BamQC report ----------------------------------- >>>>>>> Input bam file = SRR960912.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 = 126,702,336 number of mapped reads = 120,472,032 (95.08%) number of supplementary alignments = 1,989,069 (1.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 60,434,786 number of mapped paired reads (second in pair) = 60,037,246 number of mapped paired reads (both in pair) = 117,996,662 number of mapped paired reads (singletons) = 2,475,370 number of mapped bases = 10,530,021,233 bp number of sequenced bases = 10,527,121,305 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,204,587 duplication rate = 5.54% >>>>>>> Insert size mean insert size = 157,210.687 std insert size = 4,102,833.702 median insert size = 149 >>>>>>> Mapping quality mean mapping quality = 52.3824 >>>>>>> ACTG content number of A's = 3,054,340,111 bp (29.01%) number of C's = 2,166,182,815 bp (20.58%) number of T's = 3,113,484,356 bp (29.58%) number of G's = 2,191,459,628 bp (20.82%) number of N's = 1,654,395 bp (0.02%) GC percentage = 41.39% >>>>>>> Mismatches and indels general error rate = 0.016 number of mismatches = 164,848,058 number of insertions = 1,626,485 mapped reads with insertion percentage = 1.32% number of deletions = 1,365,562 mapped reads with deletion percentage = 1.1% homopolymer indels = 37.05% >>>>>>> Coverage mean coverageData = 3.4015X std coverageData = 46.866X There is a 82.73% of reference with a coverageData >= 1X There is a 69.29% of reference with a coverageData >= 2X There is a 53.6% of reference with a coverageData >= 3X There is a 39.18% of reference with a coverageData >= 4X There is a 27.23% of reference with a coverageData >= 5X There is a 18.22% of reference with a coverageData >= 6X There is a 11.83% of reference with a coverageData >= 7X There is a 7.51% of reference with a coverageData >= 8X There is a 4.7% of reference with a coverageData >= 9X There is a 2.92% of reference with a coverageData >= 10X There is a 1.82% of reference with a coverageData >= 11X There is a 1.15% of reference with a coverageData >= 12X There is a 0.75% of reference with a coverageData >= 13X There is a 0.5% of reference with a coverageData >= 14X There is a 0.35% of reference with a coverageData >= 15X There is a 0.26% of reference with a coverageData >= 16X There is a 0.21% of reference with a coverageData >= 17X There is a 0.17% of reference with a coverageData >= 18X There is a 0.15% of reference with a coverageData >= 19X There is a 0.13% of reference with a coverageData >= 20X There is a 0.11% of reference with a coverageData >= 21X There is a 0.1% of reference with a coverageData >= 22X There is a 0.09% of reference with a coverageData >= 23X There is a 0.09% of reference with a coverageData >= 24X There is a 0.08% of reference with a coverageData >= 25X There is a 0.08% of reference with a coverageData >= 26X There is a 0.07% of reference with a coverageData >= 27X There is a 0.07% of reference with a coverageData >= 28X There is a 0.06% of reference with a coverageData >= 29X There is a 0.06% of reference with a coverageData >= 30X There is a 0.06% of reference with a coverageData >= 31X There is a 0.06% of reference with a coverageData >= 32X There is a 0.05% of reference with a coverageData >= 33X There is a 0.05% of reference with a coverageData >= 34X There is a 0.05% of reference with a coverageData >= 35X There is a 0.05% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.04% of reference with a coverageData >= 38X There is a 0.04% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 972620910 3.9021804884490137 117.51446641337105 chr2 243199373 913671036 3.7568807218923217 69.16502004482786 chr3 198022430 726709264 3.6698330790102918 7.775985540777446 chr4 191154276 637519821 3.3351062520830035 21.118756575839157 chr5 180915260 513027860 2.835735691947711 4.659688595929667 chr6 171115067 525257303 3.069614571111964 14.338060488670765 chr7 159138663 595812651 3.7439842698691015 30.590613285504542 chr8 146364022 547579102 3.7412138209757586 38.093394460470456 chr9 141213431 502607976 3.559208018959613 35.804749705600805 chr10 135534747 510240249 3.764645305310527 78.48972015275704 chr11 135006516 476627078 3.530400547481723 22.840742640603054 chr12 133851895 393723180 2.9414837944580463 4.2405041459076465 chr13 115169878 328707110 2.8541066093688143 2.9452252741555816 chr14 107349540 232184741 2.1628852904260234 19.017675679750976 chr15 102531392 274487930 2.677111123196299 3.4259903496834965 chr16 90354753 371241965 4.108715398735028 39.414500488911614 chr17 81195210 210265633 2.5896310016317465 11.623443576358431 chr18 78077248 407415147 5.218103319932588 43.90207234990756 chr19 59128983 211549227 3.577758592600857 53.813453344343046 chr20 63025520 197386119 3.131844354477361 9.674272920196891 chr21 48129895 148578791 3.087037505483858 14.082205584811689 chr22 51304566 110656255 2.1568500355309506 3.291959871307163 chrMT 16571 2196086 132.52585842737312 28.073217437308458 chrX 155270560 686852410 4.423584290544196 15.519030773758796 chrY 59373566 33103389 0.5575442276786946 25.33001831256735