BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083625.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 = 1,744,402 number of mapped reads = 1,606,625 (92.1%) number of supplementary alignments = 17,920 (1.03%) number of secondary alignments = 0 number of mapped bases = 108,317,433 bp number of sequenced bases = 108,275,426 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 75,396 duplication rate = 3.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3375 >>>>>>> ACTG content number of A's = 30,054,614 bp (27.76%) number of C's = 19,957,389 bp (18.43%) number of T's = 34,438,178 bp (31.81%) number of G's = 23,819,798 bp (22%) number of N's = 5,447 bp (0.01%) GC percentage = 40.43% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 778,564 number of insertions = 8,524 mapped reads with insertion percentage = 0.53% number of deletions = 25,887 mapped reads with deletion percentage = 1.59% homopolymer indels = 48.46% >>>>>>> Coverage mean coverageData = 0.035X std coverageData = 0.4073X There is a 3.01% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 11028692 0.04424740029032866 0.9988552301043738 chr2 243199373 9831969 0.04042760833926985 0.42604079479597556 chr3 198022430 8910152 0.04499567043995976 0.24068447000563273 chr4 191154276 5407748 0.028289966163247113 0.19452605676673185 chr5 180915260 5270323 0.029131445296543806 0.1934329500436159 chr6 171115067 7628588 0.0445816264677616 0.3050893927435708 chr7 159138663 6141213 0.03859032672657304 0.4464420761176471 chr8 146364022 7643510 0.05222260153523248 0.4884546170558039 chr9 141213431 4247297 0.030077146132084277 0.2730057531873188 chr10 135534747 4885616 0.03604696292383237 0.30654587611612066 chr11 135006516 3945545 0.029224848673229966 0.2586782866923042 chr12 133851895 3804601 0.02842396067683614 0.1909046524814656 chr13 115169878 3380369 0.029351155516549213 0.19305775106290932 chr14 107349540 2384768 0.022214981079564943 0.17478639207972804 chr15 102531392 2692776 0.02626294198756221 0.1872701866755666 chr16 90354753 2932960 0.03246049491165119 0.2182023710390228 chr17 81195210 2215168 0.027282003458085766 0.20331702605737048 chr18 78077248 2962713 0.03794591991766923 0.5389630221182027 chr19 59128983 3019426 0.05106507581907844 0.5772700276219381 chr20 63025520 2299477 0.036484855658469775 0.21801464868785947 chr21 48129895 1751066 0.036382086435052474 0.21705705282610416 chr22 51304566 817189 0.015928192434178277 0.13952644518552537 chrMT 16571 4687 0.2828435218152194 0.6257638190791018 chrX 155270560 4875006 0.031396846897441474 0.2149421170374098 chrY 59373566 236574 0.003984500442503319 0.09986558272250237