BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080748.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 12,282,842 number of mapped reads = 8,769,214 (71.39%) number of supplementary alignments = 48,193 (0.39%) number of secondary alignments = 0 number of mapped bases = 553,055,474 bp number of sequenced bases = 552,872,188 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,221,092 duplication rate = 10.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3659 >>>>>>> ACTG content number of A's = 172,631,468 bp (31.22%) number of C's = 111,644,207 bp (20.19%) number of T's = 141,791,458 bp (25.65%) number of G's = 125,569,193 bp (22.71%) number of N's = 1,235,862 bp (0.22%) GC percentage = 42.91% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 5,658,653 number of insertions = 38,730 mapped reads with insertion percentage = 0.44% number of deletions = 97,568 mapped reads with deletion percentage = 1.1% homopolymer indels = 42.22% >>>>>>> Coverage mean coverageData = 0.1787X std coverageData = 1.0385X There is a 10.09% of reference with a coverageData >= 1X There is a 3.68% of reference with a coverageData >= 2X There is a 1.66% of reference with a coverageData >= 3X There is a 0.86% of reference with a coverageData >= 4X There is a 0.48% of reference with a coverageData >= 5X There is a 0.29% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.12% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 69167893 0.2775033928601526 1.3940462959167639 chr2 243199373 39426690 0.16211674197038328 0.915243347468701 chr3 198022430 31570249 0.15942764160605444 0.662990113957731 chr4 191154276 31018374 0.16226879486598564 0.7991763331367441 chr5 180915260 33455807 0.18492529043708086 0.7461084311922925 chr6 171115067 35280663 0.2061809261951199 1.9835323102301419 chr7 159138663 37780140 0.23740390479465068 1.3963617727235 chr8 146364022 24924229 0.1702893146787125 1.2331592800355669 chr9 141213431 19388700 0.13730067928170372 0.7309114343588016 chr10 135534747 23815889 0.17571795814102195 1.1365910891482247 chr11 135006516 23382887 0.1731982106700687 0.8671108952683038 chr12 133851895 23782241 0.17767578860202166 0.7578056676874736 chr13 115169878 21988080 0.19091867059197545 0.7539694103847944 chr14 107349540 16599098 0.154626633705184 0.7431444931025137 chr15 102531392 15762119 0.15372968895223815 0.6648193167492867 chr16 90354753 15642841 0.1731269300243674 0.7654764528269794 chr17 81195210 15108201 0.18607256511806547 0.7894113724193397 chr18 78077248 8136670 0.1042130736984992 1.0541155735128753 chr19 59128983 10443684 0.17662546301532026 1.4922691947379223 chr20 63025520 9819616 0.15580380772740945 0.6912697011993071 chr21 48129895 7814093 0.1623542498898034 0.8022236303429945 chr22 51304566 4679277 0.09120585875339049 0.48964995525219973 chrMT 16571 147931 8.927101562971457 8.016077325363874 chrX 155270560 32363411 0.20843237121061456 0.8156566499608212 chrY 59373566 1556691 0.02621858690448204 0.696290003320194