
|SUPER_7|	123,872,898|	0.4371868332|	0.000
|SUPER_8|	106,505,537|	0.4369205894|	0.000
|SUPER_9|	101,620,591|	0.4366290096|	0.000
|SUPER_10|	84,054,250|	0.4441273463|	0.001
|SUPER_11|	79,522,289|	0.4246977222|	0.014
|SUPER_12|	44,456,234|	0.4770332998|	0.004
|SUPER_13|	42,953,438|	0.4499156971|	0.027
|SUPER_14|	42,626,581|	0.4380274599|	0.004
|SUPER_15|	33,324,608|	0.4569506114|	0.000
|SUPER_16|	25,690,524|	0.465054508|	0.000
|SUPER_17|	25,202,864|	0.4575149872|	0.000
|SUPER_18|	23,386,534|	0.471161524|	0.000
|SUPER_19|	19,769,559|	0.4832919642|	0.000
|SUPER_20|	19,256,569|	0.4707118386|	0.000
|SUPER_21|	19,202,859|	0.5242525084|	0.005
|SUPER_24|	18,854,909|	0.4800383815|	0.000
|SUPER_25|	16,433,863|	0.5034322727|	0.000
|SUPER_26|	16,225,734|	0.4753074961|	0.000
|SUPER_27|	16,135,183|	0.5012314394|	0.000
|SUPER_22|	11,152,253|	0.5202827626|	0.024
|SUPER_23|	9,977,174|	0.4587280927|	0.164
|SUPER_23_unloc_1|	8,903,217|	0.5200635905|	0.042
|SUPER_28|	7,864,902|	0.4945411907|	0.065
|SUPER_22_unloc_1|	7,753,707|	0.533713487|	0.023
|scaffold_48_arrow_ctg1|	468,323|	0.1589821555|	0.645
|scaffold_42_arrow_ctg1|	414,693|	0.5288683436|	0.002
|scaffold_59_arrow_ctg1|	222,063|	0.4974219028|	0.002
|scaffold_49_arrow_ctg1|	200,098|	0.4521284571|	0.000
|scaffold_60_arrow_ctg1|	200,034|	0.6284581621|	0.000
|scaffold_61_arrow_ctg1|	186,729|	0.6133059139|	0.005
|scaffold_63_arrow_ctg1|	156,755|	0.5972568658|	0.000
|scaffold_45_arrow_ctg1|	139,352|	0.4775747747|	0.000
|scaffold_65_arrow_ctg1|	139,178|	0.5295592694|	0.001
|scaffold_66_arrow_ctg1|	136,476|	0.5218206864|	0.000
|scaffold_67_arrow_ctg1|	131,618|	0.5193742497|	0.000
|scaffold_68_arrow_ctg1|	130,366|	0.5817621159|	0.004
|scaffold_69_arrow_ctg1|	104,581|	0.5434256701|	0.000
|scaffold_70_arrow_ctg1|	91,510|	0.5298546607|	0.000
|scaffold_71_arrow_ctg1|	87,187|	0.529207336|	0.001
|scaffold_72_arrow_ctg1|	84,098|	0.5292159148|	0.000
|scaffold_76_arrow_ctg1|	81,177|	0.4907301329|	0.001
|scaffold_77_arrow_ctg1|	76,334|	0.5131789242|	0.002
|scaffold_78_arrow_ctg1|	74,105|	0.4520612644|	0.000
|scaffold_80_arrow_ctg1|	73,766|	0.6859799908|	0.007
|scaffold_79_arrow_ctg1|	73,540|	0.4006119119|	0.000
|scaffold_83_arrow_ctg1|	68,053|	0.6505958591|	0.000
|scaffold_84_arrow_ctg1|	67,755|	0.5005387056|	0.007
|scaffold_86_arrow_ctg1|	65,737|	0.6570272449|	0.008
|scaffold_87_arrow_ctg1|	62,133|	0.4745787263|	0.000
|scaffold_88_arrow_ctg1|	61,604|	0.5103727031|	0.000
|scaffold_89_arrow_ctg1|	61,238|	0.6525033476|	0.008
|scaffold_90_arrow_ctg1|	59,032|	0.5058612278|	0.000
|scaffold_91_arrow_ctg1|	53,571|	0.5847566781|	0.000
|scaffold_92_arrow_ctg1|	51,870|	0.5339888182|	0.010
|scaffold_93_arrow_ctg1|	51,123|	0.6870097608|	0.000
|scaffold_95_arrow_ctg1|	51,066|	0.6133826812|	0.000
|scaffold_94_arrow_ctg1|	50,289|	0.4775597049|	0.000
|scaffold_96_arrow_ctg1|	48,875|	0.4888184143|	0.000
|scaffold_97_arrow_ctg1|	48,603|	0.4761640228|	0.000
|scaffold_98_arrow_ctg1|	48,044|	0.4328532179|	0.002
|scaffold_100_arrow_ctg1|	46,898|	0.673269649|	0.000
|scaffold_99_arrow_ctg1|	46,854|	0.4942374184|	0.000
|scaffold_101_arrow_ctg1|	45,103|	0.494601246|	0.000
|scaffold_102_arrow_ctg1|	44,400|	0.4560135135|	0.000
|scaffold_103_arrow_ctg1|	44,162|	0.6547484262|	0.000
|scaffold_104_arrow_ctg1|	43,167|	0.5399031668|	0.000
|scaffold_105_arrow_ctg1|	40,978|	0.432207526|	0.000
|scaffold_106_arrow_ctg1|	39,936|	0.6700971554|	0.000
|scaffold_107_arrow_ctg1|	37,745|	0.5296065704|	0.000
|scaffold_108_arrow_ctg1|	34,665|	0.4378191259|	0.000
|scaffold_109_arrow_ctg1|	32,845|	0.6800121784|	0.000
|scaffold_110_arrow_ctg1|	31,630|	0.4792285805|	0.000
|scaffold_111_arrow_ctg1|	31,051|	0.6601719751|	0.000
|scaffold_112_arrow_ctg1|	27,483|	0.637557763|	0.000
|scaffold_113_arrow_ctg1|	27,288|	0.5906992084|	0.000
|scaffold_114_arrow_ctg1|	27,235|	0.5109601616|	0.000
|scaffold_12B_arrow_ctg1|	21,116|	0.4715381701|	0.000
|scaffold_115_arrow_ctg1|	21,067|	0.6232021645|	0.000
|scaffold_116_arrow_ctg1|	20,277|	0.6266212951|	0.000
|scaffold_117_arrow_ctg1|	16,618|	0.4925382116|	0.000
|scaffold_118_arrow_ctg1|	16,270|	0.6877688998|	0.000
|scaffold_119_arrow_ctg1|	14,461|	0.4435377913|	0.000
|scaffold_120_arrow_ctg1|	13,486|	0.4807207474|	0.000
|scaffold_121_arrow_ctg1|	11,258|	0.501598863|	0.000
|scaffold_122_arrow_ctg1|	8,758|	0.4674583238|	0.000
|scaffold_123_arrow_ctg1|	8,373|	0.6219992834|	0.012
|scaffold_124_arrow_ctg1|	8,025|	0.6343925234|	0.000
|scaffold_125_arrow_ctg1|	6,689|	0.4783973688|	0.000
|scaffold_126_arrow_ctg1|	6,663|	0.4691580369|	0.000
|scaffold_127_arrow_ctg1|	3,718|	0.7490586337|	0.000
|scaffold_128_arrow_ctg1|	3,472|	0.4282834101|	0.000
|scaffold_129_arrow_ctg1|	3,063|	0.4436826641|	0.000


We re-oriented the scaffolds (reverse complementary) 10 and 11  


![](https://i.imgur.com/D2Cadif.jpg)


We can see that scaffold CheMyd_12 match with scaffold DerCor_14 and CheMyd_14 with DerCor_12. Therefore we ask for a rename of DerCor_12 and DerCor_14

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

Scaffold 19 has a break in one of the genomes 
![](https://i.imgur.com/fNd6sxC.png)

Scaffold rCheMyd_20 map with rDerCor_22
![](https://i.imgur.com/lKX4qBk.png)

Scaffold rCheMyd1_21 map with rDerCor_24 and rCheMyd1_24 map with rDerCor_21 Therefore we ask for a rename for rDerCor_21 and rDerCor_24  

![](https://i.imgur.com/7PLhybv.png)

Scaffold rCheMyd_22 and rCheMyd_22_unloc map rDerCor_20 maybe join rCheMyd_22 and rCheMyd_22_unloc 
![](https://i.imgur.com/rWxlwmz.png)

Here after join
![](https://i.imgur.com/dqaJZax.png)




Scaffolds rCheMyd_23 and rCheMyd_23_unloc_RC map rDerCor23, maybe join

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

