Needed to pull some numbers on repeats in our Pgenerosa_v074.a3 GenSAS annotation (from 20190710) 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
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):
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