BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153370.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 36,394,422 number of mapped reads = 36,149,299 (99.33%) number of supplementary alignments = 237,406 (0.65%) number of secondary alignments = 0 number of mapped bases = 3,153,939,051 bp number of sequenced bases = 3,153,435,997 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,955,528 duplication rate = 45.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.5906 >>>>>>> ACTG content number of A's = 835,188,305 bp (26.49%) number of C's = 746,815,201 bp (23.68%) number of T's = 860,201,002 bp (27.28%) number of G's = 710,345,712 bp (22.53%) number of N's = 885,777 bp (0.03%) GC percentage = 46.21% >>>>>>> Mismatches and indels general error rate = 0.0023 number of mismatches = 6,890,009 number of insertions = 328,810 mapped reads with insertion percentage = 0.9% number of deletions = 248,900 mapped reads with deletion percentage = 0.68% homopolymer indels = 49.12% >>>>>>> Coverage mean coverageData = 1.0188X std coverageData = 12.7216X There is a 11.39% of reference with a coverageData >= 1X There is a 7.9% of reference with a coverageData >= 2X There is a 3.41% of reference with a coverageData >= 3X There is a 2.78% of reference with a coverageData >= 4X There is a 2% of reference with a coverageData >= 5X There is a 1.79% of reference with a coverageData >= 6X There is a 1.58% of reference with a coverageData >= 7X There is a 1.47% of reference with a coverageData >= 8X There is a 1.37% of reference with a coverageData >= 9X There is a 1.3% of reference with a coverageData >= 10X There is a 1.24% of reference with a coverageData >= 11X There is a 1.18% of reference with a coverageData >= 12X There is a 1.14% of reference with a coverageData >= 13X There is a 1.09% of reference with a coverageData >= 14X There is a 1.05% of reference with a coverageData >= 15X There is a 1.01% of reference with a coverageData >= 16X There is a 0.98% of reference with a coverageData >= 17X There is a 0.95% of reference with a coverageData >= 18X There is a 0.92% of reference with a coverageData >= 19X There is a 0.89% of reference with a coverageData >= 20X There is a 0.86% of reference with a coverageData >= 21X There is a 0.84% of reference with a coverageData >= 22X There is a 0.82% of reference with a coverageData >= 23X There is a 0.79% of reference with a coverageData >= 24X There is a 0.77% of reference with a coverageData >= 25X There is a 0.75% of reference with a coverageData >= 26X There is a 0.73% of reference with a coverageData >= 27X There is a 0.72% of reference with a coverageData >= 28X There is a 0.7% of reference with a coverageData >= 29X There is a 0.68% of reference with a coverageData >= 30X There is a 0.66% of reference with a coverageData >= 31X There is a 0.65% of reference with a coverageData >= 32X There is a 0.63% of reference with a coverageData >= 33X There is a 0.62% of reference with a coverageData >= 34X There is a 0.61% of reference with a coverageData >= 35X There is a 0.59% of reference with a coverageData >= 36X There is a 0.58% of reference with a coverageData >= 37X There is a 0.57% of reference with a coverageData >= 38X There is a 0.56% of reference with a coverageData >= 39X There is a 0.54% of reference with a coverageData >= 40X There is a 0.53% of reference with a coverageData >= 41X There is a 0.52% of reference with a coverageData >= 42X There is a 0.51% of reference with a coverageData >= 43X There is a 0.5% of reference with a coverageData >= 44X There is a 0.49% of reference with a coverageData >= 45X There is a 0.48% of reference with a coverageData >= 46X There is a 0.47% of reference with a coverageData >= 47X There is a 0.46% of reference with a coverageData >= 48X There is a 0.45% of reference with a coverageData >= 49X There is a 0.45% of reference with a coverageData >= 50X There is a 0.44% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 340663906 1.3667524864461622 16.552439511348826 chr2 243199373 225245252 0.9261752989799032 10.277331552102506 chr3 198022430 173260681 0.8749548270870123 10.343533024333414 chr4 191154276 125385187 0.65593712902347 8.253355528950172 chr5 180915260 191104488 1.05632044527366 12.77346853807913 chr6 171115067 107790880 0.629932138003955 8.428288532946297 chr7 159138663 147029368 0.923907271987072 11.165717932066324 chr8 146364022 199677595 1.3642532657376687 17.232354689513002 chr9 141213431 74500711 0.5275752488444247 8.63247391263857 chr10 135534747 163195585 1.204086690773105 13.943456662081143 chr11 135006516 141280485 1.0464716014151494 11.730710879608928 chr12 133851895 162225665 1.2119788442292878 13.457103692842761 chr13 115169878 42682098 0.37060122612963087 5.963764135683499 chr14 107349540 91410005 0.8515174354729419 10.03901172159995 chr15 102531392 142370888 1.3885590083474142 15.718726972507985 chr16 90354753 149101470 1.6501784914402897 18.193131134194697 chr17 81195210 124019822 1.5274278125519967 14.328017057547449 chr18 78077248 34187409 0.4378664703960877 6.16984896505184 chr19 59128983 158056078 2.673072831305081 24.728746709404376 chr20 63025520 72655933 1.1528018015559411 11.793974750318473 chr21 48129895 30700036 0.6378579467085893 8.33240517457587 chr22 51304566 39848250 0.7766998750169721 9.985046584604337 chrMT 16571 1685 0.10168366423269568 0.5490630388328734 chrX 155270560 215347810 1.3869197741027017 16.87386231463135 chrY 59373566 2197764 0.037015866623204004 1.8952163313423596