BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238318.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,601,166 number of mapped reads = 2,350,347 (90.36%) number of supplementary alignments = 34,763 (1.34%) number of secondary alignments = 0 number of mapped bases = 157,669,408 bp number of sequenced bases = 157,587,428 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 212,369 duplication rate = 7.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.355 >>>>>>> ACTG content number of A's = 45,323,165 bp (28.76%) number of C's = 29,614,486 bp (18.79%) number of T's = 49,556,666 bp (31.45%) number of G's = 33,042,639 bp (20.97%) number of N's = 50,472 bp (0.03%) GC percentage = 39.76% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,401,468 number of insertions = 12,553 mapped reads with insertion percentage = 0.53% number of deletions = 47,410 mapped reads with deletion percentage = 1.99% homopolymer indels = 45.68% >>>>>>> Coverage mean coverageData = 0.0509X std coverageData = 0.5584X There is a 3.11% of reference with a coverageData >= 1X There is a 1.15% of reference with a coverageData >= 2X There is a 0.45% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 18746687 0.07521219776619935 0.7641674503092762 chr2 243199373 19519265 0.08026034261198527 0.6429114594305302 chr3 198022430 5765779 0.02911679752642163 0.25526435580292633 chr4 191154276 5139748 0.026887957243498965 0.268504496491952 chr5 180915260 6507801 0.03597154269905148 0.2861611888505015 chr6 171115067 9553389 0.05583020342679701 0.42090925778515115 chr7 159138663 3241399 0.02036839407152742 0.2873793162480856 chr8 146364022 10734498 0.07334109744538177 1.4574683079214255 chr9 141213431 5038229 0.03567811478215553 0.44102414353415814 chr10 135534747 4673988 0.034485533071456576 0.40183472431762457 chr11 135006516 7223291 0.053503276834430714 0.508271996015834 chr12 133851895 10721768 0.08010172736067726 0.4273922719757266 chr13 115169878 7443588 0.06463137870129548 0.38492824718473106 chr14 107349540 6333889 0.059002479190874965 0.37795984052692916 chr15 102531392 3328554 0.032463755100486685 0.2676699549379517 chr16 90354753 4744779 0.052512777053355456 0.37528521313380225 chr17 81195210 2732239 0.033650248579934705 0.29535357112794236 chr18 78077248 1277043 0.01635614769618929 0.9805775896950039 chr19 59128983 2614230 0.04421232815724228 0.5609206310755566 chr20 63025520 5343348 0.08478070470501473 0.4510549911394199 chr21 48129895 2822009 0.05863318421949601 0.3746199032081868 chr22 51304566 2504626 0.048818773752028234 0.3191842877823862 chrMT 16571 13261 0.8002534548307284 1.3955636104330793 chrX 155270560 11074528 0.07132406812985025 0.45262617577404696 chrY 59373566 571472 0.009625024038475304 0.2350050407104891