BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716937.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 = 377,708 number of mapped reads = 282,719 (74.85%) number of supplementary alignments = 298 (0.08%) number of secondary alignments = 0 number of mapped bases = 14,918,943 bp number of sequenced bases = 14,914,794 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,273 duplication rate = 3.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.668 >>>>>>> ACTG content number of A's = 3,353,671 bp (22.49%) number of C's = 2,643,890 bp (17.73%) number of T's = 4,697,982 bp (31.5%) number of G's = 4,218,979 bp (28.29%) number of N's = 272 bp (0%) GC percentage = 46.01% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 98,550 number of insertions = 964 mapped reads with insertion percentage = 0.34% number of deletions = 2,392 mapped reads with deletion percentage = 0.84% homopolymer indels = 41.6% >>>>>>> Coverage mean coverageData = 0.0048X std coverageData = 0.0774X There is a 0.45% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% 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 1137271 0.004562760948948649 0.07531638263090586 chr2 243199373 1243998 0.005115136542724557 0.0994537249620368 chr3 198022430 961764 0.004856843742398273 0.07408061053241703 chr4 191154276 857470 0.004485748464240475 0.0721961637228088 chr5 180915260 861408 0.0047613893930230095 0.07316092396376829 chr6 171115067 833465 0.004870786743752962 0.07922501910303843 chr7 159138663 836685 0.005257584701462523 0.07996636707483362 chr8 146364022 738631 0.005046533908449168 0.07580393435869698 chr9 141213431 616210 0.004363678409598305 0.07132970067733622 chr10 135534747 734556 0.005419687690862034 0.08187895736720285 chr11 135006516 669758 0.004960930922771165 0.07618482226971428 chr12 133851895 680654 0.005085127857173782 0.07548115756945818 chr13 115169878 435772 0.0037837324096149515 0.06514019960417874 chr14 107349540 461237 0.004296590371975511 0.06980066998628777 chr15 102531392 446872 0.004358392013248001 0.07040224740732923 chr16 90354753 499079 0.005523550045009807 0.08263501757672997 chr17 81195210 484351 0.005965265685007774 0.08300468314154395 chr18 78077248 391278 0.005011421509118764 0.07956398577745877 chr19 59128983 387078 0.006546332785733859 0.09131184772478924 chr20 63025520 358097 0.005681777794137994 0.08090072662053858 chr21 48129895 205016 0.004259639461087542 0.07054662942939986 chr22 51304566 226790 0.0044204642526359155 0.07140183220569632 chrMT 16571 1778 0.10729587834168125 0.32822562013006157 chrX 155270560 799139 0.0051467515799517955 0.07667704682139573 chrY 59373566 50586 8.519953138741911E-4 0.03588022056949795