BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818780.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 = 718,670 number of mapped reads = 689,618 (95.96%) number of supplementary alignments = 5,953 (0.83%) number of secondary alignments = 0 number of mapped bases = 46,722,152 bp number of sequenced bases = 46,702,806 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 234,673 duplication rate = 30.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.939 >>>>>>> ACTG content number of A's = 13,222,665 bp (28.31%) number of C's = 10,693,341 bp (22.9%) number of T's = 13,513,606 bp (28.94%) number of G's = 9,270,162 bp (19.85%) number of N's = 3,032 bp (0.01%) GC percentage = 42.75% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 245,689 number of insertions = 5,876 mapped reads with insertion percentage = 0.84% number of deletions = 12,031 mapped reads with deletion percentage = 1.72% homopolymer indels = 41.78% >>>>>>> Coverage mean coverageData = 0.0151X std coverageData = 0.2348X There is a 0.88% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 3851595 0.015452699714637823 0.2943004886142342 chr2 243199373 4151837 0.01707174220387484 0.36091127333116796 chr3 198022430 3183076 0.016074320469655887 0.19599843552811125 chr4 191154276 3084933 0.016138446204572478 0.2185581620776699 chr5 180915260 2929488 0.016192597573029495 0.20161790685674685 chr6 171115067 2763375 0.016149220804734864 0.2071160403815461 chr7 159138663 2578056 0.016200060698009007 0.21722976653323303 chr8 146364022 2398007 0.016383855589866204 0.21110607444607193 chr9 141213431 1991091 0.01409986986294526 0.1975365836556903 chr10 135534747 2206514 0.016280061377913664 0.24636421952889084 chr11 135006516 2228583 0.016507225473472702 0.21338242781724326 chr12 133851895 2138808 0.01597891460557955 0.2046265386966418 chr13 115169878 1498487 0.013011101739640638 0.1759863207714907 chr14 107349540 1450390 0.013510910247030402 0.1909458345383289 chr15 102531392 1355511 0.013220448621237875 0.17947005084105228 chr16 90354753 1383711 0.015314202673986614 0.2576248022555301 chr17 81195210 1240401 0.015276775563484595 0.19854205848123518 chr18 78077248 1253826 0.016058788342539942 0.24096663769752796 chr19 59128983 913930 0.015456548610010763 0.2731490421435181 chr20 63025520 1033275 0.016394549382535838 0.20910919954146534 chr21 48129895 641784 0.01333441512806126 0.18765907252861974 chr22 51304566 557836 0.010873028338257457 0.170529397985617 chrMT 16571 20296 1.2247902963007664 1.8300409530884343 chrX 155270560 1410445 0.009083788968108313 0.15463415414468087 chrY 59373566 456897 0.007695293221902825 0.3605357345495617