BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084777.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 = 1,237,030 number of mapped reads = 1,134,575 (91.72%) number of supplementary alignments = 8,762 (0.71%) number of secondary alignments = 0 number of mapped bases = 78,761,094 bp number of sequenced bases = 78,726,778 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,048 duplication rate = 2.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9219 >>>>>>> ACTG content number of A's = 22,692,398 bp (28.82%) number of C's = 14,687,392 bp (18.66%) number of T's = 24,922,671 bp (31.66%) number of G's = 16,400,409 bp (20.83%) number of N's = 23,908 bp (0.03%) GC percentage = 39.49% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 681,262 number of insertions = 6,280 mapped reads with insertion percentage = 0.55% number of deletions = 21,027 mapped reads with deletion percentage = 1.83% homopolymer indels = 47.23% >>>>>>> Coverage mean coverageData = 0.0254X std coverageData = 0.2476X There is a 2.33% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% 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 6224766 0.024973923735981386 0.4154865744912118 chr2 243199373 6834568 0.02810273692605285 0.27179543678378454 chr3 198022430 5389312 0.02721566440730982 0.17505427452036995 chr4 191154276 5050267 0.026419848436976635 0.1779505115742097 chr5 180915260 5163947 0.028543457307028716 0.1798279737412509 chr6 171115067 4821749 0.028178401145703903 0.20747824434569423 chr7 159138663 4225709 0.026553628894067056 0.2954277706380238 chr8 146364022 4173889 0.028517178900700064 0.3298700995233717 chr9 141213431 3320022 0.023510667338717945 0.22756300532130788 chr10 135534747 3663669 0.02703121584017123 0.24244950805209103 chr11 135006516 3678880 0.0272496477133 0.22419091521060447 chr12 133851895 3532152 0.0263885094790776 0.174580274820962 chr13 115169878 2750852 0.0238851690022629 0.16395283534740615 chr14 107349540 2411621 0.022465126538967935 0.1699725528350905 chr15 102531392 2065838 0.02014834637181167 0.15329166989371218 chr16 90354753 2036498 0.022538913918562758 0.17860312072753537 chr17 81195210 1942050 0.023918282864223147 0.19045445513385276 chr18 78077248 2050943 0.026268126151167623 0.46752270618655134 chr19 59128983 1334846 0.0225751557404598 0.29738523289545865 chr20 63025520 1569983 0.02491027444121048 0.17384567838429027 chr21 48129895 1055199 0.02192398300474165 0.163320837072751 chr22 51304566 763514 0.014881989256082978 0.12853720035141727 chrMT 16571 1611 0.09721803150081468 0.3287347552944386 chrX 155270560 4518560 0.02910120244301302 0.2005149932448341 chrY 59373566 180649 0.0030425829568666973 0.08316757065557584