BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819076.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,792,796 number of mapped reads = 1,625,805 (90.69%) number of supplementary alignments = 6,690 (0.37%) number of secondary alignments = 0 number of mapped bases = 93,537,371 bp number of sequenced bases = 93,513,922 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60,979 duplication rate = 2.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3216 >>>>>>> ACTG content number of A's = 23,094,786 bp (24.7%) number of C's = 17,856,896 bp (19.1%) number of T's = 29,546,288 bp (31.6%) number of G's = 23,013,941 bp (24.61%) number of N's = 2,011 bp (0%) GC percentage = 43.71% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 445,539 number of insertions = 6,758 mapped reads with insertion percentage = 0.41% number of deletions = 13,971 mapped reads with deletion percentage = 0.85% homopolymer indels = 39.5% >>>>>>> Coverage mean coverageData = 0.0302X std coverageData = 0.2433X There is a 2.68% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.04% 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 10550962 0.04233073505562099 0.3886632042276421 chr2 243199373 7929463 0.03260478389473479 0.27506260075522715 chr3 198022430 6272815 0.031677295344774835 0.19624198956895095 chr4 191154276 5975427 0.03125970878098484 0.21202748168765487 chr5 180915260 4716547 0.026070476310290244 0.18032434467257644 chr6 171115067 4971877 0.02905575229094233 0.20244111907660547 chr7 159138663 4120827 0.02589456843683549 0.21382796337077462 chr8 146364022 6046367 0.041310473143461444 0.27066642563962096 chr9 141213431 3411806 0.024160633842258247 0.25015483966443236 chr10 135534747 4477649 0.03303690824021681 0.2341129543191867 chr11 135006516 2973829 0.022027299778626983 0.22695801841049718 chr12 133851895 4246722 0.031727021869955595 0.199208788809283 chr13 115169878 2940807 0.025534515196760043 0.17571986212145696 chr14 107349540 2334476 0.021746492812172273 0.17155957090190208 chr15 102531392 2723901 0.026566507553120903 0.18027820843812817 chr16 90354753 2749691 0.030432167746615387 0.20545001168785373 chr17 81195210 2056596 0.02532903110910114 0.18256731055205877 chr18 78077248 2338403 0.029949864523913548 0.4335516426386569 chr19 59128983 1762814 0.029813027563826016 0.27658865129356636 chr20 63025520 3053038 0.04844129806465698 0.24877474251065382 chr21 48129895 1229980 0.02555542662206099 0.18909849112888824 chr22 51304566 1077989 0.021011560647448028 0.15855410976861273 chrMT 16571 979 0.05907911411502022 0.2504189413884396 chrX 155270560 5324241 0.03429008692955059 0.2288791412168262 chrY 59373566 250165 0.004213407023590262 0.09544577176409731