BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717086.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 = 1,261,097 number of mapped reads = 1,141,327 (90.5%) number of supplementary alignments = 18,367 (1.46%) number of secondary alignments = 0 number of mapped bases = 90,191,981 bp number of sequenced bases = 90,152,926 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,456 duplication rate = 2.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.923 >>>>>>> ACTG content number of A's = 22,858,950 bp (25.36%) number of C's = 17,753,006 bp (19.69%) number of T's = 27,825,212 bp (30.86%) number of G's = 21,710,126 bp (24.08%) number of N's = 5,632 bp (0.01%) GC percentage = 43.77% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 756,668 number of insertions = 7,974 mapped reads with insertion percentage = 0.69% number of deletions = 22,719 mapped reads with deletion percentage = 1.97% homopolymer indels = 44.76% >>>>>>> Coverage mean coverageData = 0.0291X std coverageData = 0.3309X There is a 2.58% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 7097997 0.028477349310194897 0.49411546983787685 chr2 243199373 7609848 0.03129057409206396 0.4904820013817819 chr3 198022430 6050250 0.030553357011122426 0.19203090596902983 chr4 191154276 5785460 0.030265919868828883 0.20569899673165332 chr5 180915260 5339381 0.02951315991807435 0.1902310464381524 chr6 171115067 5253753 0.030703041480268947 0.22848876018603667 chr7 159138663 4953465 0.031126722486037223 0.41586558126938417 chr8 146364022 4637780 0.03168661216483925 0.4311508758125777 chr9 141213431 3945886 0.027942710350264063 0.3724489006992835 chr10 135534747 4111871 0.030338131667446134 0.3134644351351858 chr11 135006516 4110596 0.030447389665251415 0.3248338130432914 chr12 133851895 4121747 0.030793340654609334 0.19790364386328352 chr13 115169878 2813694 0.02443081514768992 0.169962758325528 chr14 107349540 2644437 0.024633892236520065 0.21729455948432144 chr15 102531392 2567592 0.025042008597718053 0.17445920285622482 chr16 90354753 2683596 0.02970066223300948 0.21044234125856562 chr17 81195210 2529237 0.031150076463870222 0.2088748555389191 chr18 78077248 2553568 0.03270566093722976 0.683440823366892 chr19 59128983 1914563 0.03237943395711711 0.38939311397763293 chr20 63025520 1865435 0.029598089789659807 0.20176542089874866 chr21 48129895 1149634 0.02388606914683691 0.18145672154955164 chr22 51304566 1008951 0.019665910437679172 0.15286359215630058 chrMT 16571 6548 0.39514815038319956 0.6923188627487686 chrX 155270560 5191097 0.033432590183225974 0.2620364181089231 chrY 59373566 245595 0.004136436743583836 0.1294729987748992