BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234091.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 = 1,576,018 number of mapped reads = 959,072 (60.85%) number of supplementary alignments = 13,433 (0.85%) number of secondary alignments = 0 number of mapped bases = 60,807,093 bp number of sequenced bases = 60,761,985 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 71,431 duplication rate = 6.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3122 >>>>>>> ACTG content number of A's = 16,299,329 bp (26.82%) number of C's = 11,305,072 bp (18.61%) number of T's = 19,228,021 bp (31.64%) number of G's = 13,919,184 bp (22.91%) number of N's = 10,379 bp (0.02%) GC percentage = 41.51% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 522,821 number of insertions = 4,621 mapped reads with insertion percentage = 0.48% number of deletions = 25,867 mapped reads with deletion percentage = 2.65% homopolymer indels = 42.27% >>>>>>> Coverage mean coverageData = 0.0196X std coverageData = 0.212X There is a 1.47% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.09% 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% 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 6180128 0.024794834914373193 0.27917901155897384 chr2 243199373 3851637 0.01583736402149359 0.28066945601431115 chr3 198022430 7106015 0.035884899503556236 0.2460275847340691 chr4 191154276 2601785 0.01361091707935427 0.15117713597932117 chr5 180915260 4105080 0.022690623223270385 0.19485827271460945 chr6 171115067 3974149 0.023225009168830236 0.2107633619791526 chr7 159138663 3753087 0.02358375349678538 0.251377022851771 chr8 146364022 2756329 0.01883201187242586 0.2464403580366888 chr9 141213431 3480672 0.024648307001336155 0.212550832580023 chr10 135534747 2132712 0.0157355368066611 0.18486970292733923 chr11 135006516 2820350 0.020890473167976573 0.20418116262903493 chr12 133851895 2086756 0.015590037033095422 0.16285370489941503 chr13 115169878 2752719 0.023901379838224712 0.200441276891009 chr14 107349540 2807015 0.02614836542382948 0.21051689869448706 chr15 102531392 1253599 0.01222648961988149 0.14331091099747453 chr16 90354753 1840554 0.020370306363407358 0.1860579340034775 chr17 81195210 1202549 0.01481059042768656 0.16193936813500504 chr18 78077248 1330490 0.017040687704566636 0.22774535943732724 chr19 59128983 1258353 0.021281492360523097 0.23232778469016033 chr20 63025520 1071690 0.017004064385347396 0.1773365165319639 chr21 48129895 711997 0.014793238173488639 0.15730911456836355 chr22 51304566 514726 0.010032752250550175 0.12713200570162278 chrMT 16571 26817 1.6183090942007121 2.123259631459027 chrX 155270560 1057334 0.0068096231507118925 0.1141289626986772 chrY 59373566 130550 0.002198789946354241 0.06420369551649652