BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438274.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP178894/SRP178894.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 = 1,267,395,646 number of mapped reads = 1,262,524,562 (99.62%) number of supplementary alignments = 20,618,781 (1.63%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 631,626,773 number of mapped paired reads (second in pair) = 630,897,789 number of mapped paired reads (both in pair) = 1,260,226,342 number of mapped paired reads (singletons) = 2,298,220 number of mapped bases = 140,115,941,180 bp number of sequenced bases = 140,082,901,483 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 598,008,774 duplication rate = 44.98% >>>>>>> Insert size mean insert size = 151,572.9013 std insert size = 3,935,033.0889 median insert size = 125 >>>>>>> Mapping quality mean mapping quality = 53.1172 >>>>>>> ACTG content number of A's = 42,837,673,681 bp (30.58%) number of C's = 27,398,255,971 bp (19.56%) number of T's = 41,803,429,775 bp (29.84%) number of G's = 28,043,157,537 bp (20.02%) number of N's = 384,519 bp (0%) GC percentage = 39.58% >>>>>>> Mismatches and indels general error rate = 0.0034 number of mismatches = 448,142,150 number of insertions = 19,942,669 mapped reads with insertion percentage = 1.56% number of deletions = 13,979,418 mapped reads with deletion percentage = 1.1% homopolymer indels = 47.64% >>>>>>> Coverage mean coverageData = 45.2616X std coverageData = 597.6107X There is a 87.39% of reference with a coverageData >= 1X There is a 85.72% of reference with a coverageData >= 2X There is a 83.17% of reference with a coverageData >= 3X There is a 81.28% of reference with a coverageData >= 4X There is a 79.17% of reference with a coverageData >= 5X There is a 77.3% of reference with a coverageData >= 6X There is a 75.4% of reference with a coverageData >= 7X There is a 73.6% of reference with a coverageData >= 8X There is a 71.83% of reference with a coverageData >= 9X There is a 70.13% of reference with a coverageData >= 10X There is a 68.46% of reference with a coverageData >= 11X There is a 66.85% of reference with a coverageData >= 12X There is a 65.27% of reference with a coverageData >= 13X There is a 63.74% of reference with a coverageData >= 14X There is a 62.25% of reference with a coverageData >= 15X There is a 60.81% of reference with a coverageData >= 16X There is a 59.39% of reference with a coverageData >= 17X There is a 58.02% of reference with a coverageData >= 18X There is a 56.69% of reference with a coverageData >= 19X There is a 55.39% of reference with a coverageData >= 20X There is a 54.12% of reference with a coverageData >= 21X There is a 52.89% of reference with a coverageData >= 22X There is a 51.7% of reference with a coverageData >= 23X There is a 50.53% of reference with a coverageData >= 24X There is a 49.4% of reference with a coverageData >= 25X There is a 48.3% of reference with a coverageData >= 26X There is a 47.22% of reference with a coverageData >= 27X There is a 46.18% of reference with a coverageData >= 28X There is a 45.17% of reference with a coverageData >= 29X There is a 44.18% of reference with a coverageData >= 30X There is a 43.22% of reference with a coverageData >= 31X There is a 42.28% of reference with a coverageData >= 32X There is a 41.37% of reference with a coverageData >= 33X There is a 40.48% of reference with a coverageData >= 34X There is a 39.62% of reference with a coverageData >= 35X There is a 38.78% of reference with a coverageData >= 36X There is a 37.96% of reference with a coverageData >= 37X There is a 37.17% of reference with a coverageData >= 38X There is a 36.39% of reference with a coverageData >= 39X There is a 35.64% of reference with a coverageData >= 40X There is a 34.9% of reference with a coverageData >= 41X There is a 34.19% of reference with a coverageData >= 42X There is a 33.49% of reference with a coverageData >= 43X There is a 32.81% of reference with a coverageData >= 44X There is a 32.15% of reference with a coverageData >= 45X There is a 31.5% of reference with a coverageData >= 46X There is a 30.87% of reference with a coverageData >= 47X There is a 30.26% of reference with a coverageData >= 48X There is a 29.66% of reference with a coverageData >= 49X There is a 29.08% of reference with a coverageData >= 50X There is a 28.51% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 10537486520 42.27667107798299 63.762350476515195 chr2 243199373 12230846068 50.291437503007046 2120.270954711297 chr3 198022430 10954296753 55.318464443649134 71.26308395194008 chr4 191154276 10529897459 55.08585881175894 67.94853704167475 chr5 180915260 9273247171 51.257407313236044 64.58906920527778 chr6 171115067 8792775015 51.38515952543209 67.3525519905672 chr7 159138663 7683231245 48.28010428238925 67.34983535567318 chr8 146364022 7289613781 49.8046834282813 63.60828057326918 chr9 141213431 5495516940 38.91638990061788 59.79201414310967 chr10 135534747 5681002402 41.915468378009365 57.453462426737225 chr11 135006516 6692752156 49.57354914632417 70.68068312917525 chr12 133851895 6305179144 47.10563973711392 64.18101294131375 chr13 115169878 5204044541 45.185812743502254 62.649169782183336 chr14 107349540 4320810539 40.24992132243883 60.57527985179294 chr15 102531392 4601070887 44.87475296346313 70.92702615315427 chr16 90354753 2374779822 26.28284338290427 45.42585289792124 chr17 81195210 2182234613 26.87639594749493 46.08269647168126 chr18 78077248 3504265614 44.882032906692615 54.64378616845811 chr19 59128983 991291895 16.764906898534008 32.42442157460268 chr20 63025520 1975857372 31.350116143428885 49.15709950833447 chr21 48129895 1453089273 30.190991960402158 52.889114019324175 chr22 51304566 709135086 13.822065778706714 34.9599048957798 chrMT 16571 334876 20.208557117856497 9.12003638717445 chrX 155270560 11233752468 72.34953276397019 98.08318878085569 chrY 59373566 99429540 1.674643224225407 11.194531934666255