BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618605.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 = 51,385,178 number of mapped reads = 46,706,301 (90.89%) number of supplementary alignments = 73,358 (0.14%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 23,980,946 number of mapped paired reads (second in pair) = 22,725,355 number of mapped paired reads (both in pair) = 44,551,842 number of mapped paired reads (singletons) = 2,154,459 number of mapped bases = 4,381,896,722 bp number of sequenced bases = 4,378,870,821 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,714,029 duplication rate = 28.47% >>>>>>> Insert size mean insert size = 62,963.7857 std insert size = 2,603,014.504 median insert size = 205 >>>>>>> Mapping quality mean mapping quality = 51.9479 >>>>>>> ACTG content number of A's = 1,177,276,367 bp (26.89%) number of C's = 984,537,277 bp (22.48%) number of T's = 1,191,708,265 bp (27.21%) number of G's = 1,022,104,626 bp (23.34%) number of N's = 3,244,286 bp (0.07%) GC percentage = 45.83% >>>>>>> Mismatches and indels general error rate = 0.0155 number of mismatches = 66,823,375 number of insertions = 842,944 mapped reads with insertion percentage = 1.78% number of deletions = 2,233,934 mapped reads with deletion percentage = 4.66% homopolymer indels = 51.95% >>>>>>> Coverage mean coverageData = 1.4155X std coverageData = 6.948X There is a 19.88% of reference with a coverageData >= 1X There is a 14.58% of reference with a coverageData >= 2X There is a 11.49% of reference with a coverageData >= 3X There is a 9.45% of reference with a coverageData >= 4X There is a 7.92% of reference with a coverageData >= 5X There is a 6.77% of reference with a coverageData >= 6X There is a 5.86% of reference with a coverageData >= 7X There is a 5.12% of reference with a coverageData >= 8X There is a 4.51% of reference with a coverageData >= 9X There is a 4.01% of reference with a coverageData >= 10X There is a 3.58% of reference with a coverageData >= 11X There is a 3.21% of reference with a coverageData >= 12X There is a 2.9% of reference with a coverageData >= 13X There is a 2.63% of reference with a coverageData >= 14X There is a 2.39% of reference with a coverageData >= 15X There is a 2.18% of reference with a coverageData >= 16X There is a 2% of reference with a coverageData >= 17X There is a 1.83% of reference with a coverageData >= 18X There is a 1.69% of reference with a coverageData >= 19X There is a 1.56% of reference with a coverageData >= 20X There is a 1.44% of reference with a coverageData >= 21X There is a 1.34% of reference with a coverageData >= 22X There is a 1.24% of reference with a coverageData >= 23X There is a 1.15% of reference with a coverageData >= 24X There is a 1.08% of reference with a coverageData >= 25X There is a 1% of reference with a coverageData >= 26X There is a 0.94% of reference with a coverageData >= 27X There is a 0.88% of reference with a coverageData >= 28X There is a 0.82% of reference with a coverageData >= 29X There is a 0.77% of reference with a coverageData >= 30X There is a 0.73% of reference with a coverageData >= 31X There is a 0.68% of reference with a coverageData >= 32X There is a 0.64% of reference with a coverageData >= 33X There is a 0.61% of reference with a coverageData >= 34X There is a 0.57% of reference with a coverageData >= 35X There is a 0.54% of reference with a coverageData >= 36X There is a 0.51% of reference with a coverageData >= 37X There is a 0.48% of reference with a coverageData >= 38X There is a 0.46% of reference with a coverageData >= 39X There is a 0.44% of reference with a coverageData >= 40X There is a 0.41% of reference with a coverageData >= 41X There is a 0.39% of reference with a coverageData >= 42X There is a 0.37% of reference with a coverageData >= 43X There is a 0.35% of reference with a coverageData >= 44X There is a 0.34% of reference with a coverageData >= 45X There is a 0.32% of reference with a coverageData >= 46X There is a 0.31% of reference with a coverageData >= 47X There is a 0.29% of reference with a coverageData >= 48X There is a 0.28% of reference with a coverageData >= 49X There is a 0.26% of reference with a coverageData >= 50X There is a 0.25% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 521073690 2.0905612507982476 9.475511386297558 chr2 243199373 300773016 1.2367343397715092 6.6701300107199275 chr3 198022430 276125581 1.3944156780623287 5.808831133012028 chr4 191154276 197952765 1.0355654560403347 6.287055422884459 chr5 180915260 242269957 1.3391350016576822 5.898002502083267 chr6 171115067 231925430 1.3553770224103059 6.100261871477756 chr7 159138663 245071451 1.5399868666736254 6.542046285615439 chr8 146364022 200341451 1.3687889158990179 6.211825127175945 chr9 141213431 304749024 2.1580739299507568 8.959976021501442 chr10 135534747 251063696 1.852393585830798 7.52486942375291 chr11 135006516 286242821 2.1202148568888335 8.704048312889404 chr12 133851895 204293547 1.5262656311290923 6.898397539160211 chr13 115169878 81440873 0.7071369216871098 4.307235201859261 chr14 107349540 5837020 0.05437396378223884 1.8246645391608975 chr15 102531392 167660774 1.6352140620503817 7.3976576259700275 chr16 90354753 9564200 0.10585165342657735 3.8015766579874466 chr17 81195210 233275929 2.8730257486864064 9.166952887941223 chr18 78077248 106207555 1.3602881469387855 6.694082477961038 chr19 59128983 126040905 2.1316264648082988 8.539035258087807 chr20 63025520 162996556 2.5861993046626193 9.106266576231928 chr21 48129895 52761976 1.0962412446567773 9.165766722386731 chr22 51304566 125991137 2.4557490068232912 9.070387938797975 chrMT 16571 11931 0.7199927584334077 3.700963919284769 chrX 155270560 11732879 0.07556409276813325 2.915011961872975 chrY 59373566 36492558 0.614626347354646 4.140408441941232