BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716192.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 = 1,891,224 number of mapped reads = 1,693,373 (89.54%) number of supplementary alignments = 52,505 (2.78%) number of secondary alignments = 0 number of mapped bases = 128,052,593 bp number of sequenced bases = 128,004,983 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,487 duplication rate = 1.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4135 >>>>>>> ACTG content number of A's = 32,718,800 bp (25.56%) number of C's = 25,936,942 bp (20.26%) number of T's = 37,587,938 bp (29.36%) number of G's = 31,745,330 bp (24.8%) number of N's = 15,973 bp (0.01%) GC percentage = 45.06% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 984,685 number of insertions = 10,249 mapped reads with insertion percentage = 0.6% number of deletions = 27,156 mapped reads with deletion percentage = 1.58% homopolymer indels = 40.8% >>>>>>> Coverage mean coverageData = 0.0414X std coverageData = 0.3371X There is a 3.59% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% 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 10251910 0.041130930622636244 0.38701035655021415 chr2 243199373 10775669 0.04430796373804796 0.48624700472875104 chr3 198022430 8366979 0.042252683193514995 0.23035184057322522 chr4 191154276 8129978 0.042530976393120284 0.2566149053299484 chr5 180915260 7737644 0.04276943802308329 0.2336331743259538 chr6 171115067 7401386 0.04325385326822214 0.2641691406834911 chr7 159138663 7036993 0.044219254248730244 0.41304554952292255 chr8 146364022 6497766 0.0443945575641533 0.4337891883974154 chr9 141213431 5444975 0.03855847819461309 0.3631813203199635 chr10 135534747 6106487 0.04505477108390515 0.349002329632181 chr11 135006516 5750227 0.042592218289671295 0.368875543153163 chr12 133851895 5818184 0.04346732633109154 0.23753734269937968 chr13 115169878 4032331 0.035012028058239324 0.2090491566236466 chr14 107349540 3849797 0.03586225893469129 0.2578022383015468 chr15 102531392 3720028 0.036281844296037646 0.21290000833641357 chr16 90354753 3874581 0.04288187252307579 0.26329860791640103 chr17 81195210 3659332 0.04506832361170074 0.26117473522327533 chr18 78077248 3529765 0.045208624668738324 0.6755633360327845 chr19 59128983 2721063 0.04601910707647382 0.3600074796108458 chr20 63025520 2738766 0.043454873517901955 0.24480683135589726 chr21 48129895 1667820 0.034652475348221724 0.2324904472989274 chr22 51304566 1588203 0.03095636750927783 0.1983560083880052 chrMT 16571 2786 0.16812503771649268 0.4297867696550744 chrX 155270560 7007339 0.045129862351240314 0.29903822811583985 chrY 59373566 342584 0.005769975143483886 0.18052363658896153