BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004118.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 = 3,690,723 number of mapped reads = 2,746,320 (74.41%) number of supplementary alignments = 18,235 (0.49%) number of secondary alignments = 0 number of mapped bases = 177,027,260 bp number of sequenced bases = 176,941,409 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 406,329 duplication rate = 11.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9075 >>>>>>> ACTG content number of A's = 47,702,748 bp (26.96%) number of C's = 30,796,131 bp (17.4%) number of T's = 59,273,761 bp (33.5%) number of G's = 39,150,012 bp (22.13%) number of N's = 18,757 bp (0.01%) GC percentage = 39.53% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 1,787,826 number of insertions = 16,031 mapped reads with insertion percentage = 0.58% number of deletions = 52,587 mapped reads with deletion percentage = 1.89% homopolymer indels = 49.37% >>>>>>> Coverage mean coverageData = 0.0572X std coverageData = 0.5853X There is a 3.1% of reference with a coverageData >= 1X There is a 1.28% of reference with a coverageData >= 2X There is a 0.61% of reference with a coverageData >= 3X There is a 0.3% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 18043527 0.07239110148495878 0.9484057118908226 chr2 243199373 15377439 0.06322976416555152 0.7166758955240555 chr3 198022430 11818690 0.05968359240920334 0.40823205213537334 chr4 191154276 10943098 0.0572474664390976 0.4172220931167104 chr5 180915260 11161338 0.061693734403609736 0.41540611262309574 chr6 171115067 11625145 0.06793758845327162 0.5072565158426128 chr7 159138663 9637332 0.060559337487961676 0.6706818076528958 chr8 146364022 10750331 0.07344927293676037 0.8587633020061787 chr9 141213431 6966435 0.0493326658142029 0.562168824795908 chr10 135534747 7286346 0.053759985253080525 0.48192654851173344 chr11 135006516 7933590 0.0587644969669464 0.527843885092446 chr12 133851895 6469976 0.0483368278050901 0.3695259301603733 chr13 115169878 4394287 0.038154828990962376 0.3275172182342167 chr14 107349540 3984795 0.037119814393242856 0.3518797055468045 chr15 102531392 4152860 0.04050330263730351 0.33340886580128065 chr16 90354753 5615575 0.0621502999405023 0.432749122751082 chr17 81195210 4068934 0.05011298080268528 0.40588540020486735 chr18 78077248 5290277 0.0677569603887678 1.1439934537626453 chr19 59128983 3052946 0.05163197209057359 0.6924941100686709 chr20 63025520 3809480 0.06044345211273148 0.42647001625813075 chr21 48129895 3164130 0.06574146899759495 0.4533056543137005 chr22 51304566 2054132 0.04003799583842109 0.31889199437189797 chrMT 16571 123028 7.424295455916964 6.873925538873899 chrX 155270560 8836767 0.056912057250260446 0.4379176370283035 chrY 59373566 466802 0.007862118303623536 0.182699908175743