BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1163161.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 = 110,077,812 number of mapped reads = 108,489,691 (98.56%) number of supplementary alignments = 1,299,649 (1.18%) number of secondary alignments = 0 number of mapped bases = 10,791,573,940 bp number of sequenced bases = 10,789,857,135 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 72,407,191 duplication rate = 54.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.8252 >>>>>>> ACTG content number of A's = 2,807,900,560 bp (26.02%) number of C's = 2,583,555,560 bp (23.94%) number of T's = 2,840,652,588 bp (26.33%) number of G's = 2,549,643,195 bp (23.63%) number of N's = 8,105,232 bp (0.08%) GC percentage = 47.57% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 71,747,842 number of insertions = 827,612 mapped reads with insertion percentage = 0.75% number of deletions = 807,587 mapped reads with deletion percentage = 0.73% homopolymer indels = 46.45% >>>>>>> Coverage mean coverageData = 3.486X std coverageData = 48.7711X There is a 9.16% of reference with a coverageData >= 1X There is a 6.39% of reference with a coverageData >= 2X There is a 5.16% of reference with a coverageData >= 3X There is a 4.57% of reference with a coverageData >= 4X There is a 4.16% of reference with a coverageData >= 5X There is a 3.88% of reference with a coverageData >= 6X There is a 3.64% of reference with a coverageData >= 7X There is a 3.46% of reference with a coverageData >= 8X There is a 3.3% of reference with a coverageData >= 9X There is a 3.16% of reference with a coverageData >= 10X There is a 3.03% of reference with a coverageData >= 11X There is a 2.92% of reference with a coverageData >= 12X There is a 2.82% of reference with a coverageData >= 13X There is a 2.73% of reference with a coverageData >= 14X There is a 2.65% of reference with a coverageData >= 15X There is a 2.57% of reference with a coverageData >= 16X There is a 2.49% of reference with a coverageData >= 17X There is a 2.43% of reference with a coverageData >= 18X There is a 2.36% of reference with a coverageData >= 19X There is a 2.3% of reference with a coverageData >= 20X There is a 2.25% of reference with a coverageData >= 21X There is a 2.19% of reference with a coverageData >= 22X There is a 2.14% of reference with a coverageData >= 23X There is a 2.09% of reference with a coverageData >= 24X There is a 2.05% of reference with a coverageData >= 25X There is a 2% of reference with a coverageData >= 26X There is a 1.96% of reference with a coverageData >= 27X There is a 1.92% of reference with a coverageData >= 28X There is a 1.88% of reference with a coverageData >= 29X There is a 1.85% of reference with a coverageData >= 30X There is a 1.81% of reference with a coverageData >= 31X There is a 1.78% of reference with a coverageData >= 32X There is a 1.74% of reference with a coverageData >= 33X There is a 1.71% of reference with a coverageData >= 34X There is a 1.68% of reference with a coverageData >= 35X There is a 1.65% of reference with a coverageData >= 36X There is a 1.62% of reference with a coverageData >= 37X There is a 1.6% of reference with a coverageData >= 38X There is a 1.57% of reference with a coverageData >= 39X There is a 1.54% of reference with a coverageData >= 40X There is a 1.52% of reference with a coverageData >= 41X There is a 1.5% of reference with a coverageData >= 42X There is a 1.47% of reference with a coverageData >= 43X There is a 1.45% of reference with a coverageData >= 44X There is a 1.43% of reference with a coverageData >= 45X There is a 1.41% of reference with a coverageData >= 46X There is a 1.39% of reference with a coverageData >= 47X There is a 1.37% of reference with a coverageData >= 48X There is a 1.35% of reference with a coverageData >= 49X There is a 1.33% of reference with a coverageData >= 50X There is a 1.31% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1397191084 5.605567113110623 77.00195904425432 chr2 243199373 718718703 2.9552654438792487 39.61318110831162 chr3 198022430 543506115 2.74466945486933 37.965014021580274 chr4 191154276 369760319 1.9343554679362758 33.0458077718837 chr5 180915260 482118509 2.6648858089693483 40.39043220273651 chr6 171115067 506895189 2.9623059961166365 40.99360208574735 chr7 159138663 522835233 3.2854067210555864 40.40660446307903 chr8 146364022 452932791 3.094563710472509 51.095156888979005 chr9 141213431 454399709 3.217822170187197 37.98062852839428 chr10 135534747 427244698 3.15228904363543 47.093980439045296 chr11 135006516 537717379 3.982899455015934 52.32604300652188 chr12 133851895 455821083 3.4054137447960673 40.42156306964923 chr13 115169878 191256671 1.6606483771737606 28.551094348696427 chr14 107349540 323245623 3.011150518204363 53.60847443082902 chr15 102531392 407977009 3.979044866571206 43.590467228408016 chr16 90354753 432337318 4.784887387163795 55.3901554382197 chr17 81195210 598974993 7.3769744914755435 69.36533228295552 chr18 78077248 166040017 2.1266120573307092 29.81548683855511 chr19 59128983 684845019 11.582222190427323 92.95213283910523 chr20 63025520 241503618 3.8318385631725054 50.28771645378857 chr21 48129895 121136922 2.5168748446261935 35.79233058183526 chr22 51304566 207312380 4.040817341676762 45.24337777821007 chrMT 16571 2500 0.1508659706716553 0.5439378539427415 chrX 155270560 535271014 3.447343875104205 56.10766633403332 chrY 59373566 12530044 0.21103741688683478 19.981929056584054