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# System prepended metadata

title: iyBomPasc1 mitochondrion

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# iyBomPasc1 mitochondrion

- Auto-generated Table of Content
[ToC]

## :memo: 1. Email Prof Ian
What Prof Ian wrote me on June, 23rd 2021

Hi Marcela
I’m not sure we’ve met, but I chair the samples working group for DToL. We (Ian, Victoria and Farhan) have run into a problem with the DToL Bombus pascuorum genome and Mark Blaxter suggested I contact you about it. Let me know if there’s someone else I should direct this to.
 
We have been using the iyBomPasc1.1 genome to align illumina NextSeq PE 75bp data of  museum specimens of B. pascuorum. Our data have been adapter trimmed and the data collapsed into single reads, as per the norm in ancient DNA analysis. These single reads have then been aligned to the reference using bwa aln and filtered for duplicates and mapping quality. Along with the autosomes we have an interest in the mitogenome. We have used the mitogenome in the tree of life assembly - HG995285. We note that the length of this contig is 21904 bp.
 
We have noticed a ~ 6kb region (between around 2900bp & 9100 bp) in our alignments where there is a lack of aligned data. This gap is present in all samples regardless of coverage, mapping quality filter 25, both when aligning to the whole genome including the mitogenome and when aligning to just the mitogenome (see attached, fig 1). This gap remains when the mapping quality filter is reduced to 15 (fig 2). However, when no mapping quality filtering is applied the gap is filled albeit with snpy data (fig 3).                                                                                               
Note also that when the alignment is just to the mt genome, a lot of poorly matching (snpy) reads map at the 11-12 Kb mark.



## 1.1 Mapping of 10x and Pacbio Hifi reads back to the mitochondrion

### 1.2 On the top 10x, botton HiFi reads

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


### 1.3 A zoom in the region 2900bp & 9100 bp

![](https://i.imgur.com/u6eV01G.png)



### 2 CG Content

The region is 90% AT and has no genes

### iyBomPasc1 Conclusions for now

By the mapping it seems the assembly is correct. The region is not great as it is a ATAT region so its hard to assemble and to map reads back.

### 3 MBG


MBG -k 201 -w 150 -a 5 -u 90

![](https://i.imgur.com/T5uoXB3.png)

MBG -k 301 -w 150 -a 5 -u 10

![](https://i.imgur.com/k0eO7EJ.png)


# 2. Other Bombus 

## iyBomCamp1	
GCA_905333015.1	Bombus campestris

```/lustre/scratch116/tol/projects/darwin/data/insects/Bombus_campestris/working/mito```

 MBG -k 301 -w 150 -a 5 -u 150

![](https://i.imgur.com/Wm32a5W.png)


MBG -k 301 -w 150 -a 5 -u 150

iyBomHort1	GCA_905332935.1	Bombus hortorum
```/lustre/scratch116/tol/projects/darwin/data/insects/Bombus_hortorum/working/mito```


![](https://i.imgur.com/Vlcc11q.png)
