BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153366.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 = 111,308,230 number of mapped reads = 108,902,312 (97.84%) number of supplementary alignments = 680,264 (0.61%) number of secondary alignments = 0 number of mapped bases = 10,659,113,588 bp number of sequenced bases = 10,657,395,637 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,802,421 duplication rate = 33.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3072 >>>>>>> ACTG content number of A's = 2,683,004,945 bp (25.18%) number of C's = 2,646,216,628 bp (24.83%) number of T's = 2,706,904,375 bp (25.4%) number of G's = 2,619,552,581 bp (24.58%) number of N's = 1,717,108 bp (0.02%) GC percentage = 49.41% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 42,002,044 number of insertions = 608,207 mapped reads with insertion percentage = 0.55% number of deletions = 777,005 mapped reads with deletion percentage = 0.7% homopolymer indels = 45.02% >>>>>>> Coverage mean coverageData = 3.4432X std coverageData = 28.1791X There is a 44.97% of reference with a coverageData >= 1X There is a 27.34% of reference with a coverageData >= 2X There is a 16.99% of reference with a coverageData >= 3X There is a 11.86% of reference with a coverageData >= 4X There is a 8.89% of reference with a coverageData >= 5X There is a 7.17% of reference with a coverageData >= 6X There is a 6.08% of reference with a coverageData >= 7X There is a 5.34% of reference with a coverageData >= 8X There is a 4.82% of reference with a coverageData >= 9X There is a 4.43% of reference with a coverageData >= 10X There is a 4.12% of reference with a coverageData >= 11X There is a 3.87% of reference with a coverageData >= 12X There is a 3.66% of reference with a coverageData >= 13X There is a 3.47% of reference with a coverageData >= 14X There is a 3.31% of reference with a coverageData >= 15X There is a 3.17% of reference with a coverageData >= 16X There is a 3.05% of reference with a coverageData >= 17X There is a 2.93% of reference with a coverageData >= 18X There is a 2.82% of reference with a coverageData >= 19X There is a 2.72% of reference with a coverageData >= 20X There is a 2.63% of reference with a coverageData >= 21X There is a 2.55% of reference with a coverageData >= 22X There is a 2.47% of reference with a coverageData >= 23X There is a 2.39% of reference with a coverageData >= 24X There is a 2.32% of reference with a coverageData >= 25X There is a 2.26% of reference with a coverageData >= 26X There is a 2.19% of reference with a coverageData >= 27X There is a 2.13% of reference with a coverageData >= 28X There is a 2.08% of reference with a coverageData >= 29X There is a 2.02% of reference with a coverageData >= 30X There is a 1.97% of reference with a coverageData >= 31X There is a 1.92% of reference with a coverageData >= 32X There is a 1.87% of reference with a coverageData >= 33X There is a 1.83% of reference with a coverageData >= 34X There is a 1.78% of reference with a coverageData >= 35X There is a 1.74% of reference with a coverageData >= 36X There is a 1.7% of reference with a coverageData >= 37X There is a 1.66% of reference with a coverageData >= 38X There is a 1.63% of reference with a coverageData >= 39X There is a 1.59% of reference with a coverageData >= 40X There is a 1.56% of reference with a coverageData >= 41X There is a 1.52% of reference with a coverageData >= 42X There is a 1.49% of reference with a coverageData >= 43X There is a 1.46% of reference with a coverageData >= 44X There is a 1.43% of reference with a coverageData >= 45X There is a 1.4% of reference with a coverageData >= 46X There is a 1.37% of reference with a coverageData >= 47X There is a 1.34% of reference with a coverageData >= 48X There is a 1.32% of reference with a coverageData >= 49X There is a 1.29% of reference with a coverageData >= 50X There is a 1.27% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1026498594 4.118339163536126 26.747339872742984 chr2 243199373 596848839 2.4541545137947374 15.590374214348639 chr3 198022430 508255955 2.5666585093415932 15.897799940967905 chr4 191154276 329845138 1.7255441254162684 16.109374843557458 chr5 180915260 700660968 3.872868258874348 56.13132986443242 chr6 171115067 265659190 1.552517815394947 10.883274066881029 chr7 159138663 563674253 3.542032101903483 31.854623740611785 chr8 146364022 609374555 4.163417666945501 50.67190350338162 chr9 141213431 259778913 1.8396190161260226 11.14987541364918 chr10 135534747 521789358 3.84985673083523 20.730036012290594 chr11 135006516 496644613 3.6786714279775947 19.1779625660769 chr12 133851895 457503737 3.4179847584526164 18.574755102123046 chr13 115169878 108413499 0.9413355374050149 6.164256507639081 chr14 107349540 252316534 2.3504202626299096 13.619123526690997 chr15 102531392 564536239 5.505984342824489 32.617024074077506 chr16 90354753 625799669 6.926029325762198 39.13831591111654 chr17 81195210 595597005 7.3353711998527995 44.78689934709402 chr18 78077248 106128585 1.3592767127243008 9.46845356152033 chr19 59128983 746671353 12.627840275893126 48.69449824123384 chr20 63025520 343345302 5.447718670151392 27.057808313300026 chr21 48129895 132946103 2.7622354671665086 31.291479136648174 chr22 51304566 287333644 5.6005472105543195 33.915000607721616 chrMT 16571 65283 3.939593265343069 2.6342672956723545 chrX 155270560 544100938 3.504211860896232 20.855093212501654 chrY 59373566 15325321 0.2581169034044544 11.591044016823883