BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053674.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 8,786,661 number of mapped reads = 6,081,609 (69.21%) number of supplementary alignments = 214 (0%) number of secondary alignments = 0 number of mapped bases = 283,718,687 bp number of sequenced bases = 283,661,725 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,602,244 duplication rate = 18.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7536 >>>>>>> ACTG content number of A's = 86,214,377 bp (30.39%) number of C's = 53,979,590 bp (19.03%) number of T's = 85,801,198 bp (30.25%) number of G's = 57,518,799 bp (20.28%) number of N's = 147,761 bp (0.05%) GC percentage = 39.31% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 3,023,271 number of insertions = 17,069 mapped reads with insertion percentage = 0.28% number of deletions = 40,117 mapped reads with deletion percentage = 0.66% homopolymer indels = 44.73% >>>>>>> Coverage mean coverageData = 0.0916X std coverageData = 1.2761X There is a 3.75% of reference with a coverageData >= 1X There is a 1.59% of reference with a coverageData >= 2X There is a 0.96% of reference with a coverageData >= 3X There is a 0.65% of reference with a coverageData >= 4X There is a 0.46% of reference with a coverageData >= 5X There is a 0.34% of reference with a coverageData >= 6X There is a 0.25% of reference with a coverageData >= 7X There is a 0.19% of reference with a coverageData >= 8X There is a 0.15% of reference with a coverageData >= 9X There is a 0.12% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% 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 22216893 0.08913475485383043 0.9242906536159449 chr2 243199373 26980227 0.11093871940204385 3.547873363246309 chr3 198022430 18713062 0.09449970894711271 0.7714619238473188 chr4 191154276 20494453 0.10721420116178829 0.8461047888813227 chr5 180915260 18708440 0.10340996110554743 0.818104156912312 chr6 171115067 17774998 0.10387745691616974 0.9465605312943687 chr7 159138663 15176956 0.09536938236058952 0.9557025799742916 chr8 146364022 14600851 0.099757104242462 0.8878218137074381 chr9 141213431 11021395 0.07804778144651127 0.7619385458042078 chr10 135534747 12512785 0.09232160222352427 0.8240736373619223 chr11 135006516 12588887 0.09324651411640013 0.9187540869064249 chr12 133851895 12864020 0.09610637189708819 0.7861024441550648 chr13 115169878 9881690 0.08580099390224238 0.7350884848909784 chr14 107349540 8869624 0.08262377277070773 0.8666370370840288 chr15 102531392 7338573 0.07157391367514059 0.666583067894349 chr16 90354753 6824581 0.07553095740298245 0.6960163804386202 chr17 81195210 5800123 0.07143430012681783 0.6700789761134073 chr18 78077248 8201251 0.10504021606909096 1.0036969709688521 chr19 59128983 3513937 0.05942833483200616 0.8747612919643645 chr20 63025520 5216620 0.08276996365916536 0.7384407910989624 chr21 48129895 3750012 0.07791440226495404 0.7202599188970721 chr22 51304566 2040008 0.03976269870404907 0.46175207018133185 chrMT 16571 12301 0.7423209220928128 1.8413753511810895 chrX 155270560 17893959 0.11524373326147597 0.9468399111363197 chrY 59373566 723041 0.012177826745322995 0.24237774219595865