BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008739.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,019,916 number of mapped reads = 764,701 (74.98%) number of supplementary alignments = 3,487 (0.34%) number of secondary alignments = 0 number of mapped bases = 48,530,130 bp number of sequenced bases = 48,503,819 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,732 duplication rate = 1.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4007 >>>>>>> ACTG content number of A's = 13,420,850 bp (27.67%) number of C's = 8,418,235 bp (17.36%) number of T's = 15,016,625 bp (30.96%) number of G's = 11,645,884 bp (24.01%) number of N's = 2,225 bp (0%) GC percentage = 41.37% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 402,522 number of insertions = 4,175 mapped reads with insertion percentage = 0.54% number of deletions = 15,965 mapped reads with deletion percentage = 2.06% homopolymer indels = 47.17% >>>>>>> Coverage mean coverageData = 0.0157X std coverageData = 0.1627X There is a 1.47% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% 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 3783046 0.015177679336654492 0.20470260064806783 chr2 243199373 4196319 0.01725464563594907 0.2179568472798003 chr3 198022430 3474391 0.017545441695670537 0.13828750723331334 chr4 191154276 2898469 0.015162982804528003 0.13350420118609926 chr5 180915260 2668415 0.014749529696942093 0.12660548136501126 chr6 171115067 2528891 0.01477889144618691 0.14778691202592092 chr7 159138663 2666533 0.016756034955502926 0.2056575537147584 chr8 146364022 3036987 0.020749545950575203 0.18469171345234045 chr9 141213431 1835020 0.012994656294414375 0.15338259481490948 chr10 135534747 2432805 0.017949677509635224 0.17633671589536587 chr11 135006516 2220320 0.01644602102020024 0.1586461682376341 chr12 133851895 2316429 0.017305911134093396 0.13801656773234908 chr13 115169878 1418465 0.012316284645191689 0.11540743738628824 chr14 107349540 1660890 0.015471794289942928 0.1344322130267616 chr15 102531392 1475910 0.014394713377147947 0.12621966443490204 chr16 90354753 1336352 0.014790057585570513 0.13895812611715033 chr17 81195210 1370021 0.016873175154051574 0.14365014951003752 chr18 78077248 1040486 0.013326366216186308 0.2321682744745961 chr19 59128983 861098 0.014563044319568291 0.17434140788843108 chr20 63025520 921529 0.014621521567771278 0.1295352998768941 chr21 48129895 525187 0.010911866730646307 0.11313817624221761 chr22 51304566 549451 0.010709592592596923 0.10742073992731788 chrMT 16571 13903 0.8389958360992095 1.0974997733323517 chrX 155270560 3162913 0.020370332920806106 0.15703203020341794 chrY 59373566 136300 0.002295634390563639 0.06608229107647363