BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082928.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,154,774 number of mapped reads = 1,920,652 (89.13%) number of supplementary alignments = 19,331 (0.9%) number of secondary alignments = 0 number of mapped bases = 127,534,558 bp number of sequenced bases = 127,485,595 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 112,727 duplication rate = 4.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0643 >>>>>>> ACTG content number of A's = 34,205,732 bp (26.83%) number of C's = 24,244,852 bp (19.02%) number of T's = 39,718,936 bp (31.16%) number of G's = 29,309,745 bp (22.99%) number of N's = 6,330 bp (0%) GC percentage = 42.01% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 935,817 number of insertions = 9,937 mapped reads with insertion percentage = 0.51% number of deletions = 29,804 mapped reads with deletion percentage = 1.54% homopolymer indels = 48.36% >>>>>>> Coverage mean coverageData = 0.0412X std coverageData = 0.3205X There is a 3.24% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 11886016 0.047687006565171206 0.4126347580378969 chr2 243199373 12340153 0.05074089150715039 0.5386969102258579 chr3 198022430 8022819 0.04051469825918205 0.24694797118519438 chr4 191154276 6497111 0.03398883423355908 0.2305287420807172 chr5 180915260 7298096 0.04033985856140604 0.24580022828180592 chr6 171115067 9395373 0.05490675464598334 0.3481880434032555 chr7 159138663 4215716 0.026490834600011687 0.22431293787372236 chr8 146364022 8547955 0.05840202314199865 0.3492464281214593 chr9 141213431 4199266 0.02973701559591736 0.2827264457819024 chr10 135534747 5049284 0.03725453517834803 0.25437979919360915 chr11 135006516 6608894 0.048952407600830174 0.33624518049686486 chr12 133851895 5413328 0.04044266986283609 0.2484536300507497 chr13 115169878 3461666 0.030057043214025112 0.22166956494433465 chr14 107349540 1846023 0.017196375503798152 0.16960665545133174 chr15 102531392 2635198 0.025701377388887885 0.2034609233239807 chr16 90354753 6583994 0.07286826405247325 0.355872886392177 chr17 81195210 2891008 0.03560564718041865 0.2609803332686731 chr18 78077248 5122065 0.0656025299457276 0.5131704993715672 chr19 59128983 2630387 0.044485578248487714 0.3767245649455739 chr20 63025520 2324379 0.036879965448916564 0.24387686643190123 chr21 48129895 2475345 0.051430509042249106 0.28248149838374065 chr22 51304566 1551754 0.030245923920299803 0.21383263307287065 chrMT 16571 120352 7.262808520910023 5.181401742150676 chrX 155270560 6184606 0.039831156659704194 0.26010227621994597 chrY 59373566 233770 0.003937274038753206 0.08186042603196621