BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472497.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 19,221,156 number of mapped reads = 18,990,745 (98.8%) number of supplementary alignments = 67,344 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,525,066 number of mapped paired reads (second in pair) = 9,465,679 number of mapped paired reads (both in pair) = 18,877,162 number of mapped paired reads (singletons) = 113,583 number of mapped bases = 1,866,658,528 bp number of sequenced bases = 1,866,405,774 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,504,916 duplication rate = 45.77% >>>>>>> Insert size mean insert size = 24,716.3574 std insert size = 1,573,263.848 median insert size = 227 >>>>>>> Mapping quality mean mapping quality = 54.9838 >>>>>>> ACTG content number of A's = 502,602,768 bp (26.93%) number of C's = 433,336,341 bp (23.22%) number of T's = 499,341,179 bp (26.75%) number of G's = 430,834,817 bp (23.08%) number of N's = 290,669 bp (0.02%) GC percentage = 46.3% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 11,026,169 number of insertions = 99,956 mapped reads with insertion percentage = 0.52% number of deletions = 95,816 mapped reads with deletion percentage = 0.49% homopolymer indels = 44.16% >>>>>>> Coverage mean coverageData = 0.603X std coverageData = 23.5467X There is a 5.67% of reference with a coverageData >= 1X There is a 2.6% of reference with a coverageData >= 2X There is a 1.12% of reference with a coverageData >= 3X There is a 0.77% of reference with a coverageData >= 4X There is a 0.53% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 205285238 0.8236097353594959 36.24189032205373 chr2 243199373 162387431 0.6677131975994034 27.609668113783453 chr3 198022430 200735457 1.013700604522427 23.49394282521836 chr4 191154276 82154973 0.42978360055100207 18.886721353077018 chr5 180915260 94688107 0.52338374883357 21.961620449232555 chr6 171115067 97929716 0.5723032910947579 16.441523548961044 chr7 159138663 83263067 0.5232107988741869 20.906673218817325 chr8 146364022 77702872 0.5308877888037267 21.888957407714962 chr9 141213431 144673654 1.0245034978294665 38.23952779394974 chr10 135534747 45610293 0.336521032499511 14.193806294572031 chr11 135006516 72780391 0.5390879874272142 18.101797775812567 chr12 133851895 70443396 0.526278660455274 16.88546384670408 chr13 115169878 34141836 0.29644761801345315 13.96304125128474 chr14 107349540 37665032 0.3508634690004261 14.176367358491703 chr15 102531392 56524873 0.5512933346306271 32.23969700983705 chr16 90354753 74422559 0.8236706595833425 25.758009724207746 chr17 81195210 80732855 0.9943056369950888 23.487322455586206 chr18 78077248 32025579 0.41017812256907416 17.46629696228057 chr19 59128983 50966616 0.8619565805824869 26.911825928387078 chr20 63025520 47760938 0.7578031565626114 29.906985273374737 chr21 48129895 7162736 0.14882093551211778 5.282096719849486 chr22 51304566 18965663 0.369668130512984 11.24039084833926 chrMT 16571 1767 0.10663206807072596 0.35074350846918123 chrX 155270560 85852972 0.5529249846203942 18.001092485392334 chrY 59373566 2780507 0.046830722614841766 1.175609666586378