BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237578.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 = 1,275,351 number of mapped reads = 1,048,754 (82.23%) number of supplementary alignments = 5,385 (0.42%) number of secondary alignments = 0 number of mapped bases = 66,590,622 bp number of sequenced bases = 66,553,498 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,878 duplication rate = 2.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.7824 >>>>>>> ACTG content number of A's = 17,376,746 bp (26.11%) number of C's = 12,225,618 bp (18.37%) number of T's = 20,156,725 bp (30.29%) number of G's = 16,755,273 bp (25.18%) number of N's = 39,136 bp (0.06%) GC percentage = 43.55% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 622,557 number of insertions = 6,164 mapped reads with insertion percentage = 0.58% number of deletions = 22,363 mapped reads with deletion percentage = 2.1% homopolymer indels = 46.83% >>>>>>> Coverage mean coverageData = 0.0215X std coverageData = 0.2139X There is a 1.86% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.05% 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 5624493 0.022565612785373963 0.25322651066765595 chr2 243199373 5791600 0.02381420613284229 0.2897245122691324 chr3 198022430 4614751 0.02330418326853175 0.1799082856671338 chr4 191154276 4293701 0.02246196679377447 0.18544007662387857 chr5 180915260 3757678 0.02077037614184674 0.16451421079614179 chr6 171115067 3611490 0.0211056224522882 0.18130559665753468 chr7 159138663 3826187 0.024043101329813233 0.2892793217357064 chr8 146364022 3494604 0.023876113489146943 0.21242452632120917 chr9 141213431 2696910 0.019098112558429376 0.22087035127262472 chr10 135534747 2932802 0.021638746261871872 0.21759076555647672 chr11 135006516 2830360 0.020964617737413503 0.21874124201819986 chr12 133851895 3743318 0.027966118821104474 0.20278205215294495 chr13 115169878 2183849 0.018961980666507262 0.16224781030129098 chr14 107349540 1909132 0.017784258786763315 0.16809414839277192 chr15 102531392 2037590 0.019872840505276667 0.16964568032202026 chr16 90354753 1830548 0.020259565094489274 0.18358877680079866 chr17 81195210 1657676 0.020415933402967983 0.17552881372992193 chr18 78077248 1752842 0.022450099675644306 0.33380768011047823 chr19 59128983 1282546 0.02169064872974392 0.2098189125365388 chr20 63025520 1375380 0.02182258869105721 0.17844869743766154 chr21 48129895 831973 0.017285992416979094 0.17291932081087796 chr22 51304566 734429 0.014315080649936694 0.14029602898650698 chrMT 16571 53970 3.2568945748596945 2.598726111580292 chrX 155270560 3490343 0.022479103572499513 0.18429683145039938 chrY 59373566 232450 0.003915041922865135 0.10028804819535903