BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237859.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 = 2,583,431 number of mapped reads = 2,259,007 (87.44%) number of supplementary alignments = 11,906 (0.46%) number of secondary alignments = 0 number of mapped bases = 146,510,255 bp number of sequenced bases = 146,456,573 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 72,514 duplication rate = 2.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4549 >>>>>>> ACTG content number of A's = 41,659,569 bp (28.44%) number of C's = 26,590,717 bp (18.16%) number of T's = 45,896,881 bp (31.34%) number of G's = 32,177,426 bp (21.97%) number of N's = 131,980 bp (0.09%) GC percentage = 40.13% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 1,076,317 number of insertions = 11,966 mapped reads with insertion percentage = 0.53% number of deletions = 32,369 mapped reads with deletion percentage = 1.42% homopolymer indels = 48.21% >>>>>>> Coverage mean coverageData = 0.0473X std coverageData = 0.3897X There is a 4.16% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 12227374 0.04905654377486987 0.551238766212377 chr2 243199373 15869668 0.06525373731123887 0.48720845894396014 chr3 198022430 11547889 0.05831606550833661 0.2667194205485623 chr4 191154276 10139193 0.05304193666062694 0.2664106178438336 chr5 180915260 9886996 0.05464987309528229 0.26105399047847583 chr6 171115067 6537742 0.0382066998226404 0.25224538625889087 chr7 159138663 7144665 0.0448958465863195 0.5467410840616573 chr8 146364022 7249314 0.049529344035107205 0.5452139525976809 chr9 141213431 6429139 0.04552781526850658 0.43565811051144815 chr10 135534747 7203632 0.05314970632586196 0.38531534856092636 chr11 135006516 5310155 0.039332583028807294 0.35895434481360555 chr12 133851895 8666482 0.0647468009324784 0.29231418759619127 chr13 115169878 5187240 0.04503990183961122 0.23140563967205477 chr14 107349540 6057807 0.056430674970754414 0.327968129947455 chr15 102531392 2611388 0.02546915582692957 0.1756382788754026 chr16 90354753 2970986 0.032881347149496386 0.2549653412666642 chr17 81195210 2660164 0.032762573063115426 0.244520367874941 chr18 78077248 3043298 0.038978038775137155 0.8239949497231019 chr19 59128983 1937806 0.03277252375539758 0.41689538360386996 chr20 63025520 1895146 0.030069502004902143 0.20832227816480542 chr21 48129895 1707528 0.035477492730869246 0.23733228549032773 chr22 51304566 1066018 0.020778228588855033 0.1560328250547993 chrMT 16571 51644 3.1165288757467864 2.588394415737404 chrX 155270560 8777907 0.056532977017665166 0.31874596923073895 chrY 59373566 331074 0.005576117829944727 0.11721252647428007