BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524511.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 = 1,389,317 number of mapped reads = 1,261,442 (90.8%) number of supplementary alignments = 6,087 (0.44%) number of secondary alignments = 0 number of mapped bases = 73,811,958 bp number of sequenced bases = 73,792,740 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,382 duplication rate = 1.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.309 >>>>>>> ACTG content number of A's = 19,095,400 bp (25.88%) number of C's = 12,928,949 bp (17.52%) number of T's = 23,225,526 bp (31.47%) number of G's = 18,540,712 bp (25.13%) number of N's = 2,153 bp (0%) GC percentage = 42.65% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 346,854 number of insertions = 4,976 mapped reads with insertion percentage = 0.39% number of deletions = 11,658 mapped reads with deletion percentage = 0.92% homopolymer indels = 43.36% >>>>>>> Coverage mean coverageData = 0.0238X std coverageData = 0.2226X There is a 2.19% of reference with a coverageData >= 1X There is a 0.14% 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 4988727 0.020014902991956837 0.34030645267418136 chr2 243199373 5819519 0.02392900494854483 0.24220703410724265 chr3 198022430 4349781 0.021966102526870316 0.1565688376430395 chr4 191154276 4378987 0.022908129975601488 0.1742192800204131 chr5 180915260 3914186 0.02163546623982963 0.15717478006927144 chr6 171115067 3792005 0.022160555855668746 0.16736189396851398 chr7 159138663 4503066 0.028296492600292867 0.29195427598943485 chr8 146364022 3837806 0.026220965696064295 0.22944935433740868 chr9 141213431 3255137 0.023051185549057298 0.22084771997242916 chr10 135534747 2684453 0.01980638219658904 0.2121021661764152 chr11 135006516 3405560 0.025225152836326804 0.21403535509424074 chr12 133851895 5248480 0.03921109970090449 0.22868892207785235 chr13 115169878 2787729 0.024205365573105844 0.16418933338294592 chr14 107349540 2486854 0.023165949290513962 0.17275407216318459 chr15 102531392 2315433 0.022582673997052532 0.16048612779247248 chr16 90354753 1926681 0.02132351576457743 0.16719513727009971 chr17 81195210 2073602 0.025538476961879893 0.17482898538889927 chr18 78077248 2204335 0.028232744576243262 0.407580170980406 chr19 59128983 1133616 0.01917191777169582 0.2607990710215023 chr20 63025520 2017406 0.03200935113268403 0.19567051301119287 chr21 48129895 861462 0.017898688538589166 0.16375580058846395 chr22 51304566 676160 0.013179333784833108 0.12040980638767289 chrMT 16571 4255 0.2567738820831573 0.5062178784341105 chrX 155270560 4924836 0.03171777058059171 0.21129641497945406 chrY 59373566 221882 0.00373705025566428 0.09427008863078172