BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438262.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 = 912,266,718 number of mapped reads = 908,973,964 (99.64%) number of supplementary alignments = 14,648,062 (1.61%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 454,771,475 number of mapped paired reads (second in pair) = 454,202,489 number of mapped paired reads (both in pair) = 907,313,014 number of mapped paired reads (singletons) = 1,660,950 number of mapped bases = 102,984,690,531 bp number of sequenced bases = 102,961,096,489 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 394,194,629 duplication rate = 41.82% >>>>>>> Insert size mean insert size = 141,775.0708 std insert size = 3,812,460.9248 median insert size = 132 >>>>>>> Mapping quality mean mapping quality = 53.1897 >>>>>>> ACTG content number of A's = 31,668,888,801 bp (30.76%) number of C's = 20,055,792,108 bp (19.48%) number of T's = 30,790,168,492 bp (29.9%) number of G's = 20,445,982,847 bp (19.86%) number of N's = 264,241 bp (0%) GC percentage = 39.34% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 299,216,074 number of insertions = 14,791,840 mapped reads with insertion percentage = 1.61% number of deletions = 10,103,945 mapped reads with deletion percentage = 1.1% homopolymer indels = 47.94% >>>>>>> Coverage mean coverageData = 33.2671X std coverageData = 386.3011X There is a 85.3% of reference with a coverageData >= 1X There is a 82.86% of reference with a coverageData >= 2X There is a 79.26% of reference with a coverageData >= 3X There is a 76.61% of reference with a coverageData >= 4X There is a 73.75% of reference with a coverageData >= 5X There is a 71.25% of reference with a coverageData >= 6X There is a 68.77% of reference with a coverageData >= 7X There is a 66.47% of reference with a coverageData >= 8X There is a 64.25% of reference with a coverageData >= 9X There is a 62.14% of reference with a coverageData >= 10X There is a 60.13% of reference with a coverageData >= 11X There is a 58.2% of reference with a coverageData >= 12X There is a 56.36% of reference with a coverageData >= 13X There is a 54.6% of reference with a coverageData >= 14X There is a 52.91% of reference with a coverageData >= 15X There is a 51.29% of reference with a coverageData >= 16X There is a 49.73% of reference with a coverageData >= 17X There is a 48.24% of reference with a coverageData >= 18X There is a 46.8% of reference with a coverageData >= 19X There is a 45.42% of reference with a coverageData >= 20X There is a 44.1% of reference with a coverageData >= 21X There is a 42.82% of reference with a coverageData >= 22X There is a 41.59% of reference with a coverageData >= 23X There is a 40.41% of reference with a coverageData >= 24X There is a 39.27% of reference with a coverageData >= 25X There is a 38.18% of reference with a coverageData >= 26X There is a 37.12% of reference with a coverageData >= 27X There is a 36.1% of reference with a coverageData >= 28X There is a 35.12% of reference with a coverageData >= 29X There is a 34.17% of reference with a coverageData >= 30X There is a 33.26% of reference with a coverageData >= 31X There is a 32.38% of reference with a coverageData >= 32X There is a 31.52% of reference with a coverageData >= 33X There is a 30.7% of reference with a coverageData >= 34X There is a 29.9% of reference with a coverageData >= 35X There is a 29.13% of reference with a coverageData >= 36X There is a 28.39% of reference with a coverageData >= 37X There is a 27.67% of reference with a coverageData >= 38X There is a 26.98% of reference with a coverageData >= 39X There is a 26.31% of reference with a coverageData >= 40X There is a 25.65% of reference with a coverageData >= 41X There is a 25.02% of reference with a coverageData >= 42X There is a 24.41% of reference with a coverageData >= 43X There is a 23.82% of reference with a coverageData >= 44X There is a 23.25% of reference with a coverageData >= 45X There is a 22.69% of reference with a coverageData >= 46X There is a 22.16% of reference with a coverageData >= 47X There is a 21.63% of reference with a coverageData >= 48X There is a 21.13% of reference with a coverageData >= 49X There is a 20.64% of reference with a coverageData >= 50X There is a 20.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 8217617314 32.969295246008635 53.14519742141764 chr2 243199373 9351639562 38.45256443979401 1367.184357968276 chr3 198022430 7711385924 38.941982097684594 51.9416487306788 chr4 191154276 7981137019 41.75233317302303 53.97431908534362 chr5 180915260 6936578816 38.34159051038591 52.05902396317282 chr6 171115067 6508883447 38.03804984046203 53.44860470581355 chr7 159138663 5551067018 34.88195083051565 50.25107372383991 chr8 146364022 5325301527 36.383951836196466 49.053089652999255 chr9 141213431 4538401882 32.13859935178545 55.00366270616974 chr10 135534747 4087655261 30.159463543322953 44.673199930559 chr11 135006516 4818128104 35.68811526104414 51.74759541548349 chr12 133851895 4599644789 34.363688231683234 49.69899386693035 chr13 115169878 3519844160 30.562194048690404 46.41687832698417 chr14 107349540 3102487881 28.900802751460322 46.69982987172641 chr15 102531392 2780374112 27.117296056996867 48.325901994091105 chr16 90354753 1674529231 18.53282949044197 31.701235508666347 chr17 81195210 1662638430 20.477050678235823 36.35915282023641 chr18 78077248 2676978135 34.286276778095456 47.58633255886983 chr19 59128983 744714398 12.594743900804112 24.902209781081904 chr20 63025520 1443591700 22.90487567575801 37.74039118696093 chr21 48129895 1046353447 21.740197999600873 40.15866268495398 chr22 51304566 508981687 9.9207873038045 24.956917178925575 chrMT 16571 17059 1.029449037475107 2.1791395351452305 chrX 155270560 8123929511 52.32111941246299 74.47923599021335 chrY 59373566 72810117 1.226305271945431 8.498538501582741