BamQC report ----------------------------------- >>>>>>> Input bam file = SRR960895.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 = 221,315,980 number of mapped reads = 217,350,267 (98.21%) number of supplementary alignments = 368,740 (0.17%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 109,010,315 number of mapped paired reads (second in pair) = 108,339,952 number of mapped paired reads (both in pair) = 215,897,206 number of mapped paired reads (singletons) = 1,453,061 number of mapped bases = 21,230,552,662 bp number of sequenced bases = 21,224,416,217 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,614,984 duplication rate = 9.44% >>>>>>> Insert size mean insert size = 15,239.1484 std insert size = 1,152,644.8437 median insert size = 164 >>>>>>> Mapping quality mean mapping quality = 53.6045 >>>>>>> ACTG content number of A's = 6,476,894,265 bp (30.52%) number of C's = 4,145,530,854 bp (19.53%) number of T's = 6,469,410,016 bp (30.48%) number of G's = 4,129,448,192 bp (19.46%) number of N's = 3,132,890 bp (0.01%) GC percentage = 38.99% >>>>>>> Mismatches and indels general error rate = 0.0139 number of mismatches = 289,132,095 number of insertions = 2,646,980 mapped reads with insertion percentage = 1.19% number of deletions = 2,709,944 mapped reads with deletion percentage = 1.21% homopolymer indels = 39.93% >>>>>>> Coverage mean coverageData = 6.8581X std coverageData = 91.8602X There is a 89.3% of reference with a coverageData >= 1X There is a 84.95% of reference with a coverageData >= 2X There is a 78.57% of reference with a coverageData >= 3X There is a 70.72% of reference with a coverageData >= 4X There is a 62.05% of reference with a coverageData >= 5X There is a 53.19% of reference with a coverageData >= 6X There is a 44.65% of reference with a coverageData >= 7X There is a 36.78% of reference with a coverageData >= 8X There is a 29.78% of reference with a coverageData >= 9X There is a 23.72% of reference with a coverageData >= 10X There is a 18.62% of reference with a coverageData >= 11X There is a 14.42% of reference with a coverageData >= 12X There is a 11.03% of reference with a coverageData >= 13X There is a 8.34% of reference with a coverageData >= 14X There is a 6.25% of reference with a coverageData >= 15X There is a 4.64% of reference with a coverageData >= 16X There is a 3.43% of reference with a coverageData >= 17X There is a 2.53% of reference with a coverageData >= 18X There is a 1.87% of reference with a coverageData >= 19X There is a 1.38% of reference with a coverageData >= 20X There is a 1.03% of reference with a coverageData >= 21X There is a 0.77% of reference with a coverageData >= 22X There is a 0.59% of reference with a coverageData >= 23X There is a 0.46% of reference with a coverageData >= 24X There is a 0.37% of reference with a coverageData >= 25X There is a 0.3% of reference with a coverageData >= 26X There is a 0.25% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.17% of reference with a coverageData >= 30X There is a 0.16% of reference with a coverageData >= 31X There is a 0.14% of reference with a coverageData >= 32X There is a 0.13% of reference with a coverageData >= 33X There is a 0.13% of reference with a coverageData >= 34X There is a 0.12% of reference with a coverageData >= 35X There is a 0.11% of reference with a coverageData >= 36X There is a 0.11% of reference with a coverageData >= 37X There is a 0.1% of reference with a coverageData >= 38X There is a 0.1% of reference with a coverageData >= 39X There is a 0.09% of reference with a coverageData >= 40X There is a 0.09% of reference with a coverageData >= 41X There is a 0.09% of reference with a coverageData >= 42X There is a 0.08% of reference with a coverageData >= 43X There is a 0.08% of reference with a coverageData >= 44X There is a 0.08% of reference with a coverageData >= 45X There is a 0.07% of reference with a coverageData >= 46X There is a 0.07% of reference with a coverageData >= 47X There is a 0.07% of reference with a coverageData >= 48X There is a 0.07% of reference with a coverageData >= 49X There is a 0.07% of reference with a coverageData >= 50X There is a 0.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1799676487 7.220349059832433 229.83739763700441 chr2 243199373 2232022714 9.17774863671215 48.91680620418206 chr3 198022430 1396398856 7.0517206358895805 13.818020824097573 chr4 191154276 1181875904 6.182837908370932 72.56789090216428 chr5 180915260 1148677616 6.349257746416748 8.006115176380408 chr6 171115067 1301304713 7.604851728223324 27.200180062626668 chr7 159138663 1101358949 6.920750295608554 58.407934797873025 chr8 146364022 1212665947 8.28527346016769 91.86223892213334 chr9 141213431 1074353632 7.608013093315465 74.46228804642641 chr10 135534747 941488556 6.946473703898233 214.9226370508081 chr11 135006516 941102285 6.970791580163435 35.407885626664964 chr12 133851895 1073807962 8.022359055880381 7.681150037791671 chr13 115169878 597313761 5.186371396520886 4.6313056633540235 chr14 107349540 422175202 3.932715519787043 6.770219836373167 chr15 102531392 519117578 5.063011121510962 4.558674325934938 chr16 90354753 574894483 6.36263687201934 84.05398822700403 chr17 81195210 452102271 5.568090420604861 23.696500743607217 chr18 78077248 670011396 8.581391034684009 78.18955277289608 chr19 59128983 368838554 6.237863993026905 101.181809044228 chr20 63025520 410808783 6.518133971762549 21.25887364878823 chr21 48129895 265473173 5.51576464066668 29.605170611804283 chr22 51304566 244183929 4.75949702020674 6.0815114422943735 chrMT 16571 8426348 508.49966809486455 110.86110917591724 chrX 155270560 1234192890 7.94866000354478 25.156911432665755 chrY 59373566 58280673 0.9815929364929841 62.81750113242026