BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716982.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt
>>>>>>> Reference
number of bases = 3,095,693,983 bp
number of contigs = 25
>>>>>>> Globals
number of windows = 424
number of reads = 2,363,378
number of mapped reads = 2,168,626 (91.76%)
number of supplementary alignments = 10,886 (0.46%)
number of secondary alignments = 0
number of mapped bases = 125,821,417 bp
number of sequenced bases = 125,784,909 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 77,570
duplication rate = 2.46%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 43.9242
>>>>>>> ACTG content
number of A's = 30,095,640 bp (23.93%)
number of C's = 24,085,223 bp (19.15%)
number of T's = 39,824,149 bp (31.66%)
number of G's = 31,778,504 bp (25.26%)
number of N's = 1,393 bp (0%)
GC percentage = 44.41%
>>>>>>> Mismatches and indels
general error rate = 0.0051
number of mismatches = 626,817
number of insertions = 7,604
mapped reads with insertion percentage = 0.35%
number of deletions = 23,369
mapped reads with deletion percentage = 1.07%
homopolymer indels = 42.62%
>>>>>>> Coverage
mean coverageData = 0.0406X
std coverageData = 0.376X
There is a 3.58% of reference with a coverageData >= 1X
There is a 0.34% of reference with a coverageData >= 2X
There is a 0.05% of reference with a coverageData >= 3X
There is a 0.01% of reference with a coverageData >= 4X
There is a 0.01% of reference with a coverageData >= 5X
There is a 0% of reference with a coverageData >= 6X
There is a 0% of reference with a coverageData >= 7X
There is a 0% of reference with a coverageData >= 8X
There is a 0% of reference with a coverageData >= 9X
There is a 0% of reference with a coverageData >= 10X
There is a 0% of reference with a coverageData >= 11X
There is a 0% of reference with a coverageData >= 12X
There is a 0% of reference with a coverageData >= 13X
There is a 0% of reference with a coverageData >= 14X
There is a 0% of reference with a coverageData >= 15X
There is a 0% of reference with a coverageData >= 16X
There is a 0% of reference with a coverageData >= 17X
There is a 0% of reference with a coverageData >= 18X
There is a 0% of reference with a coverageData >= 19X
There is a 0% of reference with a coverageData >= 20X
There is a 0% of reference with a coverageData >= 21X
There is a 0% of reference with a coverageData >= 22X
There is a 0% of reference with a coverageData >= 23X
There is a 0% of reference with a coverageData >= 24X
There is a 0% of reference with a coverageData >= 25X
There is a 0% of reference with a coverageData >= 26X
There is a 0% of reference with a coverageData >= 27X
There is a 0% of reference with a coverageData >= 28X
There is a 0% of reference with a coverageData >= 29X
There is a 0% of reference with a coverageData >= 30X
There is a 0% of reference with a coverageData >= 31X
There is a 0% of reference with a coverageData >= 32X
There is a 0% of reference with a coverageData >= 33X
There is a 0% of reference with a coverageData >= 34X
There is a 0% of reference with a coverageData >= 35X
There is a 0% of reference with a coverageData >= 36X
There is a 0% of reference with a coverageData >= 37X
There is a 0% of reference with a coverageData >= 38X
There is a 0% of reference with a coverageData >= 39X
There is a 0% of reference with a coverageData >= 40X
There is a 0% of reference with a coverageData >= 41X
There is a 0% of reference with a coverageData >= 42X
There is a 0% of reference with a coverageData >= 43X
There is a 0% of reference with a coverageData >= 44X
There is a 0% of reference with a coverageData >= 45X
There is a 0% of reference with a coverageData >= 46X
There is a 0% of reference with a coverageData >= 47X
There is a 0% of reference with a coverageData >= 48X
There is a 0% of reference with a coverageData >= 49X
There is a 0% of reference with a coverageData >= 50X
There is a 0% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 10091430 0.040487080672107933 0.5499867856676465
chr2 243199373 12093776 0.04972782557297136 0.43880488563718795
chr3 198022430 9176031 0.04633834157069985 0.25081978503232977
chr4 191154276 6769724 0.03541497549340722 0.217807661067204
chr5 180915260 6664151 0.03683575945998143 0.21345810989036695
chr6 171115067 6853646 0.04005284934961338 0.2491992274376192
chr7 159138663 8269149 0.05196191072687346 0.9075590368419454
chr8 146364022 9801548 0.06696692169336532 0.3954184949422814
chr9 141213431 4275421 0.030276305658206125 0.2378531618217781
chr10 135534747 5474586 0.04039249064300832 0.43935484115843587
chr11 135006516 4410239 0.03266686031657909 0.2586596154744019
chr12 133851895 6818657 0.0509418039991141 0.26767314542983145
chr13 115169878 4066525 0.03530892860718321 0.20608531938272912
chr14 107349540 3935560 0.036661172465201064 0.2167343703442819
chr15 102531392 2904492 0.02832783153865696 0.19527160071021596
chr16 90354753 3649547 0.04039131178854531 0.23730575489985653
chr17 81195210 5118437 0.06303865708334272 0.2943756089322076
chr18 78077248 2934588 0.03758569974187615 0.42420618472779636
chr19 59128983 2464162 0.04167435113842564 0.4707120762438976
chr20 63025520 2741762 0.043502409817483455 0.24108200383400813
chr21 48129895 930221 0.019327301669783407 0.1593120675466944
chr22 51304566 1828108 0.0356324620307674 0.21029607711580556
chrMT 16571 7111 0.4291231669784563 0.7649898114351285
chrX 155270560 4294483 0.027658063447442968 0.21527315207483075
chrY 59373566 248063 0.004178004063289714 0.0877496625678476