---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
layout: post
title: Genome Feature Counts - Panopea-generosa-vv0.74.a4
date: '2019-10-29 14:45'
tags:
  - jupyter notebook
  - Panopea generosa
  - geoduck
  - genome
categories:
  - 2019
  - Geoduck Genome Sequencing
---
#### UPDATE 20191203

Due to a bug with GenSAS, the final GFF generated by their system to did not properly merge all of the repeats data properly. The _repeats data below should be ignored_! It appears that the other features data (e.g. CDS, exons, etc) was unaffected by the bug.

Here's the updated analysis: https://robertslab.github.io/sams-notebook/posts/2019/2019-12-03-Data-Wrangling---Renaming,-Splitting,-and-Feature-Counts-of-Updated-Pgenerosa_v074-GenSAS-Merged-GFF/

I'll leave original notebook entry below for posterity.

---

In preparation for a paper we're writing, we needed some summary stats for [Panopea-generosa-vv0.74.a4](https://robertslab.github.io/sams-notebook/posts/2019/2019-09-28-Genome-Annotation---Pgenerosa_v074-a4-Using-GenSAS/). This info will be compiled in to a table for the manuscript. See our Genomic Resources wiki for more info on GFFs:

- [Genomic Resources Wiki](https://github.com/RobertsLab/resources/wiki/Genomic-Resources) (GitHub)

Calculations were performed using Python in  Jupyter Notebooks.

Genome Features Jupyter Notebook (GitHub):

 - [20191029_swoose_pgen_v074.a4_genome_feature_counts.ipynb](https://github.com/RobertsLab/code/blob/master/notebooks/sam/20191029_swoose_pgen_v074.a4_genome_feature_counts.ipynb)

 Repeat Features Jupyter Notbooke (GitHub):

 - [20191029_swoose_pgen_v074.a4_genome_repeats_counts.ipyn](https://github.com/RobertsLab/code/blob/master/notebooks/sam/20191029_swoose_pgen_v074.a4_genome_repeats_counts.ipynb)

---

# RESULTS

I've copied/pasted the summary data for each of the GFFs that were analyzed, for quick reference. Will get this compiled in to a table of some sort for people to use for the manuscript.

Also, the repeats were split into individual GFFs by repeat type. Those GFFs can be found here:

- [20191029_pgen_v074.a4_repeats_counts](https://gannet.fish.washington.edu/Atumefaciens/20191029_pgen_v074.a4_repeats_counts/)


#### Genome Features
```
Panopea-generosa-vv0.74.a4.mRNA.gff3
-------------------------
mean       12903.649559
min          166.000000
median      5453.000000
max       283066.000000
Name: seqlength, dtype: float64



Panopea-generosa-vv0.74.a4.gene.gff3
-------------------------
mean       10811.04461
min          166.00000
median      4464.00000
max       283066.00000
Name: seqlength, dtype: float64



Panopea-generosa-vv0.74.a4.CDS.gff3
-------------------------
mean        201.476988
min           3.000000
median      133.000000
max       13221.000000
Name: seqlength, dtype: float64



Panopea-generosa-vv0.74.a4.tRNA.gff3
-------------------------
mean       74.805659
min        53.000000
median     75.000000
max       314.000000
Name: seqlength, dtype: float64



Panopea-generosa-vv0.74.a4.rRNA.gff3
-------------------------
mean      118.428571
min       113.000000
median    115.000000
max       138.000000
Name: seqlength, dtype: float64



Panopea-generosa-vv0.74.a4.exon.gff3
-------------------------
mean        201.476988
min           3.000000
median      133.000000
max       13221.000000
Name: seqlength, dtype: float64
```

---

#### Repeats Features
```
Panopea-generosa-vv0.74.a4.repeats.LINE.gff3
-------------------------
percent 2.91
sum       27388849.00
mean           394.85
min             11.00
median         226.00
max           6604.00
Name: seqlength, dtype: float64



Panopea-generosa-vv0.74.a4.repeats.Simple_repeat.gff3
-------------------------
percent 0.5
sum       4733271.0
mean          261.2
min             6.0
median        125.0
max          5981.0
Name: seqlength, dtype: float64



Panopea-generosa-vv0.74.a4.repeats.Unknown.gff3
-------------------------
percent 29.09
sum       2.740281e+08
mean      1.991900e+02
min       1.100000e+01
median    1.440000e+02
max       6.574000e+03
Name: seqlength, dtype: float64



Panopea-generosa-vv0.74.a4.repeats.LTR.gff3
-------------------------
percent 0.22
sum       2060084.00
mean          712.83
min            11.00
median        316.00
max          6541.00
Name: seqlength, dtype: float64



Panopea-generosa-vv0.74.a4.repeats.RC.gff3
-------------------------
percent 0.02
sum       232303.00
mean         425.46
min           13.00
median       464.00
max          674.00
Name: seqlength, dtype: float64



Panopea-generosa-vv0.74.a4.repeats.SINE.gff3
-------------------------
percent 0.65
sum       6133778.00
mean          155.69
min            11.00
median        164.00
max           934.00
Name: seqlength, dtype: float64



Panopea-generosa-vv0.74.a4.repeats.DNA.gff3
-------------------------
percent 0.91
sum       8602532.00
mean          407.82
min            11.00
median        247.00
max          7012.00
Name: seqlength, dtype: float64



-------------------------
Repeats composition of genome (percent): 34.3
```