BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8751225.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP188831/SRP188831.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 = 5,222,297 number of mapped reads = 4,908,410 (93.99%) number of supplementary alignments = 188,410 (3.61%) number of secondary alignments = 0 number of mapped bases = 480,842,179 bp number of sequenced bases = 480,699,742 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 157,506 duplication rate = 1.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.159 >>>>>>> ACTG content number of A's = 140,658,444 bp (29.26%) number of C's = 99,790,726 bp (20.76%) number of T's = 141,335,571 bp (29.4%) number of G's = 98,912,419 bp (20.58%) number of N's = 2,582 bp (0%) GC percentage = 41.34% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 1,795,722 number of insertions = 138,088 mapped reads with insertion percentage = 2.75% number of deletions = 64,451 mapped reads with deletion percentage = 1.29% homopolymer indels = 49.1% >>>>>>> Coverage mean coverageData = 0.1553X std coverageData = 1.4563X There is a 11.88% of reference with a coverageData >= 1X There is a 2.46% of reference with a coverageData >= 2X There is a 0.59% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 57214909 0.22954770893028187 4.128698578117092 chr2 243199373 35533289 0.14610765053247074 0.6059920912273838 chr3 198022430 32167868 0.16244557750351815 0.5304627642919003 chr4 191154276 22389779 0.1171293651835442 0.48931768352424315 chr5 180915260 40380140 0.2231991928154651 0.5749211809585008 chr6 171115067 27143987 0.1586300229190221 0.9841722248267089 chr7 159138663 27085087 0.17019803038058703 0.8316564441491466 chr8 146364022 23941949 0.16357810254763291 0.5743653133217587 chr9 141213431 20813689 0.14739170950389271 0.7110535961907009 chr10 135534747 23916479 0.17646012944562475 1.9522714301604205 chr11 135006516 21671331 0.1605206299820373 0.722781162454077 chr12 133851895 25291070 0.18894816543314535 0.5259980937935123 chr13 115169878 13983551 0.12141673884555126 0.4154858365137334 chr14 107349540 10294350 0.09589561352568442 0.3821821725847718 chr15 102531392 11423792 0.11141750616240537 0.3949827293932372 chr16 90354753 13353261 0.14778703451272784 1.0340896516001747 chr17 81195210 12763946 0.15720072649605807 0.7251343761467948 chr18 78077248 9932092 0.12720853071050864 1.3963727537672213 chr19 59128983 8583798 0.14517073632062977 2.9328189416952033 chr20 63025520 8541826 0.13552963942225307 0.4526126711650748 chr21 48129895 6137230 0.12751388715890613 0.46863002604055193 chr22 51304566 5015503 0.09775938851134615 0.37715318574368484 chrMT 16571 1120372 67.61040371733752 27.82604920278666 chrX 155270560 21013858 0.1353370400673508 0.49618466113584453 chrY 59373566 1129023 0.019015583466891646 0.7349742630633832