BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153335.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 = 69,873,768 number of mapped reads = 69,085,529 (98.87%) number of supplementary alignments = 486,126 (0.7%) number of secondary alignments = 0 number of mapped bases = 6,874,478,615 bp number of sequenced bases = 6,873,547,876 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,547,096 duplication rate = 35.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.9865 >>>>>>> ACTG content number of A's = 1,774,264,385 bp (25.81%) number of C's = 1,658,392,882 bp (24.13%) number of T's = 1,775,093,741 bp (25.83%) number of G's = 1,665,485,675 bp (24.23%) number of N's = 311,193 bp (0%) GC percentage = 48.36% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 20,651,643 number of insertions = 581,293 mapped reads with insertion percentage = 0.83% number of deletions = 404,912 mapped reads with deletion percentage = 0.58% homopolymer indels = 47.86% >>>>>>> Coverage mean coverageData = 2.2207X std coverageData = 24.2272X There is a 12.86% of reference with a coverageData >= 1X There is a 7.15% of reference with a coverageData >= 2X There is a 5.55% of reference with a coverageData >= 3X There is a 4.91% of reference with a coverageData >= 4X There is a 4.49% of reference with a coverageData >= 5X There is a 4.19% of reference with a coverageData >= 6X There is a 3.94% of reference with a coverageData >= 7X There is a 3.73% of reference with a coverageData >= 8X There is a 3.54% of reference with a coverageData >= 9X There is a 3.38% of reference with a coverageData >= 10X There is a 3.23% of reference with a coverageData >= 11X There is a 3.1% of reference with a coverageData >= 12X There is a 2.98% of reference with a coverageData >= 13X There is a 2.86% of reference with a coverageData >= 14X There is a 2.76% of reference with a coverageData >= 15X There is a 2.66% of reference with a coverageData >= 16X There is a 2.57% of reference with a coverageData >= 17X There is a 2.48% of reference with a coverageData >= 18X There is a 2.4% of reference with a coverageData >= 19X There is a 2.33% 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 2.12% of reference with a coverageData >= 23X There is a 2.06% of reference with a coverageData >= 24X There is a 2% of reference with a coverageData >= 25X There is a 1.95% of reference with a coverageData >= 26X There is a 1.89% of reference with a coverageData >= 27X There is a 1.84% of reference with a coverageData >= 28X There is a 1.79% of reference with a coverageData >= 29X There is a 1.74% of reference with a coverageData >= 30X There is a 1.7% of reference with a coverageData >= 31X There is a 1.66% of reference with a coverageData >= 32X There is a 1.62% of reference with a coverageData >= 33X There is a 1.58% of reference with a coverageData >= 34X There is a 1.54% of reference with a coverageData >= 35X There is a 1.5% of reference with a coverageData >= 36X There is a 1.46% of reference with a coverageData >= 37X There is a 1.43% of reference with a coverageData >= 38X There is a 1.4% of reference with a coverageData >= 39X There is a 1.37% of reference with a coverageData >= 40X There is a 1.33% of reference with a coverageData >= 41X There is a 1.3% of reference with a coverageData >= 42X There is a 1.28% of reference with a coverageData >= 43X There is a 1.25% of reference with a coverageData >= 44X There is a 1.22% of reference with a coverageData >= 45X There is a 1.2% of reference with a coverageData >= 46X There is a 1.17% of reference with a coverageData >= 47X There is a 1.15% of reference with a coverageData >= 48X There is a 1.12% of reference with a coverageData >= 49X There is a 1.1% of reference with a coverageData >= 50X There is a 1.08% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 736894854 2.9564413963887377 24.23462825933066 chr2 243199373 506158148 2.0812477505852782 17.748953264253544 chr3 198022430 312823000 1.5797351845444982 13.802346264333732 chr4 191154276 214505594 1.122159537775655 12.79215443115043 chr5 180915260 432442749 2.390305544153655 29.927238436288135 chr6 171115067 283162400 1.6548069376029872 14.803782015579985 chr7 159138663 331820180 2.085100966318914 19.16176161695366 chr8 146364022 489791564 3.3463931730435776 65.07795531610482 chr9 141213431 207072259 1.4663779325636526 14.32160446363485 chr10 135534747 310266995 2.2892062874474544 20.369637715746887 chr11 135006516 263496420 1.9517311297774693 14.948144185990088 chr12 133851895 263871636 1.9713701924055689 16.08904434704007 chr13 115169878 73783491 0.640649206904604 7.467486769151466 chr14 107349540 176222958 1.6415809327175506 14.385971309023954 chr15 102531392 335414718 3.2713368214097787 25.292406994949946 chr16 90354753 274463798 3.037624351648662 22.510683154580967 chr17 81195210 291208978 3.586529032931869 22.75583312238508 chr18 78077248 47943072 0.614046642627568 7.7845702217700605 chr19 59128983 467923399 7.91360472071708 43.38606636142092 chr20 63025520 169143266 2.6837266237549486 20.336587776731722 chr21 48129895 116229730 2.4149175891615804 31.263163905367556 chr22 51304566 116280251 2.2664698303850774 16.839998265104086 chrMT 16571 1999 0.12063243014905557 0.3513036006667594 chrX 155270560 444953512 2.8656656612818296 26.005315474152873 chrY 59373566 8603644 0.14490697762704702 6.5098115307857665