BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504604.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 = 427,936,432 number of mapped reads = 368,306,117 (86.07%) number of supplementary alignments = 2,058,602 (0.48%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 184,476,120 number of mapped paired reads (second in pair) = 183,829,997 number of mapped paired reads (both in pair) = 366,033,658 number of mapped paired reads (singletons) = 2,272,459 number of mapped bases = 36,578,563,450 bp number of sequenced bases = 36,568,958,784 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,825,810 duplication rate = 21.98% >>>>>>> Insert size mean insert size = 29,875.9449 std insert size = 1,684,809.5666 median insert size = 213 >>>>>>> Mapping quality mean mapping quality = 53.9775 >>>>>>> ACTG content number of A's = 9,650,268,143 bp (26.39%) number of C's = 8,556,305,784 bp (23.4%) number of T's = 9,665,964,139 bp (26.43%) number of G's = 8,689,859,795 bp (23.76%) number of N's = 6,560,923 bp (0.02%) GC percentage = 47.16% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 172,526,973 number of insertions = 2,761,344 mapped reads with insertion percentage = 0.73% number of deletions = 3,728,211 mapped reads with deletion percentage = 0.98% homopolymer indels = 40.59% >>>>>>> Coverage mean coverageData = 11.8159X std coverageData = 24.5864X There is a 78.43% of reference with a coverageData >= 1X There is a 69.8% of reference with a coverageData >= 2X There is a 62.52% of reference with a coverageData >= 3X There is a 56.45% of reference with a coverageData >= 4X There is a 51.21% of reference with a coverageData >= 5X There is a 46.69% of reference with a coverageData >= 6X There is a 42.73% of reference with a coverageData >= 7X There is a 39.25% of reference with a coverageData >= 8X There is a 36.17% of reference with a coverageData >= 9X There is a 33.42% of reference with a coverageData >= 10X There is a 30.97% of reference with a coverageData >= 11X There is a 28.76% of reference with a coverageData >= 12X There is a 26.77% of reference with a coverageData >= 13X There is a 24.96% of reference with a coverageData >= 14X There is a 23.32% of reference with a coverageData >= 15X There is a 21.83% of reference with a coverageData >= 16X There is a 20.47% of reference with a coverageData >= 17X There is a 19.22% of reference with a coverageData >= 18X There is a 18.08% of reference with a coverageData >= 19X There is a 17.02% of reference with a coverageData >= 20X There is a 16.05% of reference with a coverageData >= 21X There is a 15.16% of reference with a coverageData >= 22X There is a 14.33% of reference with a coverageData >= 23X There is a 13.56% of reference with a coverageData >= 24X There is a 12.85% of reference with a coverageData >= 25X There is a 12.18% of reference with a coverageData >= 26X There is a 11.57% of reference with a coverageData >= 27X There is a 10.99% of reference with a coverageData >= 28X There is a 10.46% of reference with a coverageData >= 29X There is a 9.95% of reference with a coverageData >= 30X There is a 9.48% of reference with a coverageData >= 31X There is a 9.04% of reference with a coverageData >= 32X There is a 8.63% of reference with a coverageData >= 33X There is a 8.24% of reference with a coverageData >= 34X There is a 7.88% of reference with a coverageData >= 35X There is a 7.54% of reference with a coverageData >= 36X There is a 7.21% of reference with a coverageData >= 37X There is a 6.91% of reference with a coverageData >= 38X There is a 6.62% of reference with a coverageData >= 39X There is a 6.35% of reference with a coverageData >= 40X There is a 6.09% of reference with a coverageData >= 41X There is a 5.85% of reference with a coverageData >= 42X There is a 5.62% of reference with a coverageData >= 43X There is a 5.4% of reference with a coverageData >= 44X There is a 5.19% of reference with a coverageData >= 45X There is a 5% of reference with a coverageData >= 46X There is a 4.81% of reference with a coverageData >= 47X There is a 4.64% of reference with a coverageData >= 48X There is a 4.47% of reference with a coverageData >= 49X There is a 4.31% of reference with a coverageData >= 50X There is a 4.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3756575245 15.07147797637784 25.541852471916453 chr2 243199373 2509187925 10.317411159608541 18.81221661801312 chr3 198022430 2705829552 13.66425789240138 22.74378956204852 chr4 191154276 1527198309 7.9893494456802 12.780981896304612 chr5 180915260 1485601346 8.211586717449926 13.90529364815469 chr6 171115067 1868690756 10.920667529528536 17.896052531833785 chr7 159138663 2975900274 18.700045720504765 27.97939942895483 chr8 146364022 2787465932 19.044748114396583 47.000816832957064 chr9 141213431 1438511620 10.186790376901188 19.965091503474085 chr10 135534747 1722316999 12.707567890321144 24.141134130798292 chr11 135006516 1867170594 13.830225749992689 23.545700274298333 chr12 133851895 1246972649 9.316062719918907 15.82670586782572 chr13 115169878 829798698 7.204997629675357 13.595336982202564 chr14 107349540 1220926289 11.373372340486974 19.872292917192787 chr15 102531392 815231888 7.951046719428134 14.914679016245984 chr16 90354753 1068660350 11.827383889810424 20.41326102283775 chr17 81195210 1330834008 16.390548260174462 50.66672137007677 chr18 78077248 478360779 6.126762805471833 28.6817068985026 chr19 59128983 1081882369 18.296989295418797 31.89736613106219 chr20 63025520 1648393469 26.154381098323345 39.17085976117555 chr21 48129895 347042176 7.210532580634136 18.422260690485246 chr22 51304566 754154646 14.699561945422168 27.4247309947217 chrMT 16571 246255 14.86059984309939 11.355281746253983 chrX 155270560 1074710305 6.921533000203 12.291339266621728 chrY 59373566 36901017 0.6215058229785289 14.875302064564888