BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153323.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 = 341,589,716 number of mapped reads = 331,604,824 (97.08%) number of supplementary alignments = 2,321,494 (0.68%) number of secondary alignments = 0 number of mapped bases = 32,573,796,576 bp number of sequenced bases = 32,569,264,924 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 286,382,609 duplication rate = 79.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.2702 >>>>>>> ACTG content number of A's = 6,927,960,505 bp (21.27%) number of C's = 9,375,944,433 bp (28.79%) number of T's = 6,958,366,318 bp (21.36%) number of G's = 9,298,020,283 bp (28.55%) number of N's = 8,973,385 bp (0.03%) GC percentage = 57.34% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 116,357,231 number of insertions = 1,439,703 mapped reads with insertion percentage = 0.42% number of deletions = 1,582,005 mapped reads with deletion percentage = 0.47% homopolymer indels = 39.11% >>>>>>> Coverage mean coverageData = 10.5223X std coverageData = 163.9733X There is a 10.82% of reference with a coverageData >= 1X There is a 9.15% of reference with a coverageData >= 2X There is a 7.56% of reference with a coverageData >= 3X There is a 6.71% of reference with a coverageData >= 4X There is a 5.93% of reference with a coverageData >= 5X There is a 5.54% of reference with a coverageData >= 6X There is a 5.14% of reference with a coverageData >= 7X There is a 4.91% of reference with a coverageData >= 8X There is a 4.66% of reference with a coverageData >= 9X There is a 4.5% of reference with a coverageData >= 10X There is a 4.33% of reference with a coverageData >= 11X There is a 4.21% of reference with a coverageData >= 12X There is a 4.08% of reference with a coverageData >= 13X There is a 3.98% of reference with a coverageData >= 14X There is a 3.88% of reference with a coverageData >= 15X There is a 3.79% of reference with a coverageData >= 16X There is a 3.71% of reference with a coverageData >= 17X There is a 3.64% of reference with a coverageData >= 18X There is a 3.57% of reference with a coverageData >= 19X There is a 3.5% of reference with a coverageData >= 20X There is a 3.44% of reference with a coverageData >= 21X There is a 3.38% of reference with a coverageData >= 22X There is a 3.33% of reference with a coverageData >= 23X There is a 3.27% of reference with a coverageData >= 24X There is a 3.22% of reference with a coverageData >= 25X There is a 3.18% of reference with a coverageData >= 26X There is a 3.13% of reference with a coverageData >= 27X There is a 3.09% of reference with a coverageData >= 28X There is a 3.05% of reference with a coverageData >= 29X There is a 3.01% of reference with a coverageData >= 30X There is a 2.97% of reference with a coverageData >= 31X There is a 2.93% of reference with a coverageData >= 32X There is a 2.89% of reference with a coverageData >= 33X There is a 2.86% of reference with a coverageData >= 34X There is a 2.83% of reference with a coverageData >= 35X There is a 2.79% of reference with a coverageData >= 36X There is a 2.76% of reference with a coverageData >= 37X There is a 2.73% of reference with a coverageData >= 38X There is a 2.7% of reference with a coverageData >= 39X There is a 2.67% of reference with a coverageData >= 40X There is a 2.65% of reference with a coverageData >= 41X There is a 2.62% of reference with a coverageData >= 42X There is a 2.59% of reference with a coverageData >= 43X There is a 2.57% of reference with a coverageData >= 44X There is a 2.54% of reference with a coverageData >= 45X There is a 2.52% of reference with a coverageData >= 46X There is a 2.49% of reference with a coverageData >= 47X There is a 2.47% of reference with a coverageData >= 48X There is a 2.45% of reference with a coverageData >= 49X There is a 2.43% of reference with a coverageData >= 50X There is a 2.4% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3398629105 13.635388715841955 167.5730666505895 chr2 243199373 1343687494 5.525045058401528 71.55196728145677 chr3 198022430 1440676927 7.275321926915047 94.94755528937407 chr4 191154276 775981791 4.059452957254275 91.24230750838468 chr5 180915260 1899133631 10.497365622999409 296.0233337987429 chr6 171115067 618542893 3.6147774935564265 52.42213851805762 chr7 159138663 2144601157 13.476304981901224 277.7586701244448 chr8 146364022 2032137118 13.88413006305607 268.34553918176573 chr9 141213431 848451522 6.008291959140912 65.44219969052499 chr10 135534747 1410674939 10.408216123353224 131.1384552526443 chr11 135006516 1824945538 13.517462653432224 142.52139359294657 chr12 133851895 1324203086 9.893046983010588 102.370910103192 chr13 115169878 181595613 1.5767630925162568 26.33900486410507 chr14 107349540 717839797 6.68693873303975 91.09258457149602 chr15 102531392 1489521064 14.527463588907484 158.5184304101821 chr16 90354753 2211469033 24.475403446678673 221.08056469468409 chr17 81195210 1920077648 23.647671432834525 197.56160117931637 chr18 78077248 137422768 1.760087240779798 24.90107327659042 chr19 59128983 2889433939 48.866626693038164 296.53739969950027 chr20 63025520 913643254 14.496401679827473 139.3365158443241 chr21 48129895 539250251 11.204060407777744 292.9651006027988 chr22 51304566 987020728 19.238457801202333 167.05328679514759 chrMT 16571 6460 0.3898376682155573 1.1546739368793986 chrX 155270560 1496314559 9.636820779161226 113.1586207518508 chrY 59373566 28536261 0.4806223193668374 30.604112784200968