BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231800.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 = 2,364,480 number of mapped reads = 1,985,580 (83.98%) number of supplementary alignments = 12,981 (0.55%) number of secondary alignments = 0 number of mapped bases = 128,896,293 bp number of sequenced bases = 128,849,630 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 104,272 duplication rate = 2.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1167 >>>>>>> ACTG content number of A's = 37,970,737 bp (29.47%) number of C's = 25,513,036 bp (19.8%) number of T's = 36,516,685 bp (28.34%) number of G's = 28,839,103 bp (22.38%) number of N's = 10,069 bp (0.01%) GC percentage = 42.18% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 780,342 number of insertions = 9,178 mapped reads with insertion percentage = 0.46% number of deletions = 27,960 mapped reads with deletion percentage = 1.4% homopolymer indels = 44.56% >>>>>>> Coverage mean coverageData = 0.0416X std coverageData = 4.2793X There is a 3.56% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% 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 11513023 0.04619054890940472 0.873864373408325 chr2 243199373 7104455 0.029212472517353077 15.185386026038985 chr3 198022430 11353410 0.05733395959235527 0.2645003383918255 chr4 191154276 5549587 0.029031979384023823 0.2051497744985997 chr5 180915260 8746246 0.04834443484756344 0.24660991766200255 chr6 171115067 8732683 0.05103398054363033 0.3189652665986489 chr7 159138663 10903559 0.06851609027279562 0.9294064892485255 chr8 146364022 6587099 0.04500490564545978 0.5743589825147668 chr9 141213431 4494388 0.031826915953908096 0.34977714714737124 chr10 135534747 6504442 0.04799095541160379 0.3980512059573634 chr11 135006516 4431863 0.032827030363482605 0.3360649183063816 chr12 133851895 4681346 0.03497407339657014 0.2151095834042901 chr13 115169878 5234858 0.045453360643483535 0.2349055171361524 chr14 107349540 4679288 0.04358926922276518 0.2662649425328207 chr15 102531392 2779254 0.027106371480843643 0.18132886820247843 chr16 90354753 4019364 0.04448425640652241 0.2718491829186417 chr17 81195210 3709525 0.04568650047213376 0.2760756098292701 chr18 78077248 2923299 0.037441112166248486 0.8250922508310534 chr19 59128983 2168300 0.036670679757843966 0.527907245995499 chr20 63025520 3373151 0.05352039935568957 0.26583904953777265 chr21 48129895 3085439 0.06410649763520157 0.29583693851245496 chr22 51304566 916456 0.017863049460354073 0.14540198316572073 chrMT 16571 185417 11.189246273610525 6.728971482006425 chrX 155270560 4868818 0.03135699388216285 0.2308622774419845 chrY 59373566 351023 0.00591210910255921 0.13101327600557852