BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365349.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 516,081,342 number of mapped reads = 486,922,596 (94.35%) number of supplementary alignments = 1,992,911 (0.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 244,036,888 number of mapped paired reads (second in pair) = 242,885,708 number of mapped paired reads (both in pair) = 484,084,054 number of mapped paired reads (singletons) = 2,838,542 number of mapped bases = 49,902,602,800 bp number of sequenced bases = 49,885,659,628 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 366,685,795 duplication rate = 43.01% >>>>>>> Insert size mean insert size = 60,830.6678 std insert size = 2,350,454.5829 median insert size = 198 >>>>>>> Mapping quality mean mapping quality = 53.7391 >>>>>>> ACTG content number of A's = 15,012,578,487 bp (30.09%) number of C's = 9,704,809,710 bp (19.45%) number of T's = 14,537,050,100 bp (29.14%) number of G's = 10,624,221,356 bp (21.3%) number of N's = 6,999,975 bp (0.01%) GC percentage = 40.75% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 293,741,252 number of insertions = 15,121,203 mapped reads with insertion percentage = 3.03% number of deletions = 8,033,552 mapped reads with deletion percentage = 1.61% homopolymer indels = 49.76% >>>>>>> Coverage mean coverageData = 16.12X std coverageData = 162.1095X There is a 76.13% of reference with a coverageData >= 1X There is a 70.8% of reference with a coverageData >= 2X There is a 65.84% of reference with a coverageData >= 3X There is a 62.3% of reference with a coverageData >= 4X There is a 58.75% of reference with a coverageData >= 5X There is a 56% of reference with a coverageData >= 6X There is a 53.11% of reference with a coverageData >= 7X There is a 50.76% of reference with a coverageData >= 8X There is a 48.26% of reference with a coverageData >= 9X There is a 46.16% of reference with a coverageData >= 10X There is a 43.93% of reference with a coverageData >= 11X There is a 42.03% of reference with a coverageData >= 12X There is a 40.02% of reference with a coverageData >= 13X There is a 38.28% of reference with a coverageData >= 14X There is a 36.45% of reference with a coverageData >= 15X There is a 34.85% of reference with a coverageData >= 16X There is a 33.19% of reference with a coverageData >= 17X There is a 31.72% of reference with a coverageData >= 18X There is a 30.2% of reference with a coverageData >= 19X There is a 28.85% of reference with a coverageData >= 20X There is a 27.45% of reference with a coverageData >= 21X There is a 26.21% of reference with a coverageData >= 22X There is a 24.93% of reference with a coverageData >= 23X There is a 23.78% of reference with a coverageData >= 24X There is a 22.61% of reference with a coverageData >= 25X There is a 21.55% of reference with a coverageData >= 26X There is a 20.49% of reference with a coverageData >= 27X There is a 19.52% of reference with a coverageData >= 28X There is a 18.55% of reference with a coverageData >= 29X There is a 17.66% of reference with a coverageData >= 30X There is a 16.78% of reference with a coverageData >= 31X There is a 15.97% of reference with a coverageData >= 32X There is a 15.17% of reference with a coverageData >= 33X There is a 14.44% of reference with a coverageData >= 34X There is a 13.72% of reference with a coverageData >= 35X There is a 13.06% of reference with a coverageData >= 36X There is a 12.41% of reference with a coverageData >= 37X There is a 11.82% of reference with a coverageData >= 38X There is a 11.23% of reference with a coverageData >= 39X There is a 10.69% of reference with a coverageData >= 40X There is a 10.16% of reference with a coverageData >= 41X There is a 9.68% of reference with a coverageData >= 42X There is a 9.21% of reference with a coverageData >= 43X There is a 8.78% of reference with a coverageData >= 44X There is a 8.35% of reference with a coverageData >= 45X There is a 7.97% of reference with a coverageData >= 46X There is a 7.58% of reference with a coverageData >= 47X There is a 7.24% of reference with a coverageData >= 48X There is a 6.89% of reference with a coverageData >= 49X There is a 6.58% of reference with a coverageData >= 50X There is a 6.27% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3239427634 12.99666825704719 452.9752439986845 chr2 243199373 4348924306 17.882136176395488 95.91121097978557 chr3 198022430 3418616173 17.26378255735979 26.842857561925857 chr4 191154276 3469667286 18.15113613257597 103.5676308210617 chr5 180915260 3120300475 17.247303931133285 24.284043472939146 chr6 171115067 2971824998 17.367406915721805 68.81263916317464 chr7 159138663 3550151828 22.308543763497624 105.73742557642234 chr8 146364022 2550446907 17.425367738254693 54.499183341318854 chr9 141213431 2126840400 15.061176440079556 125.10567215594514 chr10 135534747 2555804277 18.857188533358165 265.71779727436643 chr11 135006516 2334130962 17.289024494195523 99.92602466802532 chr12 133851895 2231642469 16.672475716537296 35.70268001481606 chr13 115169878 1673986803 14.534935975186151 21.014076210732735 chr14 107349540 1532911152 14.279624784605504 22.829144594764095 chr15 102531392 1399450165 13.648992154519856 23.993219555273836 chr16 90354753 1437050778 15.904539941578944 59.542230524893824 chr17 81195210 1319758274 16.25413954837976 94.81507499631883 chr18 78077248 1413573261 18.104803860402455 168.22136189436128 chr19 59128983 943444825 15.955708641225911 226.43540240030944 chr20 63025520 1021100823 16.201386723981017 34.15835888248294 chr21 48129895 709626857 14.743993457704406 60.13447476007461 chr22 51304566 583639828 11.375982168916506 45.19377569117292 chrMT 16571 67077282 4047.8717035785407 776.9576876101735 chrX 155270560 1375224790 8.856957751681968 38.207450112343395 chrY 59373566 507980247 8.555663424359588 183.91381606818464