---
# System prepended metadata

title: MitoHiFi paper - comparison with olders references

---

# MitoHiFi paper - comparison with olders references

- Table of Content
[ToC]

# 0. All assemblies that had references on NCBI

![](https://i.imgur.com/fjH1aQX.png)



# 1. Tridacna crocea

```
Mito by MitoHiFi in path bellow

/lustre/scratch124/tol/projects/asg/data/molluscs/Tridacna_crocea/working/xbTriCroc3.hifiasm.20220328/mito

python /lustre/scratch123/tol/teams/tola/users/jf18/softwares/MitoHiFi/compareGenesLists.py /lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/had_reference_on_ncbi/references_fasta/MT902179.1.gb genbank /lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/new_datafreeze/more2/Tridacna_crocea/final_mitogenome.gb genbank True
Shared genes:
{'12S ribosomal RNA': [1, 1], '16S ribosomal RNA': [1, 1], 'ATP6': [1, 1], 'ATP8': [1, 1], 'COX1': [1, 1], 'COX2': [1, 1], 'COX3': [1, 1], 'CYTB': [1, 1], 'ND1': [1, 1], 'ND2': [1, 1], 'ND3': [1, 1], 'ND4': [1, 1], 'ND4L': [1, 1], 'ND5': [1, 1], 'ND6': [1, 1], 'tRNA-Ala': [1, 1], 'tRNA-Arg': [2, 1], 'tRNA-Asn': [1, 1], 'tRNA-Asp': [1, 1], 'tRNA-Cys': [1, 1], 'tRNA-Gln': [1, 1], 'tRNA-Glu': [1, 1], 'tRNA-Gly': [1, 1], 'tRNA-His': [1, 1], 'tRNA-Ile': [1, 1], 'tRNA-Leu': [2, 2], 'tRNA-Lys': [1, 1], 'tRNA-Met': [2, 3], 'tRNA-Phe': [2, 2], 'tRNA-Pro': [1, 1], 'tRNA-Ser': [2, 2], 'tRNA-Thr': [1, 1], 'tRNA-Trp': [1, 1], 'tRNA-Tyr': [1, 1], 'tRNA-Val': [1, 1]}


Specific to /lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/had_reference_on_ncbi/references_fasta/MT902179.1.gb:
{}


Specific to /lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/new_datafreeze/more2/Tridacna_crocea/final_mitogenome.gb:
{}


(fastani) mu2@tol-head2:/lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/had_reference_on_ncbi/compare_discrepancies$ fastANI -r MT902179.1.rot1.fa -q Tridacna_crocea.fa --visualize -o MT902179.1.rot1.Tridacna_crocea.out


mu2@tol-head2:/lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/had_reference_on_ncbi/compare_discrepancies$ python3 /software/team311/jf18/git_softwares/MitoHiFi_2/rotate_genbank.py MT902179.1.gb "trnF(gaa)" MT902179.1.rot1.gb

```

![](https://i.imgur.com/nLngHy3.png)


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



Repeats:

```
/lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/new_datafreeze/more2/Tridacna_crocea/

trf

2940 3406 8 57.9 8 96 1 835 11 0 37 49 1.43 GTATGTGT GTATGTGTGTATGTGTGTATGTGTGTATGTGTGTATGTGTGTATGTGTGAATGTGTGTATGTGTGTATGTGTGTATGTGTGTATGTCTGTGTGTATGTGTGTATGTGTGTATGT
GTGTATGTGTGTATGTGTGTATGTGTGTATGTGTGTATGTGTGTATGTGTGTATGTGTGTATGTGTGTATGTGTGTATGTGTGTATGTGTGTATGTGTGTATGTGTGTATGTGTGTATGTGTGTATGTGTGTATGTGTGTATGTGTGTATGTGTGTATGTGTGTATG
TGTGTATGTGTGTATGTGTGTATGTGTGTATGTGTGTATGTGTGTATGTGTGTATGTGTGTATGTGTGTATGTGTGTATGTGTGTATGTGTGTATGTGTGTATGTGTATATGTGTGTATGTGTGTATGTGTGTATGTGTGTATGTGTGTATGTCTGTGTGTGTGTGT
GTGTGTGTGTGTGTGTGTG
3557 3952 6 66.2 6 93 1 607 0 45 0 54 1.02 TCTCTC TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTCTCTCTCTCTTTCTCTCTCTTTCT
CTCTCTTTCTCTCTCTTTCTCCCTCTTTCTCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCATCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTCTCTTTCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC
TCTCTCTCTCTCTCTCTCTCTCTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT
3557 3952 10 39.7 10 91 1 607 0 45 0 54 1.02 TCTCTCTCTC TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTCTCTCTCTCTTTCTCTCT
CTTTCTCTCTCTTTCTCTCTCTTTCTCCCTCTTTCTCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCATCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTCTCTTTCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC
TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT
4053 4105 22 2.4 23 76 17 58 9 11 1 77 1.07 TTTACTTTTATTTATTCTTTCCT TTTACTTTTATTTTTCTTTCTTTTTATGTTTATTTATTTTTTCCTTTTCTTTT
4051 4093 16 2.7 16 77 0 50 13 6 2 76 1.08 TATTTATTTTTATGTT TATTTACTTTTATTTTTCTTTCTTTTTATGTTTATTTATTTTT
4035 4093 29 2.1 28 84 9 77 11 6 5 76 1.14 TTTTCTTTCTTTTTATATTTACTTTTAT TTTTCTTTGTTGTTTATATTTACTTTTATTTTTCTTTCTTTTTATGTTTATTTATTTTT



TRASH
qall.repeats.from.final_mitogenome.fasta.csv


"start","end","width","seq","strand","class","region.name"
6876,6970,95,"CCTGGGAAGGGCTAAAGTTGGGCTAGGTTCTGTTTCTATACTACTGATTTTTCCGGTGGGTGGAAGAAACACCTAGAAAAACCATAAAAATTTTA","-",NA,"final_mitogenome.fasta_atg001776l_1.rc.rotated_r
otated"
6971,7067,97,"CCGGGGAAGGGCTAAAGTTGGGCTAGGTTCTGTTTCTATACTACTGATTTTTCCGGTGGGTGGAAGAAACACCTAGAAAAGCCCTAGAGTATCTCCA","-",NA,"final_mitogenome.fasta_atg001776l_1.rc.rotated
_rotated"
7068,7164,97,"CCGGGGAAGGGCTAAAGTTGGGCTAGGTTCTGTTTCTATACTACTGATTTTTCCGGTGGGTGGAAGAAACACCTAGAAAAGCCCTAGAGTATCTCCA","-",NA,"final_mitogenome.fasta_atg001776l_1.rc.rotated
_rotated"
7165,7261,97,"CCGGGGAAGGGCTAAAGTTGGGCTAGGTTCTGTTTCTATACTACTGATTTTTCCGGTGGGTGGAAGAAACACCTAGAAAAGCCCTAGAGTATCTCCA","-",NA,"final_mitogenome.fasta_atg001776l_1.rc.rotated
_rotated"

```


mu2@tol-head2:/lustre/scratch124/tol/projects/darwin/data/insects/Phymatocera_aterrima/working/iyPhyAter2.hicanu.20220711/mito.reads.v3/mito.reads.v3.1.5$ ./trf409.linux64 final_mitogenome.fasta 2 7 7 80 10 50 500 -f -d -m


# 2 . Tridacna gigas



```
(biopython) mu2@tol-head2:/lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/had_reference_on_ncbi/compare_discrepancies$ python /lustre/scratch123/tol/teams/tola/users/jf18/softwares/MitoHiFi/compareGenesLists.py NC_050683.1.gb genbank Tridacna_gigas.gb genbank True
Shared genes:
{'12S ribosomal RNA': [1, 1], '16S ribosomal RNA': [1, 1], 'ATP6': [1, 1], 'ATP8': [1, 1], 'COX1': [1, 1], 'COX2': [1, 1], 'COX3': [1, 1], 'CYTB': [1, 1], 'ND1': [1, 1], 'ND2': [1, 1], 'ND3': [1, 1], 'ND4': [1, 1], 'ND4L': [1, 1], 'ND5': [1, 1], 'ND6': [1, 1], 'tRNA-Ala': [1, 1], 'tRNA-Arg': [1, 1], 'tRNA-Asn': [1, 1], 'tRNA-Asp': [1, 1], 'tRNA-Cys': [1, 1], 'tRNA-Gln': [1, 1], 'tRNA-Glu': [1, 1], 'tRNA-Gly': [1, 1], 'tRNA-His': [1, 1], 'tRNA-Ile': [1, 1], 'tRNA-Leu': [2, 2], 'tRNA-Lys': [1, 1], 'tRNA-Met': [2, 2], 'tRNA-Phe': [1, 1], 'tRNA-Pro': [1, 1], 'tRNA-Ser': [2, 2], 'tRNA-Thr': [1, 1], 'tRNA-Trp': [1, 1], 'tRNA-Tyr': [1, 1], 'tRNA-Val': [1, 1]}


Specific to NC_050683.1.gb:
{}


Specific to Tridacna_gigas.gb:
{}
```

```
mu2@tol-head2:/lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/had_reference_on_ncbi/compare_discrepancies$ python3 /software/team311/jf18/git_softwares/MitoHiFi_2/rotate_genbank.py MT902179.1.gb "trnF(gaa)" MT902179.1.rot1.gb

(fastani) mu2@tol-head2:/lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/had_reference_on_ncbi/compare_discrepancies$ fastANI -r NC_050683.1.rot.fa -q Tridacna_gigas.fa --visualize -o NC_050683.1.rot.Tridacna_gigas.out

(biopython) mu2@tol-head2:/lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/had_reference_on_ncbi/compare_discrepancies$ Rscript visualize.R Tridacna_gigas.fa NC_050683.1.rot.fa NC_050683.1.rot.Tridacna_gigas.out.visual

```

![](https://i.imgur.com/pk1MDR7.png)

```
(biopython) mu2@tol-head2:/lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/had_reference_on_ncbi/compare_discrepancies$ python /software/team311/mu2/plot_geneFromgb_nodups.py NC_050683.1.rot.gb NC_050683.1.rot
(biopython) mu2@tol-head2:/lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/had_reference_on_ncbi/compare_discrepancies$ python /software/team311/mu2/plot_geneFromgb_nodups.py Tridacna_gigas.gb Tridacna_gigas
```

![](https://i.imgur.com/8hm59dF.png)



# 3. Nebria brevicollis

```
Shared genes:
{'12S ribosomal RNA': [1, 1], '16S ribosomal RNA': [1, 1], 'atp6': [1, 1], 'atp8': [1, 1], 'cob': [1, 1], 'cox1': [1, 1], 'cox2': [1, 1], 'cox3': [1, 1], 'nad1': [1, 1], 'nad2': [1, 1], 'nad3': [1, 1], 'nad4': [1, 1], 'nad4l': [1, 1], 'nad5': [1, 1], 'nad6': [1, 1], 'tRNA-Ala': [1, 1], 'tRNA-Arg': [1, 1], 'tRNA-Asn': [1, 1], 'tRNA-Asp': [1, 1], 'tRNA-Cys': [1, 1], 'tRNA-Gln': [1, 1], 'tRNA-Glu': [1, 1], 'tRNA-Gly': [1, 1], 'tRNA-His': [1, 1], 'tRNA-Ile': [1, 1], 'tRNA-Leu': [2, 2], 'tRNA-Lys': [1, 1], 'tRNA-Met': [1, 1], 'tRNA-Phe': [1, 1], 'tRNA-Pro': [1, 1], 'tRNA-Ser': [2, 2], 'tRNA-Thr': [1, 1], 'tRNA-Trp': [1, 1], 'tRNA-Tyr': [1, 1], 'tRNA-Val': [1, 1]}


Specific to KT876906.1.gb:
{}


Specific to Nebria_brevicollis.gb:
{}
```
![](https://i.imgur.com/4MY1pnx.png)


With reverse complement

![](https://i.imgur.com/1zIWTkw.png)


```
(biopython) mu2@tol-head2:/lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/had_reference_on_ncbi/compare_discrepancies$ mitofinder -j annotateRC.KT876906 -a KT876906.1.RC.fasta -r KT876906.1.gb -o 5 
```
```
mu2@tol-head2:/lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/had_reference_on_ncbi/compare_discrepancies$ python3 /software/team311/jf18/git_softwares/MitoHiFi_2/rotate_genbank.py annotateRC.KT876906_mtDNA_contig.gb ND1 annotateRC.KT876906_mtDNA_contig.rot.gb

mu2@tol-head2:/lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/had_reference_on_ncbi/compare_discrepancies$ python3 /software/team311/jf18/git_softwares/MitoHiFi_2/rotate_genbank.py Nebria_brevicollis.gb ND1 Nebria_brevicollis.rot.gb 
```



# 4 . Bombus terrestris

```
(biopython) mu2@tol-head2:/lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/had_reference_on_ncbi/compare_discrepancies$ python /lustre/scratch123/tol/teams/tola/users/jf18/softwares/MitoHiFi/compareGenesLists.py NC_045179.1.gb genbank Bombus_terrestris.gb genbank True
Shared genes:
{'16S ribosomal RNA': [1, 1], 'ATP6': [1, 1], 'COX1': [1, 1], 'COX2': [1, 1], 'COX3': [1, 1], 'CYTB': [1, 1], 'ND1': [1, 1], 'ND2': [1, 1], 'ND3': [1, 1], 'ND4': [1, 1], 'ND4L': [1, 1], 'ND5': [1, 1], 'ND6': [1, 1], 'tRNA-Ala': [1, 1], 'tRNA-Arg': [1, 1], 'tRNA-Asn': [1, 1], 'tRNA-Asp': [1, 1], 'tRNA-Cys': [1, 1], 'tRNA-Gln': [1, 1], 'tRNA-Glu': [1, 1], 'tRNA-Gly': [1, 1], 'tRNA-His': [1, 1], 'tRNA-Ile': [1, 2], 'tRNA-Leu': [2, 3], 'tRNA-Lys': [1, 1], 'tRNA-Met': [1, 2], 'tRNA-Phe': [1, 1], 'tRNA-Pro': [1, 1], 'tRNA-Ser': [2, 2], 'tRNA-Thr': [1, 1], 'tRNA-Trp': [1, 1], 'tRNA-Tyr': [1, 1], 'tRNA-Val': [1, 1]}


Specific to NC_045179.1.gb:
{'12S ribosomal RNA': [1, 0], 'ATP8': [1, 0]}


Specific to Bombus_terrestris.gb:
{}

(fastani) mu2@tol-head2:/lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/had_reference_on_ncbi/compare_discrepancies$ fastANI -q Bombus_terrestris.fa -r NC_045179.1.fasta --visualize -o Bombus_terrestris-NC_045179.1.out

(biopython) mu2@tol-head2:/lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/had_reference_on_ncbi/compare_discrepancies$ Rscript visualize.R Bombus_terrestris.fa NC_045179.1.fasta Bombus_terrestris-NC_045179.1.out.visual

```

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

Running a Mitos annotation

```
mu2@tol-head2:/lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/checking_replace_old_leps/Bombus_terrestris/mitos$ echo ' singularity exec --bind /lustre/:/lustre/ /software/tola/images/mitohifi-2.2.sif mitohifi.py -c final_mitogenome.fasta -f NC_045179.1.fasta -g NC_045179.1.gb -o 5 -t 8 ' | bsub -n 8 -q normal -R"span[hosts=1] select[mem>78000] rusage[mem=78000]" -M78000 -P team311 -o species-%J -e s.error.%J 
```

Here results, no genes missing

```
(biopython) mu2@tol-head2:/lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/had_reference_on_ncbi/compare_discrepancies$ python /lustre/scratch123/tol/teams/tola/users/jf18/softwares/MitoHiFi/compareGenesLists.py NC_045179.1.gb genbank /lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/checking_replace_old_leps/Bombus_terrestris/mitos/final_mitogenome.gb genbank True
Shared genes:
{'12S ribosomal RNA': [1, 1], '16S ribosomal RNA': [1, 1], 'ATP6': [1, 1], 'ATP8': [1, 1], 'COX1': [1, 1], 'COX2': [1, 1], 'COX3': [1, 1], 'CYTB': [1, 1], 'ND1': [1, 1], 'ND2': [1, 1], 'ND3': [1, 1], 'ND4': [1, 1], 'ND4L': [1, 1], 'ND5': [1, 1], 'ND6': [1, 1], 'tRNA-Ala': [1, 1], 'tRNA-Arg': [1, 1], 'tRNA-Asn': [1, 1], 'tRNA-Asp': [1, 1], 'tRNA-Cys': [1, 1], 'tRNA-Gln': [1, 1], 'tRNA-Glu': [1, 1], 'tRNA-Gly': [1, 1], 'tRNA-His': [1, 1], 'tRNA-Ile': [1, 2], 'tRNA-Leu': [2, 3], 'tRNA-Lys': [1, 1], 'tRNA-Met': [1, 2], 'tRNA-Phe': [1, 1], 'tRNA-Pro': [1, 1], 'tRNA-Ser': [2, 2], 'tRNA-Thr': [1, 1], 'tRNA-Trp': [1, 1], 'tRNA-Tyr': [1, 1], 'tRNA-Val': [1, 1]}


Specific to NC_045179.1.gb:
{}


Specific to /lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/checking_replace_old_leps/Bombus_terrestris/mitos/final_mitogenome.gb:
{}
```

Lets rotate both by ND1

![](https://i.imgur.com/ZX5KTmT.png)

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



# 5 . Sarcophaga_caerulescens

```
(biopython) mu2@tol-head2:/lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/had_reference_on_ncbi/compare_discrepancies$ python /lustre/scratch123/tol/teams/tola/users/jf18/softwares/MitoHiFi/compareGenesLists.py Sarcophaga_caerulescens.gb genbank MW551788.1.gb genbank True
Shared genes:
{'ATP6': [1, 1], 'ATP8': [1, 1], 'COX1': [1, 1], 'COX2': [1, 1], 'COX3': [1, 1], 'CYTB': [1, 1], 'ND1': [1, 1], 'ND2': [1, 1], 'ND3': [1, 1], 'ND4': [1, 1], 'ND4L': [1, 1], 'ND5': [1, 1], 'ND6': [1, 1], 'rrnL': [1, 1], 'rrnS': [1, 1], 'tRNA-Ala': [1, 1], 'tRNA-Arg': [1, 1], 'tRNA-Asn': [1, 1], 'tRNA-Asp': [1, 1], 'tRNA-Cys': [1, 1], 'tRNA-Gln': [1, 1], 'tRNA-Glu': [1, 1], 'tRNA-Gly': [1, 1], 'tRNA-His': [1, 1], 'tRNA-Ile': [1, 1], 'tRNA-Leu': [2, 2], 'tRNA-Lys': [1, 1], 'tRNA-Met': [1, 1], 'tRNA-Phe': [1, 1], 'tRNA-Pro': [1, 1], 'tRNA-Ser': [2, 2], 'tRNA-Thr': [1, 1], 'tRNA-Trp': [1, 1], 'tRNA-Tyr': [1, 1], 'tRNA-Val': [1, 1]}


Specific to Sarcophaga_caerulescens.gb:
{}


Specific to MW551788.1.gb:
{}
```

![](https://i.imgur.com/TqD5Q1Z.png)


![](https://i.imgur.com/6zNwLDT.png)


# 6. Pterostichus_madidus

```
mu2@tol-head2:/lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/had_reference_on_ncbi/compare_discrepancies$ python /lustre/scratch123/tol/teams/tola/users/jf18/softwares/MitoHiFi/compareGenesLists.py Pterostichus_madidus.gb genbank KT876910.1.gb genbank True
Shared genes:
{'ATP6': [1, 1], 'ATP8': [1, 1], 'COX1': [1, 1], 'COX2': [1, 1], 'COX3': [1, 1], 'CYTB': [1, 1], 'ND1': [1, 1], 'ND2': [1, 1], 'ND3': [1, 1], 'ND4': [1, 1], 'ND4L': [1, 1], 'ND5': [1, 1], 'ND6': [1, 1], 'rrnL': [1, 1], 'rrnS': [1, 1], 'tRNA-Ala': [1, 1], 'tRNA-Arg': [1, 1], 'tRNA-Asn': [1, 1], 'tRNA-Asp': [1, 1], 'tRNA-Cys': [1, 1], 'tRNA-Gln': [1, 1], 'tRNA-Glu': [1, 1], 'tRNA-Gly': [1, 1], 'tRNA-His': [1, 1], 'tRNA-Ile': [1, 1], 'tRNA-Leu': [2, 2], 'tRNA-Lys': [1, 1], 'tRNA-Met': [1, 1], 'tRNA-Phe': [1, 1], 'tRNA-Pro': [1, 1], 'tRNA-Ser': [2, 2], 'tRNA-Thr': [1, 1], 'tRNA-Trp': [1, 1], 'tRNA-Tyr': [1, 1], 'tRNA-Val': [1, 1]}


Specific to Pterostichus_madidus.gb:
{}


Specific to KT876910.1.gb:
{}
```

![](https://i.imgur.com/LcBd4It.png)

![](https://i.imgur.com/kLI21K4.png)

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


# 7. Eupeodes latifasciatus

```
(biopython) mu2@tol-head2:/lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/had_reference_on_ncbi/compare_discrepancies$ python /lustre/scratch123/tol/teams/tola/users/jf18/softwares/MitoHiFi/compareGenesLists.py MZ329813.1.gb genbank Eupeodes_latifasciatus.gb genbank True
Shared genes:
{'12S ribosomal RNA': [1, 1], '16S ribosomal RNA': [1, 1], 'ATP6': [1, 1], 'ATP8': [1, 1], 'COX1': [1, 1], 'COX2': [1, 1], 'COX3': [1, 1], 'CYTB': [1, 1], 'ND1': [1, 1], 'ND2': [1, 1], 'ND3': [1, 1], 'ND4': [1, 1], 'ND4L': [1, 1], 'ND5': [1, 1], 'ND6': [1, 1], 'tRNA-Ala': [1, 1], 'tRNA-Arg': [1, 1], 'tRNA-Asn': [1, 1], 'tRNA-Asp': [1, 1], 'tRNA-Cys': [1, 1], 'tRNA-Gln': [1, 1], 'tRNA-Glu': [1, 1], 'tRNA-Gly': [1, 1], 'tRNA-His': [1, 1], 'tRNA-Ile': [1, 1], 'tRNA-Leu': [2, 2], 'tRNA-Lys': [1, 1], 'tRNA-Met': [1, 1], 'tRNA-Phe': [1, 1], 'tRNA-Pro': [1, 1], 'tRNA-Ser': [2, 2], 'tRNA-Thr': [1, 1], 'tRNA-Trp': [1, 1], 'tRNA-Tyr': [1, 1], 'tRNA-Val': [1, 1]}


Specific to MZ329813.1.gb:
{}


Specific to Eupeodes_latifasciatus.gb:
{}
```



![](https://i.imgur.com/ibe3Mob.png)

```
(biopython) mu2@tol-head2:/lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/had_reference_on_ncbi/compare_discrepancies$ echo ' mitofinder -j annotateMZ329813.1.RC -a MZ329813.1.RC.fa -r MZ329813.1.gb -o 5 ' | bsub -n 1 -q long -R"span[hosts=1] select[mem>78000] rusage[mem=78000]" -M78000 -P team311 -o anot.%J -e anot.error.%J 
Job <538664> is submitted to queue <long>.
```


![](https://i.imgur.com/7ik6Mxj.png)

![](https://i.imgur.com/pQz1sQj.png)


# 7. Acridotheres tristis

![](https://i.imgur.com/sMyMBf5.png)

# 8 . Agaricus_bisporus

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


```
(biopython) mu2@tol-head2:/lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/had_reference_on_ncbi/compare_discrepancies$ python /lustre/scratch123/tol/teams/tola/users/jf18/softwares/MitoHiFi/compareGenesLists.py Agaricus_bisporus.gb genbank JX271275.1.gb genbank True
Shared genes:
{'ATP6': [1, 1], 'ATP8': [1, 1], 'COX1': [1, 18], 'COX2': [1, 3], 'COX3': [1, 2], 'CYTB': [1, 5], 'ND1': [1, 1], 'ND2': [1, 1], 'ND3': [1, 1], 'ND4': [1, 2], 'ND4L': [1, 1], 'ND5': [1, 2], 'ND6': [1, 1], 'P3': [1, 1], 'atp9': [1, 1], 'dpo2': [1, 1], 'rps3': [1, 1], 'tRNA-Ala': [1, 1], 'tRNA-Arg': [2, 3], 'tRNA-Asn': [1, 1], 'tRNA-Asp': [1, 1], 'tRNA-Cys': [1, 1], 'tRNA-Gln': [1, 1], 'tRNA-Glu': [2, 2], 'tRNA-Gly': [2, 2], 'tRNA-His': [2, 2], 'tRNA-Ile': [2, 2], 'tRNA-Leu': [2, 3], 'tRNA-Lys': [2, 2], 'tRNA-Met': [5, 5], 'tRNA-Phe': [1, 1], 'tRNA-Pro': [1, 1], 'tRNA-Ser': [2, 3], 'tRNA-Thr': [1, 1], 'tRNA-Trp': [1, 1], 'tRNA-Tyr': [1, 1], 'tRNA-Val': [1, 1]}


Specific to Agaricus_bisporus.gb:
{'rrnL': [1, 0], 'rrnS': [1, 0]}


Specific to JX271275.1.gb:
{'large subunit ribosomal RNA': [0, 1], 'rnl': [0, 1], 'small subunit ribosomal RNA': [0, 1]}
```

```
mu2@tol-head1:/lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/had_reference_on_ncbi/mitohifi-bAcrTri1.MT.20220617$ echo ' singularity exec --bind /lustre/:/lustre/ /software/tola/images/mitohifi-2.2.sif mitohifi.py -c bAcrTri1.MT.20220617.fasta -f OK542103.1.fasta -g OK542103.1.gb -o 2 -t 8 ' | bsub -n 8 -q normal -R"span[hosts=1] select[mem>78000] rusage[mem=78000]" -M78000 -P team311 -o species-%J -e s.error.%J 
Job <538717> is submitted to queue <normal>.
```



# 9. Eupeodes_corollae

```
biopython) mu2@tol-head2:/lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/had_reference_on_ncbi/compare_discrepancies$ python /lustre/scratch123/tol/teams/tola/users/jf18/softwares/MitoHiFi/compareGenesLists.py NC_036482.1.gb genbank Eupeodes_corollae.gb genbank True
Shared genes:
{'12S ribosomal RNA': [1, 1], '16S ribosomal RNA': [1, 1], 'ATP6': [1, 1], 'ATP8': [1, 1], 'COX1': [1, 1], 'COX2': [1, 1], 'COX3': [1, 1], 'CYTB': [1, 1], 'ND1': [1, 1], 'ND2': [1, 1], 'ND3': [1, 1], 'ND4': [1, 1], 'ND4L': [1, 1], 'ND5': [1, 1], 'ND6': [1, 1], 'tRNA-Ala': [1, 1], 'tRNA-Arg': [1, 1], 'tRNA-Asn': [1, 1], 'tRNA-Asp': [1, 1], 'tRNA-Cys': [1, 1], 'tRNA-Gln': [1, 1], 'tRNA-Glu': [1, 1], 'tRNA-Gly': [1, 1], 'tRNA-His': [1, 1], 'tRNA-Ile': [1, 1], 'tRNA-Leu': [2, 2], 'tRNA-Lys': [1, 1], 'tRNA-Met': [1, 1], 'tRNA-Phe': [1, 1], 'tRNA-Pro': [1, 1], 'tRNA-Ser': [2, 2], 'tRNA-Thr': [1, 1], 'tRNA-Trp': [1, 1], 'tRNA-Tyr': [1, 1], 'tRNA-Val': [1, 1]}


Specific to NC_036482.1.gb:
{}


Specific to Eupeodes_corollae.gb:
{}

```

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


```
(biopython) mu2@tol-head2:/lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/had_reference_on_ncbi/compare_discrepancies$ echo ' mitofinder -j annotateRC.NC_036482.1.RC -a NC_036482.1.RC.fa -r NC_036482.1.gb -o 5  ' | bsub -n 1 -q long -R"span[hosts=1] select[mem>78000] rusage[mem=78000]" -M78000 -P team311 -o anot.%J -e anot.error.%J
Job <538724> is submitted to queue <long>.
```


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


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



# 10 . Platycheirus_albimanus


```
(biopython) mu2@tol-head2:/lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/had_reference_on_ncbi/compare_discrepancies$ echo ' mitofinder -j annotateOK299510.1.RC -a OK299510.1.RC.fa -r OK299510.1.gb -o 5  ' | bsub -n 1 -q long -R"span[hosts=1] select[mem>78000] rusage[mem=78000]" -M78000 -P team311 -o anot.%J -e anot.error.%J
Job <538756> is submitted to queue <long>.
```



# 11. Flammulina_velutipes

nesLists.py Flammulina_velutipes.gb genbank JN190941.1.rot.gb genbank True
Shared genes:
{'ATP6': [1, 1], 'ATP8': [1, 1], 'COX1': [1, 1], 'COX2': [1, 1], 'COX3': [1, 1], 'CYTB': [1, 1], 'ND1': [1, 1], 'ND2': [1, 1], 'ND3': [1, 1], 'ND4': [1, 1], 'ND4L': [1, 1], 'ND5': [1, 1], 'ND6': [1, 1], 'atp9': [1, 1], 'oi1cox1': [1, 1], 'oi2cox1': [1, 1], 'oi3cox1': [1, 1], 'oi4cox1': [1, 1], 'oi6cox1': [1, 1], 'oi7cox1': [1, 1], 'orf1014': [1, 1], 'orf107': [1, 1], 'orf1077': [1, 1], 'orf928': [1, 1], 'rps3': [1, 1], 'tRNA-Ala': [1, 1], 'tRNA-Arg': [2, 2], 'tRNA-Asn': [1, 1], 'tRNA-Asp': [1, 1], 'tRNA-Cys': [1, 1], 'tRNA-Gln': [1, 1], 'tRNA-Glu': [1, 1], 'tRNA-Gly': [1, 1], 'tRNA-His': [1, 1], 'tRNA-Ile': [1, 2], 'tRNA-Leu': [2, 2], 'tRNA-Lys': [1, 1], 'tRNA-Met': [3, 3], 'tRNA-Phe': [1, 1], 'tRNA-Pro': [1, 1], 'tRNA-Ser': [2, 2], 'tRNA-Thr': [1, 1], 'tRNA-Trp': [1, 1], 'tRNA-Tyr': [1, 1], 'tRNA-Val': [1, 1]}


Specific to Flammulina_velutipes.gb:
{'rrnL': [1, 0], 'rrnS': [1, 0]}


Specific to JN190941.1.rot.gb:
{'large subunit ribosomal RNA': [0, 1], 'oi1nad5': [0, 1], 'oi5cox1': [0, 1], 'orf174': [0, 1], 'orf230': [0, 1], 'orf245': [0, 1], 'orf370': [0, 1], 'orf418': [0, 1], 'small subunit ribosomal RNA': [0, 1]}


Plot of reads coverage mapping QV>60
![](https://i.imgur.com/1EJvtGf.png)

Flamulina against itself
![](https://i.imgur.com/GrQ3Ccp.png)


Flamulina against NCBI reference

![](https://i.imgur.com/HP2XlcW.png)



Mapped our reads to ncbi ref and didnt find that region covered.
![](https://i.imgur.com/yawH6vO.png)



# 12. Agaricus bisporus

![](https://i.imgur.com/vtj9wx1.png)


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

Agaricus against itself
![](https://i.imgur.com/USCB2OP.png)




```
mu2@tol-head1:/lustre/scratch123/tol/teams/tola/users/mu2/mitohifi-paper/had_reference_on_ncbi/compare_discrepancies$ python3 /lustre/scratch123/tol/teams/tola/users/jf18/softwares/MitoHiFi/compareGenesLists.py Agaricus_bisporus.gb genbank JX271275.1.gb genbank True 
Shared genes:
{'ATP6': [1, 1], 'ATP8': [1, 1], 'COX1': [1, 18], 'COX2': [1, 3], 'COX3': [1, 2], 'CYTB': [1, 5], 'ND1': [1, 1], 'ND2': [1, 1], 'ND3': [1, 1], 'ND4': [1, 2], 'ND4L': [1, 1], 'ND5': [1, 2], 'ND6': [1, 1], 'P3': [1, 1], 'atp9': [1, 1], 'dpo2': [1, 1], 'rps3': [1, 1], 'tRNA-Ala': [1, 1], 'tRNA-Arg': [2, 3], 'tRNA-Asn': [1, 1], 'tRNA-Asp': [1, 1], 'tRNA-Cys': [1, 1], 'tRNA-Gln': [1, 1], 'tRNA-Glu': [2, 2], 'tRNA-Gly': [2, 2], 'tRNA-His': [2, 2], 'tRNA-Ile': [2, 2], 'tRNA-Leu': [2, 3], 'tRNA-Lys': [2, 2], 'tRNA-Met': [5, 5], 'tRNA-Phe': [1, 1], 'tRNA-Pro': [1, 1], 'tRNA-Ser': [2, 3], 'tRNA-Thr': [1, 1], 'tRNA-Trp': [1, 1], 'tRNA-Tyr': [1, 1], 'tRNA-Val': [1, 1]}


Specific to Agaricus_bisporus.gb:
{'rrnL': [1, 0], 'rrnS': [1, 0]}


Specific to JX271275.1.gb:
{'large subunit ribosomal RNA': [0, 1], 'rnl': [0, 1], 'small subunit ribosomal RNA': [0, 1]}
```

# 13. Pleurotus_ostreatus

![](https://i.imgur.com/CxY4lSJ.png)

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