BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524516.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 = 1,396,990 number of mapped reads = 1,264,580 (90.52%) number of supplementary alignments = 5,557 (0.4%) number of secondary alignments = 0 number of mapped bases = 73,327,087 bp number of sequenced bases = 73,304,436 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 71,475 duplication rate = 4.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6494 >>>>>>> ACTG content number of A's = 18,574,538 bp (25.34%) number of C's = 12,462,407 bp (17%) number of T's = 23,641,480 bp (32.25%) number of G's = 18,624,997 bp (25.41%) number of N's = 1,014 bp (0%) GC percentage = 42.41% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 378,780 number of insertions = 5,090 mapped reads with insertion percentage = 0.4% number of deletions = 13,541 mapped reads with deletion percentage = 1.06% homopolymer indels = 43.94% >>>>>>> Coverage mean coverageData = 0.0237X std coverageData = 0.2479X There is a 2.05% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.04% 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 7252590 0.029097580462999127 0.45656718419316844 chr2 243199373 5763174 0.023697322607817744 0.3044866564634024 chr3 198022430 3836709 0.01937512331305095 0.15666740122296877 chr4 191154276 4216067 0.0220558341054322 0.2025283965431195 chr5 180915260 3976448 0.021979616313184416 0.1674500928314043 chr6 171115067 3194402 0.018668151531039637 0.18367815792145037 chr7 159138663 3684166 0.02315066578132556 0.2830626472079833 chr8 146364022 6691801 0.045720259040162206 0.28687324325944724 chr9 141213431 3172355 0.02246496652290815 0.20251441443171006 chr10 135534747 3928425 0.028984633733812923 0.2704008900680095 chr11 135006516 2506998 0.018569459269654805 0.20928508355699624 chr12 133851895 3382961 0.02527391188596919 0.1799009734792451 chr13 115169878 1637680 0.0142196903256249 0.13478670996306527 chr14 107349540 1673180 0.015586280108885422 0.14342030826945534 chr15 102531392 1946662 0.018986009670092063 0.15525105297917915 chr16 90354753 2269333 0.02511581211449939 0.18782424060994188 chr17 81195210 2558745 0.03151349691687478 0.20831058933233076 chr18 78077248 1749311 0.022404875233307402 0.34576983193361777 chr19 59128983 1505648 0.025463789898094474 0.3055216720130539 chr20 63025520 2064270 0.03275292294296025 0.20879073971386566 chr21 48129895 1016542 0.021120802362024682 0.1826073746441875 chr22 51304566 611915 0.011927106059137115 0.12459403776974336 chrMT 16571 8758 0.5285136684569428 0.9625599801707018 chrX 155270560 4390442 0.028276075000953176 0.20123597805093885 chrY 59373566 288505 0.004859148935066491 0.1614904552945395