BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237818.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 = 3,209,236 number of mapped reads = 2,337,475 (72.84%) number of supplementary alignments = 23,620 (0.74%) number of secondary alignments = 0 number of mapped bases = 163,731,098 bp number of sequenced bases = 163,661,063 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 394,813 duplication rate = 12.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1763 >>>>>>> ACTG content number of A's = 47,515,550 bp (29.03%) number of C's = 31,351,516 bp (19.16%) number of T's = 50,361,010 bp (30.77%) number of G's = 34,148,592 bp (20.87%) number of N's = 284,395 bp (0.17%) GC percentage = 40.02% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,382,922 number of insertions = 13,670 mapped reads with insertion percentage = 0.58% number of deletions = 38,139 mapped reads with deletion percentage = 1.61% homopolymer indels = 47.21% >>>>>>> Coverage mean coverageData = 0.0529X std coverageData = 0.863X There is a 1.15% of reference with a coverageData >= 1X There is a 0.71% of reference with a coverageData >= 2X There is a 0.55% of reference with a coverageData >= 3X There is a 0.44% of reference with a coverageData >= 4X There is a 0.36% of reference with a coverageData >= 5X There is a 0.3% of reference with a coverageData >= 6X There is a 0.25% of reference with a coverageData >= 7X There is a 0.21% of reference with a coverageData >= 8X There is a 0.18% of reference with a coverageData >= 9X There is a 0.15% of reference with a coverageData >= 10X There is a 0.13% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% 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 11003168 0.04414499733583412 1.153361463370517 chr2 243199373 13245312 0.05446277199078141 0.9003876562994474 chr3 198022430 10992072 0.05550922690929507 0.8067196622381014 chr4 191154276 10352677 0.054158751855490794 0.798333947510544 chr5 180915260 11004730 0.06082809156065663 0.8303983987598662 chr6 171115067 7948091 0.04644880862536786 0.7427569084850335 chr7 159138663 10085635 0.06337639647003947 1.0343577842243428 chr8 146364022 8559863 0.058483381933847105 0.9363583985240271 chr9 141213431 5993227 0.042440913428411775 0.7199099863777364 chr10 135534747 7249353 0.053487044174731074 0.8746370298080219 chr11 135006516 6936706 0.051380527440616275 0.7773520045290538 chr12 133851895 7548609 0.056395234449239585 0.806429774620888 chr13 115169878 5753738 0.0499587053482856 0.7548012365904512 chr14 107349540 4689232 0.043681901198645096 0.717191465873668 chr15 102531392 5161108 0.05033685683307606 0.7532284268893951 chr16 90354753 4220812 0.04671377940682324 0.7303896835689173 chr17 81195210 4392510 0.05409814199630742 0.8090683126228191 chr18 78077248 4203547 0.05383830895269259 1.0326117639316446 chr19 59128983 3456323 0.058453956497103964 1.0048908067653133 chr20 63025520 3808699 0.06043106030699945 0.8429671700507652 chr21 48129895 2617703 0.054388296504698376 0.7660937959527998 chr22 51304566 1759788 0.034300806676739064 0.5960668358170205 chrMT 16571 52572 3.172530324060105 5.013295436684732 chrX 155270560 11952616 0.07697928055389251 0.9503068366220644 chrY 59373566 743007 0.012514104340642096 0.34514920674739047