BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8751178.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 = 4,862,328 number of mapped reads = 3,310,338 (68.08%) number of supplementary alignments = 192,309 (3.96%) number of secondary alignments = 0 number of mapped bases = 325,881,082 bp number of sequenced bases = 325,772,028 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 127,124 duplication rate = 1.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.0341 >>>>>>> ACTG content number of A's = 97,575,216 bp (29.95%) number of C's = 65,263,273 bp (20.03%) number of T's = 97,999,922 bp (30.08%) number of G's = 64,931,280 bp (19.93%) number of N's = 2,337 bp (0%) GC percentage = 39.96% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 1,331,698 number of insertions = 172,997 mapped reads with insertion percentage = 5.05% number of deletions = 49,428 mapped reads with deletion percentage = 1.46% homopolymer indels = 51.6% >>>>>>> Coverage mean coverageData = 0.1053X std coverageData = 1.4389X There is a 8.39% of reference with a coverageData >= 1X There is a 1.43% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% 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% 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 30669456 0.12304665832708196 4.193540458710849 chr2 243199373 25471902 0.10473670916906516 0.5596880948663739 chr3 198022430 21577235 0.10896359063970683 0.45656096539368657 chr4 191154276 19016815 0.09948412035522554 0.44305476661202203 chr5 180915260 26537198 0.1466830271807917 0.4788906377693607 chr6 171115067 16755799 0.09792123682480865 0.6536354939213562 chr7 159138663 19557658 0.12289696062106542 0.8358383188558666 chr8 146364022 18054410 0.12335278679346486 1.0031407184169896 chr9 141213431 14299246 0.10125981571823717 0.6832087599299067 chr10 135534747 14279097 0.10535377322835154 1.9313137121481712 chr11 135006516 14634655 0.10839961976353793 0.5575791386735237 chr12 133851895 14285353 0.1067250710197267 0.3936809692500791 chr13 115169878 13328480 0.11572887139812721 0.3958207617460103 chr14 107349540 8517373 0.07934242661868882 0.3597817888545114 chr15 102531392 10295398 0.10041215474768937 0.3679889533062489 chr16 90354753 8945774 0.09900723208219052 0.7364565446643588 chr17 81195210 8604983 0.10597894875818413 0.587233262388404 chr18 78077248 5933923 0.0760006679538705 1.5349129231474936 chr19 59128983 5756516 0.09735523440340585 2.773006281202315 chr20 63025520 5741718 0.09110147762366737 0.3652638677558066 chr21 48129895 3764761 0.0782208438227426 0.3793813915189482 chr22 51304566 2650219 0.05165659134510562 0.2654436488058022 chrMT 16571 337454 20.364130106813107 12.583606474201353 chrX 155270560 15706747 0.10115727669173087 0.42175747473384334 chrY 59373566 1158912 0.019518989309148114 0.8739446714632466