BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524636.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 = 939,852 number of mapped reads = 856,758 (91.16%) number of supplementary alignments = 3,653 (0.39%) number of secondary alignments = 0 number of mapped bases = 50,141,995 bp number of sequenced bases = 50,125,447 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,756 duplication rate = 3.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0903 >>>>>>> ACTG content number of A's = 12,398,755 bp (24.74%) number of C's = 9,386,594 bp (18.73%) number of T's = 16,155,324 bp (32.23%) number of G's = 12,184,340 bp (24.31%) number of N's = 434 bp (0%) GC percentage = 43.03% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 252,220 number of insertions = 3,961 mapped reads with insertion percentage = 0.46% number of deletions = 9,542 mapped reads with deletion percentage = 1.11% homopolymer indels = 40.54% >>>>>>> Coverage mean coverageData = 0.0162X std coverageData = 0.1785X There is a 1.46% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 5175181 0.0207629613087303 0.3098868466346643 chr2 243199373 4421068 0.01817878041979985 0.20550164191326062 chr3 198022430 3092503 0.015616932889875153 0.13504680847243886 chr4 191154276 2294057 0.012001076031383154 0.14437979317669422 chr5 180915260 3083053 0.01704142038653898 0.1410168876745936 chr6 171115067 3210509 0.018762281173054153 0.15359376503073863 chr7 159138663 3023993 0.01900225214283722 0.1940538513537868 chr8 146364022 4386734 0.029971395566049695 0.23982040283285094 chr9 141213431 1793815 0.012702863936504737 0.14501658976609477 chr10 135534747 2216615 0.016354588392008436 0.19816493381258182 chr11 135006516 2538666 0.01880402572569164 0.16430844100486308 chr12 133851895 1542053 0.0115205914716411 0.11757154426121126 chr13 115169878 1187302 0.010309136560863597 0.10991796533334305 chr14 107349540 920402 0.008573879310521499 0.10268955516861293 chr15 102531392 1275231 0.012437468907083598 0.12067258559673963 chr16 90354753 1478254 0.01636055604069882 0.14312204598091202 chr17 81195210 1101365 0.013564408540848654 0.1289193735658548 chr18 78077248 1315464 0.016848237273936705 0.22492962297116562 chr19 59128983 1019443 0.01724100345172519 0.21941896478147896 chr20 63025520 944741 0.014989816823407408 0.13675132579522958 chr21 48129895 744039 0.015458978250420035 0.14919895552175205 chr22 51304566 938535 0.01829340102009634 0.14701695838743967 chrMT 16571 6364 0.3840444149417657 0.6542887272898228 chrX 155270560 2274336 0.014647567446140467 0.13619687001051356 chrY 59373566 158272 0.0026656980650277937 0.10869830254076258