BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506106.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 = 5,784,728 number of mapped reads = 4,321,687 (74.71%) number of supplementary alignments = 76,406 (1.32%) number of secondary alignments = 0 number of mapped bases = 338,134,259 bp number of sequenced bases = 337,996,976 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 718,278 duplication rate = 11.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5436 >>>>>>> ACTG content number of A's = 90,162,557 bp (26.68%) number of C's = 65,445,452 bp (19.36%) number of T's = 98,512,635 bp (29.15%) number of G's = 83,818,780 bp (24.8%) number of N's = 57,552 bp (0.02%) GC percentage = 44.16% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 2,604,834 number of insertions = 26,707 mapped reads with insertion percentage = 0.6% number of deletions = 66,542 mapped reads with deletion percentage = 1.51% homopolymer indels = 42.09% >>>>>>> Coverage mean coverageData = 0.1092X std coverageData = 0.7571X There is a 6.4% of reference with a coverageData >= 1X There is a 2.29% of reference with a coverageData >= 2X There is a 0.98% of reference with a coverageData >= 3X There is a 0.47% of reference with a coverageData >= 4X There is a 0.24% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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% 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 24954672 0.10011879569198746 1.1815358849356885 chr2 243199373 26148865 0.10752028131256737 0.7828199402808644 chr3 198022430 19835002 0.10016543075448574 0.4951334500884025 chr4 191154276 20371639 0.10657171488018401 0.7120086569532701 chr5 180915260 24290704 0.1342656445896272 0.5859145106906192 chr6 171115067 12622821 0.07376802768630537 0.4535872560854767 chr7 159138663 16675709 0.10478728855476183 0.8940256613962902 chr8 146364022 21626240 0.14775652994832295 0.8476438661472985 chr9 141213431 9584323 0.0678711857089571 0.6554651231842799 chr10 135534747 19439330 0.14342691029629473 1.0030690704451481 chr11 135006516 13735012 0.10173591917593074 0.6759271834418086 chr12 133851895 14736793 0.1100977539391579 0.5709828402288337 chr13 115169878 6155509 0.05344721299435604 0.36276760626771337 chr14 107349540 10269915 0.09566799261552494 0.5440671492748733 chr15 102531392 12356975 0.12051894311548994 0.5650360337137934 chr16 90354753 12699519 0.14055175381863974 0.7228243000219009 chr17 81195210 9519376 0.1172406106222276 0.6549378083943732 chr18 78077248 5880533 0.0753168579917161 1.1034517053917285 chr19 59128983 9066131 0.15332803880628218 1.0012109451680273 chr20 63025520 9520064 0.15105093936551417 0.6956096726349358 chr21 48129895 5921115 0.12302364258222462 0.760201629008668 chr22 51304566 4550853 0.08870268973720585 0.5258734024673346 chrMT 16571 23315 1.4069760424838573 2.0364662900006976 chrX 155270560 26867487 0.17303658207969366 0.7146889046767803 chrY 59373566 1282357 0.021598113207483612 0.6985309730067001