---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
layout: post
title: Data Wrangling - Pgenerosa_v074.a3 Annotation Genome Repeats Compostion
date: '2019-09-05 15:30'
tags:
  - Panopea generosa
  - geoduck
  - repeats
  - Jupyter
  - Pgenerosa_v074.a3
categories:
  - 2019
  - Geoduck Genome Sequencing
---
Needed to pull some numbers on repeats in our Pgenerosa_v074.a3 GenSAS annotation ([from 20190710](https://robertslab.github.io/sams-notebook/posts/2019/2019-07-10-Genome-Annotation---Pgenerosa_v074-Using-GenSAS/)) for the manuscript we're putting together.

Used the following file (repeats identified via RepeatMasker; original file name t_5d25021b0d20b-5d250896def4c-repeatmasker.gensas.gff3):

[Panopea-generosa-vv0.74.a3.TE.gff3](https://owl.fish.washington.edu/halfshell/genomic-databank/Panopea-generosa-vv0.74.a3.TE.gff3)

Repeats were analyzed by type of repeats:

- DNA transposons (DNA)

- Simple repeats

- LINE (Long Interspersed Nuclear Elements)

- LTR (Long Terminal Repeats)

- SINE (Short Interspersed Nuclear Elements)

- Unknown repeats

Analysis was done in a Jupyter notebook (link below).

Jupyter Notebook (GitHub):

- [20190905_swoose_pgen_v074.a3_genome_repeats_counts.ipynb](https://github.com/RobertsLab/code/blob/master/notebooks/sam/20190905_swoose_pgen_v074.a3_genome_repeats_counts.ipynb)

---

# RESULTS

Will add info to manuscript and create a table.

```
Panopea-generosa-vv0.74.a3.repeats.DNA.gff3
-------------------------
percent 1.2
sum       11316890.00
mean           293.09
min              1.00
median         154.00
max           7012.00




Panopea-generosa-vv0.74.a3.repeats.Simple_repeat.gff3
-------------------------
percent 2.03
sum       19132744.00
mean            63.78
min              1.00
median          41.00
max          12422.00




Panopea-generosa-vv0.74.a3.repeats.LINE.gff3
-------------------------
percent 3.11
sum       29258694.00
mean           396.48
min             11.00
median         227.00
max           6604.00




Panopea-generosa-vv0.74.a3.repeats.LTR.gff3
-------------------------
percent 0.46
sum       4355629.00
mean          370.63
min             1.00
median        276.00
max          6541.00




Panopea-generosa-vv0.74.a3.repeats.SINE.gff3
-------------------------
percent 2.3
sum       21645991.00
mean           147.84
min              1.00
median         142.00
max            934.00




Panopea-generosa-vv0.74.a3.repeats.Unknown.gff3
-------------------------
percent 31.14
sum       2.933161e+08
mean      2.001500e+02
min       1.100000e+01
median    1.450000e+02
max       1.098100e+04




-------------------------
Repeats composition of genome (percent): 40.24
```
