BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173849.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 2,292,424 number of mapped reads = 2,226,731 (97.13%) number of supplementary alignments = 219,574 (9.58%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,115,710 number of mapped paired reads (second in pair) = 1,111,021 number of mapped paired reads (both in pair) = 2,184,610 number of mapped paired reads (singletons) = 42,121 number of mapped bases = 260,987,868 bp number of sequenced bases = 260,832,150 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,667,758 duplication rate = 63.13% >>>>>>> Insert size mean insert size = 1,032,009.0324 std insert size = 9,272,371.4807 median insert size = 197 >>>>>>> Mapping quality mean mapping quality = 52.8107 >>>>>>> ACTG content number of A's = 78,659,587 bp (30.16%) number of C's = 51,018,045 bp (19.56%) number of T's = 78,418,685 bp (30.06%) number of G's = 52,732,316 bp (20.22%) number of N's = 3,517 bp (0%) GC percentage = 39.78% >>>>>>> Mismatches and indels general error rate = 0.0109 number of mismatches = 2,746,367 number of insertions = 31,283 mapped reads with insertion percentage = 1.35% number of deletions = 61,611 mapped reads with deletion percentage = 2.69% homopolymer indels = 42.93% >>>>>>> Coverage mean coverageData = 0.0843X std coverageData = 1.4039X There is a 1.93% of reference with a coverageData >= 1X There is a 1.49% of reference with a coverageData >= 2X There is a 1.11% of reference with a coverageData >= 3X There is a 0.89% of reference with a coverageData >= 4X There is a 0.66% of reference with a coverageData >= 5X There is a 0.52% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.3% of reference with a coverageData >= 8X There is a 0.21% of reference with a coverageData >= 9X There is a 0.18% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 21236921 0.08520308160034634 1.0310410829118446 chr2 243199373 20913751 0.08599426364475043 3.795392362689809 chr3 198022430 19077368 0.096339429831257 0.8586000534395647 chr4 191154276 17012862 0.08900068759121035 1.1782690964263007 chr5 180915260 16380336 0.09054148334419108 0.8305988782237781 chr6 171115067 16871507 0.09859743677627172 0.9570490535615541 chr7 159138663 14173483 0.08906373054045326 0.9946293255445245 chr8 146364022 12070650 0.08247006221241994 1.181893590584238 chr9 141213431 11362790 0.08046536309991646 1.0333516234628424 chr10 135534747 13233856 0.0976417951331698 1.2548889278983966 chr11 135006516 11937396 0.08842088777403899 0.8395948339077276 chr12 133851895 12392879 0.09258650391165549 0.8422450865963572 chr13 115169878 9533439 0.08277719109852665 0.8079998240628568 chr14 107349540 8574007 0.07986999292218672 0.7793028848026861 chr15 102531392 7559768 0.07373125296104437 0.7385294485543128 chr16 90354753 8099527 0.0896414049186765 0.9596109882677883 chr17 81195210 6704324 0.08257043734476455 0.8115519981923026 chr18 78077248 7453596 0.09546437907237715 1.290492872970157 chr19 59128983 4428521 0.07489594400769585 0.8357772988673655 chr20 63025520 5321081 0.08442740337564847 0.8129962916946369 chr21 48129895 3821093 0.07939125983964852 0.9459878703725606 chr22 51304566 3051722 0.05948246399745395 0.7033842103334312 chrMT 16571 271957 16.411622714380545 16.10569679896567 chrX 155270560 7154286 0.04607625553743092 0.5945987365491499 chrY 59373566 2350748 0.03959250148458322 0.8739406870619074