BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1505958.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 = 5,830,171 number of mapped reads = 4,460,864 (76.51%) number of supplementary alignments = 215 (0%) number of secondary alignments = 0 number of mapped bases = 209,615,061 bp number of sequenced bases = 209,575,332 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 409,712 duplication rate = 7.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9089 >>>>>>> ACTG content number of A's = 61,492,457 bp (29.34%) number of C's = 43,701,480 bp (20.85%) number of T's = 60,441,107 bp (28.84%) number of G's = 43,939,343 bp (20.97%) number of N's = 945 bp (0%) GC percentage = 41.82% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 1,026,568 number of insertions = 9,342 mapped reads with insertion percentage = 0.21% number of deletions = 28,758 mapped reads with deletion percentage = 0.64% homopolymer indels = 45.91% >>>>>>> Coverage mean coverageData = 0.0677X std coverageData = 0.5788X There is a 4.77% of reference with a coverageData >= 1X There is a 1.25% of reference with a coverageData >= 2X There is a 0.4% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 16390090 0.06575746906564377 1.0746329690027572 chr2 243199373 18010876 0.0740580692204334 0.5211062561651137 chr3 198022430 14224735 0.07183395840562103 0.3643541110789012 chr4 191154276 13027494 0.06815172682822956 0.36074490962047134 chr5 180915260 13251180 0.07324523094403423 0.3687553128368197 chr6 171115067 11986928 0.07005185580764785 0.39868294333640925 chr7 159138663 11468779 0.0720678355831103 0.7724032990384725 chr8 146364022 10477247 0.07158348654835407 0.7768248329521461 chr9 141213431 9100252 0.06444324690333457 0.4983101238428529 chr10 135534747 10323684 0.07617001712483368 0.5875387545661056 chr11 135006516 9502264 0.07038374355205196 0.5751359377881171 chr12 133851895 9194782 0.06869370060095152 0.3739560100698331 chr13 115169878 6391858 0.055499390213819624 0.31673237477442395 chr14 107349540 6541611 0.060937485153639226 0.3876966993671258 chr15 102531392 5813044 0.056695260706106476 0.31915395079125086 chr16 90354753 6293483 0.06965303751093205 0.39177875127822037 chr17 81195210 5840909 0.07193662039915902 0.4251262405726367 chr18 78077248 5702694 0.07303912658396976 1.1438997937306523 chr19 59128983 4043762 0.06838883056723638 0.7613949482410146 chr20 63025520 4234668 0.06718973520567542 0.36611314324143346 chr21 48129895 2651683 0.05509430261586899 0.3424452186967577 chr22 51304566 2644949 0.0515538714429433 0.3107461722403966 chrMT 16571 73736 4.44970128537807 3.719579795349846 chrX 155270560 11873115 0.0764672646250519 0.4185796550818399 chrY 59373566 551238 0.009284232649930443 0.15520618488928595