BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153375.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 = 46,448,628 number of mapped reads = 46,123,599 (99.3%) number of supplementary alignments = 237,774 (0.51%) number of secondary alignments = 0 number of mapped bases = 4,483,060,172 bp number of sequenced bases = 4,482,518,724 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,972,499 duplication rate = 59.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.7515 >>>>>>> ACTG content number of A's = 1,179,456,709 bp (26.31%) number of C's = 1,054,455,892 bp (23.52%) number of T's = 1,215,163,091 bp (27.11%) number of G's = 1,032,010,271 bp (23.02%) number of N's = 1,432,761 bp (0.03%) GC percentage = 46.55% >>>>>>> Mismatches and indels general error rate = 0.0027 number of mismatches = 11,569,650 number of insertions = 310,812 mapped reads with insertion percentage = 0.67% number of deletions = 269,448 mapped reads with deletion percentage = 0.58% homopolymer indels = 49.71% >>>>>>> Coverage mean coverageData = 1.4482X std coverageData = 15.2975X There is a 9.44% of reference with a coverageData >= 1X There is a 6.74% of reference with a coverageData >= 2X There is a 4.65% of reference with a coverageData >= 3X There is a 3.92% of reference with a coverageData >= 4X There is a 3.15% of reference with a coverageData >= 5X There is a 2.89% of reference with a coverageData >= 6X There is a 2.55% of reference with a coverageData >= 7X There is a 2.4% of reference with a coverageData >= 8X There is a 2.22% of reference with a coverageData >= 9X There is a 2.12% of reference with a coverageData >= 10X There is a 2% of reference with a coverageData >= 11X There is a 1.92% of reference with a coverageData >= 12X There is a 1.84% of reference with a coverageData >= 13X There is a 1.78% of reference with a coverageData >= 14X There is a 1.71% of reference with a coverageData >= 15X There is a 1.65% of reference with a coverageData >= 16X There is a 1.6% of reference with a coverageData >= 17X There is a 1.55% of reference with a coverageData >= 18X There is a 1.5% of reference with a coverageData >= 19X There is a 1.46% of reference with a coverageData >= 20X There is a 1.42% of reference with a coverageData >= 21X There is a 1.38% of reference with a coverageData >= 22X There is a 1.34% of reference with a coverageData >= 23X There is a 1.3% of reference with a coverageData >= 24X There is a 1.27% of reference with a coverageData >= 25X There is a 1.24% of reference with a coverageData >= 26X There is a 1.21% of reference with a coverageData >= 27X There is a 1.18% of reference with a coverageData >= 28X There is a 1.15% of reference with a coverageData >= 29X There is a 1.12% of reference with a coverageData >= 30X There is a 1.1% of reference with a coverageData >= 31X There is a 1.07% of reference with a coverageData >= 32X There is a 1.05% of reference with a coverageData >= 33X There is a 1.02% of reference with a coverageData >= 34X There is a 1% of reference with a coverageData >= 35X There is a 0.98% of reference with a coverageData >= 36X There is a 0.96% of reference with a coverageData >= 37X There is a 0.94% of reference with a coverageData >= 38X There is a 0.92% of reference with a coverageData >= 39X There is a 0.9% of reference with a coverageData >= 40X There is a 0.88% of reference with a coverageData >= 41X There is a 0.86% of reference with a coverageData >= 42X There is a 0.84% of reference with a coverageData >= 43X There is a 0.83% of reference with a coverageData >= 44X There is a 0.81% of reference with a coverageData >= 45X There is a 0.8% of reference with a coverageData >= 46X There is a 0.78% of reference with a coverageData >= 47X There is a 0.76% of reference with a coverageData >= 48X There is a 0.75% of reference with a coverageData >= 49X There is a 0.74% of reference with a coverageData >= 50X There is a 0.72% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 437372723 1.7547507855557158 15.894847646899322 chr2 243199373 335917046 1.3812414146314431 13.267699564679273 chr3 198022430 239321556 1.2085578184249128 11.687930648641723 chr4 191154276 175666093 0.9189754824004042 10.01781122937729 chr5 180915260 284858235 1.5745395662035364 15.965896712552254 chr6 171115067 155869293 0.9109033805889226 9.534937717749184 chr7 159138663 216901858 1.3629739870316744 16.10559779856729 chr8 146364022 237374860 1.6218115405437548 26.669310890070044 chr9 141213431 111610705 0.7903689061984479 8.421358415972582 chr10 135534747 225248586 1.6619250117462498 15.629191249027 chr11 135006516 213856467 1.5840455211806221 13.598508574103855 chr12 133851895 224087701 1.6741466454397227 14.135477206915686 chr13 115169878 57049891 0.4953542713659903 6.43256245739239 chr14 107349540 132356636 1.2329501924274664 11.55666403449923 chr15 102531392 219194674 2.137829885309662 18.7932632955183 chr16 90354753 216836162 2.399831273956335 22.794887477161772 chr17 81195210 185292153 2.282057685422576 16.407423207707037 chr18 78077248 49323962 0.6317328448871559 7.319670320859875 chr19 59128983 214136474 3.6215145794068535 24.96657950070344 chr20 63025520 111846256 1.7746185354757882 16.01729336611992 chr21 48129895 46016314 0.9560859004575015 10.543575666442726 chr22 51304566 64412807 1.2554985261935556 11.895929578335803 chrMT 16571 8307 0.5012974473477763 1.5900301725160835 chrX 155270560 325886403 2.098829314456005 22.03010539972035 chrY 59373566 2615010 0.04404333740035086 1.702922955942259