BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472668.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 = 19,158,152 number of mapped reads = 19,022,128 (99.29%) number of supplementary alignments = 118,030 (0.62%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,529,272 number of mapped paired reads (second in pair) = 9,492,856 number of mapped paired reads (both in pair) = 18,933,236 number of mapped paired reads (singletons) = 88,892 number of mapped bases = 1,861,813,460 bp number of sequenced bases = 1,861,589,284 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,943,784 duplication rate = 49.78% >>>>>>> Insert size mean insert size = 22,485.2824 std insert size = 1,450,614.3673 median insert size = 192 >>>>>>> Mapping quality mean mapping quality = 54.6444 >>>>>>> ACTG content number of A's = 506,724,972 bp (27.22%) number of C's = 426,182,103 bp (22.89%) number of T's = 507,373,691 bp (27.25%) number of G's = 420,957,609 bp (22.61%) number of N's = 350,909 bp (0.02%) GC percentage = 45.51% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 10,506,271 number of insertions = 115,555 mapped reads with insertion percentage = 0.6% number of deletions = 92,763 mapped reads with deletion percentage = 0.48% homopolymer indels = 45.89% >>>>>>> Coverage mean coverageData = 0.6014X std coverageData = 30.6835X There is a 3.49% of reference with a coverageData >= 1X There is a 1.74% of reference with a coverageData >= 2X There is a 0.81% of reference with a coverageData >= 3X There is a 0.61% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.31% of reference with a coverageData >= 9X There is a 0.29% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.25% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.24% of reference with a coverageData >= 16X There is a 0.23% of reference with a coverageData >= 17X There is a 0.23% of reference with a coverageData >= 18X There is a 0.22% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.21% of reference with a coverageData >= 21X There is a 0.21% of reference with a coverageData >= 22X There is a 0.2% of reference with a coverageData >= 23X There is a 0.2% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.19% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.17% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 225304096 0.9039259163972153 41.43935068086448 chr2 243199373 163599386 0.6726965780458652 43.542723877890154 chr3 198022430 164046949 0.8284260979930405 30.81267668540459 chr4 191154276 70953457 0.37118425224241386 22.966761468307975 chr5 180915260 77115181 0.42625028424910094 28.863814955509888 chr6 171115067 190041840 1.1106084539007894 49.48613910569008 chr7 159138663 117663597 0.7393778154338271 38.256867922509265 chr8 146364022 75070071 0.512899754831826 26.31672569587442 chr9 141213431 94777761 0.6711667603345747 24.693937986493122 chr10 135534747 31423479 0.23184814001976925 11.606420016166703 chr11 135006516 37867823 0.2804888543305569 13.305235441971002 chr12 133851895 64085189 0.4787768525802343 18.615313097328297 chr13 115169878 61645223 0.5352547390907195 21.8330993833871 chr14 107349540 43141204 0.401876002449568 25.595225715596015 chr15 102531392 22279732 0.21729668899842888 11.974080460730908 chr16 90354753 96784705 1.0711634063124493 44.58404658000498 chr17 81195210 64167646 0.7902885650520517 29.306764583921538 chr18 78077248 10912176 0.13976127847129038 9.667993349775127 chr19 59128983 38999473 0.6595661048322107 25.983436124491032 chr20 63025520 85759045 1.3607034896340402 42.594806320260496 chr21 48129895 12027101 0.24988836979594492 18.241534961057702 chr22 51304566 16383858 0.31934502671750503 9.68506271864601 chrMT 16571 4336 0.26166193953291894 0.6012758323100015 chrX 155270560 95346550 0.6140671483377145 23.45865222912037 chrY 59373566 2413582 0.04065078388587945 2.944330490697798