BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618568.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 239,567,132 number of mapped reads = 231,060,690 (96.45%) number of supplementary alignments = 2,464,696 (1.03%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 116,120,505 number of mapped paired reads (second in pair) = 114,940,185 number of mapped paired reads (both in pair) = 228,036,496 number of mapped paired reads (singletons) = 3,024,194 number of mapped bases = 21,774,981,280 bp number of sequenced bases = 21,760,178,897 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 95,472,687 duplication rate = 33.48% >>>>>>> Insert size mean insert size = 130,736.4881 std insert size = 3,581,372.9605 median insert size = 189 >>>>>>> Mapping quality mean mapping quality = 53.5649 >>>>>>> ACTG content number of A's = 5,830,241,817 bp (26.79%) number of C's = 4,831,680,507 bp (22.2%) number of T's = 5,886,474,147 bp (27.05%) number of G's = 5,209,485,882 bp (23.94%) number of N's = 2,296,544 bp (0.01%) GC percentage = 46.14% >>>>>>> Mismatches and indels general error rate = 0.0134 number of mismatches = 285,084,974 number of insertions = 3,637,363 mapped reads with insertion percentage = 1.55% number of deletions = 10,775,057 mapped reads with deletion percentage = 4.55% homopolymer indels = 52.35% >>>>>>> Coverage mean coverageData = 7.034X std coverageData = 24.4325X There is a 44.25% of reference with a coverageData >= 1X There is a 36.49% of reference with a coverageData >= 2X There is a 31.43% of reference with a coverageData >= 3X There is a 27.84% of reference with a coverageData >= 4X There is a 25% of reference with a coverageData >= 5X There is a 22.71% of reference with a coverageData >= 6X There is a 20.79% of reference with a coverageData >= 7X There is a 19.16% of reference with a coverageData >= 8X There is a 17.75% of reference with a coverageData >= 9X There is a 16.52% of reference with a coverageData >= 10X There is a 15.44% of reference with a coverageData >= 11X There is a 14.47% of reference with a coverageData >= 12X There is a 13.6% of reference with a coverageData >= 13X There is a 12.82% of reference with a coverageData >= 14X There is a 12.11% of reference with a coverageData >= 15X There is a 11.46% of reference with a coverageData >= 16X There is a 10.87% of reference with a coverageData >= 17X There is a 10.33% of reference with a coverageData >= 18X There is a 9.83% of reference with a coverageData >= 19X There is a 9.36% of reference with a coverageData >= 20X There is a 8.93% of reference with a coverageData >= 21X There is a 8.53% of reference with a coverageData >= 22X There is a 8.16% of reference with a coverageData >= 23X There is a 7.81% of reference with a coverageData >= 24X There is a 7.49% of reference with a coverageData >= 25X There is a 7.18% of reference with a coverageData >= 26X There is a 6.9% of reference with a coverageData >= 27X There is a 6.63% of reference with a coverageData >= 28X There is a 6.37% of reference with a coverageData >= 29X There is a 6.13% of reference with a coverageData >= 30X There is a 5.9% of reference with a coverageData >= 31X There is a 5.69% of reference with a coverageData >= 32X There is a 5.49% of reference with a coverageData >= 33X There is a 5.29% of reference with a coverageData >= 34X There is a 5.11% of reference with a coverageData >= 35X There is a 4.94% of reference with a coverageData >= 36X There is a 4.77% of reference with a coverageData >= 37X There is a 4.61% of reference with a coverageData >= 38X There is a 4.46% of reference with a coverageData >= 39X There is a 4.32% of reference with a coverageData >= 40X There is a 4.18% of reference with a coverageData >= 41X There is a 4.05% of reference with a coverageData >= 42X There is a 3.93% of reference with a coverageData >= 43X There is a 3.81% of reference with a coverageData >= 44X There is a 3.69% of reference with a coverageData >= 45X There is a 3.58% of reference with a coverageData >= 46X There is a 3.48% of reference with a coverageData >= 47X There is a 3.38% of reference with a coverageData >= 48X There is a 3.28% of reference with a coverageData >= 49X There is a 3.19% of reference with a coverageData >= 50X There is a 3.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1870661589 7.505143142652391 29.639655495164916 chr2 243199373 1839417646 7.563414425414658 26.543667921624458 chr3 198022430 1406700316 7.10374231848382 21.08364177033249 chr4 191154276 1095691189 5.731973209953201 19.653518902873287 chr5 180915260 1241379016 6.8616600722349235 20.503565675368332 chr6 171115067 1197071530 6.99571084526414 21.71175774899364 chr7 159138663 1072725423 6.740822140751553 21.26038816488288 chr8 146364022 1068964092 7.303462130878038 21.90738782387217 chr9 141213431 926473759 6.56080482174532 26.00494703979002 chr10 135534747 1085139786 8.006358590834274 24.36801958208564 chr11 135006516 1110257351 8.223731593814332 30.93291475499838 chr12 133851895 959879263 7.1712041357352465 21.617773509990528 chr13 115169878 585051078 5.079896654922218 16.747764396353332 chr14 107349540 665742432 6.20163283419752 20.719748034412625 chr15 102531392 724600214 7.067105984477418 23.094908944051372 chr16 90354753 799568030 8.84920829787449 35.702562823840196 chr17 81195210 675299097 8.316981962359602 26.591288712725365 chr18 78077248 563145982 7.212677142514039 26.447209513903644 chr19 59128983 452861768 7.658879707097279 28.06001889122062 chr20 63025520 606484618 9.622841953545167 28.225010215101644 chr21 48129895 286975384 5.962518389038663 33.103683570344174 chr22 51304566 378862175 7.384570312903533 27.130221477160877 chrMT 16571 45229 2.729406795003319 7.32380093767257 chrX 155270560 1132309183 7.292491139337683 21.041275252531456 chrY 59373566 29675130 0.4998037342072396 11.653087595472776