BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524575.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 = 3,361,107
number of mapped reads = 3,087,492 (91.86%)
number of supplementary alignments = 14,538 (0.43%)
number of secondary alignments = 0
number of mapped bases = 180,101,299 bp
number of sequenced bases = 180,045,593 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 195,830
duplication rate = 4.73%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.8623
>>>>>>> ACTG content
number of A's = 45,885,764 bp (25.49%)
number of C's = 33,965,932 bp (18.87%)
number of T's = 57,595,874 bp (31.99%)
number of G's = 42,595,396 bp (23.66%)
number of N's = 2,627 bp (0%)
GC percentage = 42.52%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 909,950
number of insertions = 12,777
mapped reads with insertion percentage = 0.41%
number of deletions = 33,456
mapped reads with deletion percentage = 1.08%
homopolymer indels = 42.4%
>>>>>>> Coverage
mean coverageData = 0.0582X
std coverageData = 0.4918X
There is a 4.81% of reference with a coverageData >= 1X
There is a 0.71% of reference with a coverageData >= 2X
There is a 0.13% of reference with a coverageData >= 3X
There is a 0.04% of reference with a coverageData >= 4X
There is a 0.01% of reference with a coverageData >= 5X
There is a 0.01% of reference with a coverageData >= 6X
There is a 0.01% of reference with a coverageData >= 7X
There is a 0.01% 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 17734454 0.07115109253830104 0.9900418763383892
chr2 243199373 14159957 0.058223657509182805 0.5692177652083197
chr3 198022430 10082901 0.05091797429210418 0.2702200370479537
chr4 191154276 10083227 0.05274915743972162 0.32637961396531795
chr5 180915260 9758363 0.05393886065774661 0.2755493039709099
chr6 171115067 7619329 0.044527516679755616 0.3567322559873017
chr7 159138663 9033741 0.05676647541018992 0.6566968929875749
chr8 146364022 16491973 0.11267777951606167 0.5087185705480388
chr9 141213431 7676010 0.05435750654624347 0.40694240565256057
chr10 135534747 9429755 0.06957444647017344 0.472047974007335
chr11 135006516 6106657 0.04523231308331814 0.4526841197253676
chr12 133851895 8358994 0.06244957533100297 0.2967694866124347
chr13 115169878 3940021 0.03421051639908831 0.21704277062664415
chr14 107349540 4282865 0.039896444828734244 0.24531776534875716
chr15 102531392 4854128 0.047342846959495095 0.27228348968999405
chr16 90354753 5601758 0.06199738048091394 0.32447912942079093
chr17 81195210 6361749 0.07835128451542893 0.3668535713429043
chr18 78077248 4157162 0.053244217828989054 0.7951400286673491
chr19 59128983 3721146 0.0629326907246147 0.6587754776232077
chr20 63025520 5065335 0.08036958679595187 0.3409131620180392
chr21 48129895 2498687 0.05191548828436048 0.3078590898256114
chr22 51304566 1487595 0.028995372458661867 0.19742345613393553
chrMT 16571 14852 0.8962645585661698 1.241776799802397
chrX 155270560 10986551 0.07075746361705658 0.37441908059102696
chrY 59373566 594089 0.010005951133202948 0.26578840879867593