BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472830.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 = 2,529,789 number of mapped reads = 2,192,559 (86.67%) number of supplementary alignments = 22,677 (0.9%) number of secondary alignments = 0 number of mapped bases = 142,210,288 bp number of sequenced bases = 142,151,604 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,363 duplication rate = 2.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7304 >>>>>>> ACTG content number of A's = 38,409,067 bp (27.02%) number of C's = 28,555,682 bp (20.09%) number of T's = 42,052,340 bp (29.58%) number of G's = 33,131,213 bp (23.31%) number of N's = 3,302 bp (0%) GC percentage = 43.4% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,223,263 number of insertions = 11,502 mapped reads with insertion percentage = 0.52% number of deletions = 32,937 mapped reads with deletion percentage = 1.48% homopolymer indels = 44.68% >>>>>>> Coverage mean coverageData = 0.0459X std coverageData = 0.3544X There is a 4.02% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 9302524 0.03732196919982799 0.43285721571269975 chr2 243199373 13792393 0.056712288481105586 0.5495734526563614 chr3 198022430 10304307 0.052036059753432985 0.25199340922772645 chr4 191154276 7893125 0.04129190915928033 0.2631557114350522 chr5 180915260 7221059 0.039914040418702106 0.22202977989967784 chr6 171115067 8703111 0.05086116116238905 0.270062680906934 chr7 159138663 8656377 0.05439518490864788 0.44555252496304404 chr8 146364022 7938403 0.054237393121104586 0.35326653476528014 chr9 141213431 8381935 0.059356499878542 0.42691002330455097 chr10 135534747 5969370 0.04404309693365938 0.34175902346671405 chr11 135006516 4724963 0.03499803668735515 0.32779031693221744 chr12 133851895 5957247 0.04450625820426375 0.2442902351099437 chr13 115169878 5729857 0.049751350782884396 0.2558317207457638 chr14 107349540 2802317 0.02610460184552258 0.22298728596316914 chr15 102531392 2606793 0.025424340283998096 0.19354739449911035 chr16 90354753 4600752 0.05091876018962721 0.28290001310999335 chr17 81195210 3203597 0.039455492509964565 0.24169669895720444 chr18 78077248 2392713 0.030645457688262785 0.6998954974235692 chr19 59128983 3642030 0.061594666696702695 0.3789989586328236 chr20 63025520 6597750 0.10468378523493341 0.38009950133916726 chr21 48129895 2133550 0.04432899760117906 0.2758251627763472 chr22 51304566 1699004 0.03311603883365859 0.21017414499813328 chrMT 16571 187737 11.32924989439382 7.0825001158779886 chrX 155270560 6998355 0.04507200205885778 0.269959744584838 chrY 59373566 771019 0.01298589678780621 0.19108186822431125