BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472646.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 8,852,802 number of mapped reads = 8,754,415 (98.89%) number of supplementary alignments = 48,079 (0.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,380,624 number of mapped paired reads (second in pair) = 4,373,791 number of mapped paired reads (both in pair) = 8,695,308 number of mapped paired reads (singletons) = 59,107 number of mapped bases = 861,181,524 bp number of sequenced bases = 861,081,381 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,800,428 duplication rate = 41.55% >>>>>>> Insert size mean insert size = 20,830.8348 std insert size = 1,450,867.8856 median insert size = 212 >>>>>>> Mapping quality mean mapping quality = 54.4236 >>>>>>> ACTG content number of A's = 231,373,097 bp (26.87%) number of C's = 201,180,521 bp (23.36%) number of T's = 230,720,730 bp (26.79%) number of G's = 197,698,307 bp (22.96%) number of N's = 108,726 bp (0.01%) GC percentage = 46.32% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 7,121,424 number of insertions = 53,738 mapped reads with insertion percentage = 0.61% number of deletions = 42,867 mapped reads with deletion percentage = 0.48% homopolymer indels = 46.8% >>>>>>> Coverage mean coverageData = 0.2782X std coverageData = 20.0937X There is a 2.14% of reference with a coverageData >= 1X There is a 0.92% of reference with a coverageData >= 2X There is a 0.45% of reference with a coverageData >= 3X There is a 0.35% of reference with a coverageData >= 4X There is a 0.28% of reference with a coverageData >= 5X There is a 0.25% of reference with a coverageData >= 6X There is a 0.22% of reference with a coverageData >= 7X There is a 0.21% of reference with a coverageData >= 8X There is a 0.2% of reference with a coverageData >= 9X There is a 0.19% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.17% of reference with a coverageData >= 12X There is a 0.16% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.15% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.14% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.13% of reference with a coverageData >= 19X There is a 0.13% of reference with a coverageData >= 20X There is a 0.12% of reference with a coverageData >= 21X There is a 0.12% of reference with a coverageData >= 22X There is a 0.12% of reference with a coverageData >= 23X There is a 0.12% of reference with a coverageData >= 24X There is a 0.11% of reference with a coverageData >= 25X There is a 0.11% of reference with a coverageData >= 26X There is a 0.11% of reference with a coverageData >= 27X There is a 0.11% of reference with a coverageData >= 28X There is a 0.1% of reference with a coverageData >= 29X There is a 0.1% of reference with a coverageData >= 30X There is a 0.1% of reference with a coverageData >= 31X There is a 0.1% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.09% of reference with a coverageData >= 34X There is a 0.09% of reference with a coverageData >= 35X There is a 0.09% of reference with a coverageData >= 36X There is a 0.09% of reference with a coverageData >= 37X There is a 0.09% of reference with a coverageData >= 38X There is a 0.09% of reference with a coverageData >= 39X There is a 0.08% of reference with a coverageData >= 40X There is a 0.08% of reference with a coverageData >= 41X There is a 0.08% 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 0.08% of reference with a coverageData >= 46X There is a 0.08% 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 0.07% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 112062370 0.4495971546646618 27.12730274901339 chr2 243199373 77911487 0.32036055865982843 23.607358269120244 chr3 198022430 68323075 0.3450269497248367 18.058785801341156 chr4 191154276 19061915 0.09972005543836225 5.829472123075689 chr5 180915260 57893005 0.3200006732433737 37.70942418552449 chr6 171115067 65407321 0.3822417402904678 17.418623712146083 chr7 159138663 41149506 0.25857642149475646 12.728359237704161 chr8 146364022 31928323 0.2181432469790971 12.31249076502051 chr9 141213431 22908344 0.16222496569749092 6.593567745349678 chr10 135534747 15418884 0.11376332889749667 8.37876714833769 chr11 135006516 43029629 0.31872260891466897 17.732995170072716 chr12 133851895 34913225 0.26083474574640875 15.888008650332244 chr13 115169878 16234324 0.1409598089528236 8.289289653068737 chr14 107349540 21864328 0.2036741657206915 11.267154579661547 chr15 102531392 13084976 0.12761921734174836 7.379506841220816 chr16 90354753 39077726 0.43249220104668984 16.21724195701726 chr17 81195210 66670054 0.8211082156201086 40.259451405175696 chr18 78077248 8273367 0.10596386542722408 5.229348168660499 chr19 59128983 30098426 0.5090299963386822 24.258319572066537 chr20 63025520 13825632 0.2193656157061457 12.96643459952855 chr21 48129895 13344414 0.2772583235429872 25.759081479695396 chr22 51304566 30467860 0.5938625423709851 52.70533565065138 chrMT 16571 3102 0.1871944964093899 0.5832598586981415 chrX 155270560 16872381 0.10866439201352787 6.286385193330554 chrY 59373566 1357850 0.022869604968648843 1.5884119510160708