BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525254.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 = 1,518,921 number of mapped reads = 1,387,921 (91.38%) number of supplementary alignments = 6,353 (0.42%) number of secondary alignments = 0 number of mapped bases = 80,916,788 bp number of sequenced bases = 80,889,727 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,201 duplication rate = 2.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9237 >>>>>>> ACTG content number of A's = 19,697,589 bp (24.35%) number of C's = 14,752,189 bp (18.24%) number of T's = 26,417,735 bp (32.66%) number of G's = 20,020,732 bp (24.75%) number of N's = 1,482 bp (0%) GC percentage = 42.99% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 409,135 number of insertions = 5,342 mapped reads with insertion percentage = 0.38% number of deletions = 16,899 mapped reads with deletion percentage = 1.21% homopolymer indels = 44.98% >>>>>>> Coverage mean coverageData = 0.0261X std coverageData = 0.2686X There is a 2.39% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 8493757 0.03407717487692839 0.47660881145345135 chr2 243199373 6637811 0.027293701123152155 0.31774687973240057 chr3 198022430 5031684 0.025409666975604733 0.17245050105291576 chr4 191154276 4570414 0.023909556697544136 0.17004643719970938 chr5 180915260 3608595 0.019946327357902256 0.15186406441526046 chr6 171115067 4903069 0.02865363691205521 0.2058971446414234 chr7 159138663 5909496 0.03713425693415559 0.48081627219444584 chr8 146364022 5347978 0.03653888385220789 0.28093968338717307 chr9 141213431 2619345 0.01854883761021287 0.1864074814944457 chr10 135534747 5359561 0.039543815284504125 0.3092269405881808 chr11 135006516 3631591 0.02689937573087213 0.22413235948061777 chr12 133851895 3581715 0.026758791872165875 0.17784505559722422 chr13 115169878 2515417 0.021840927885675106 0.16002081061512158 chr14 107349540 1798918 0.01675757530027609 0.14298240997875925 chr15 102531392 2142435 0.020895405379846983 0.15639631593374928 chr16 90354753 2052783 0.02271914793458624 0.18138014744705375 chr17 81195210 1312313 0.016162443572718146 0.14003027110789285 chr18 78077248 1724358 0.022085281489429544 0.3889862746080559 chr19 59128983 1458437 0.02466534897107904 0.3385312965448654 chr20 63025520 1394496 0.02212589439960194 0.16143560715800087 chr21 48129895 1135516 0.02359273794384966 0.17038111724371535 chr22 51304566 819758 0.015978265950052088 0.13463162493226064 chrMT 16571 79873 4.8200470701828495 3.473122934120419 chrX 155270560 4560386 0.02937057739728639 0.19790661033665105 chrY 59373566 227082 0.0038246313182536485 0.09792899764185507