BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716437.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 = 1,258,976 number of mapped reads = 1,088,165 (86.43%) number of supplementary alignments = 4,128 (0.33%) number of secondary alignments = 0 number of mapped bases = 61,622,931 bp number of sequenced bases = 61,604,394 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,512 duplication rate = 1.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.9537 >>>>>>> ACTG content number of A's = 16,063,132 bp (26.07%) number of C's = 12,359,003 bp (20.06%) number of T's = 18,942,152 bp (30.75%) number of G's = 14,239,251 bp (23.11%) number of N's = 856 bp (0%) GC percentage = 43.18% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 317,941 number of insertions = 4,986 mapped reads with insertion percentage = 0.46% number of deletions = 11,912 mapped reads with deletion percentage = 1.09% homopolymer indels = 40.66% >>>>>>> Coverage mean coverageData = 0.0199X std coverageData = 0.2022X There is a 1.84% of reference with a coverageData >= 1X There is a 0.1% 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 5234178 0.02099965881328737 0.2664173610039173 chr2 243199373 6191822 0.02545986004659642 0.2485314055262697 chr3 198022430 4523256 0.022842139650543627 0.16489710494149876 chr4 191154276 3697011 0.019340456710474005 0.1508444469537193 chr5 180915260 3484826 0.019262200435717806 0.14644078953131703 chr6 171115067 3563343 0.02082425038585293 0.16209961247935153 chr7 159138663 3164315 0.019884011467408143 0.39298170821939926 chr8 146364022 4404599 0.030093454250662774 0.21856229121169268 chr9 141213431 2274895 0.016109622037297572 0.1533239509975878 chr10 135534747 2955239 0.021804290526325328 0.2594421655392732 chr11 135006516 2141054 0.01585889380331835 0.15307126487058648 chr12 133851895 2901919 0.021680074084868203 0.1610352026518538 chr13 115169878 1714916 0.01489031706710673 0.12843977409645524 chr14 107349540 1637383 0.015252818037226801 0.13693200313749318 chr15 102531392 1533283 0.014954278588161566 0.13111276978585548 chr16 90354753 1933802 0.021402327335231605 0.16289903500514402 chr17 81195210 2008183 0.024732776724144194 0.16895048742301547 chr18 78077248 1625827 0.02082331334219157 0.24049091014747082 chr19 59128983 1264671 0.021388343513366364 0.23750488291725205 chr20 63025520 1383269 0.021947760208880465 0.15999894882376517 chr21 48129895 672865 0.013980188404732651 0.1280915223698452 chr22 51304566 799465 0.015582726106678301 0.1325459717146924 chrMT 16571 22374 1.3501900911230462 1.464339845228877 chrX 155270560 2354503 0.015163872662016548 0.14373805181563704 chrY 59373566 135933 0.002289453188646274 0.06140468468964031