BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082973.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 = 3,032,312 number of mapped reads = 2,525,387 (83.28%) number of supplementary alignments = 23,802 (0.78%) number of secondary alignments = 0 number of mapped bases = 169,407,775 bp number of sequenced bases = 169,339,801 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 91,430 duplication rate = 2.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1016 >>>>>>> ACTG content number of A's = 49,107,686 bp (29%) number of C's = 30,935,306 bp (18.27%) number of T's = 52,859,933 bp (31.22%) number of G's = 36,420,866 bp (21.51%) number of N's = 16,010 bp (0.01%) GC percentage = 39.78% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 1,572,340 number of insertions = 14,295 mapped reads with insertion percentage = 0.56% number of deletions = 38,993 mapped reads with deletion percentage = 1.53% homopolymer indels = 47.44% >>>>>>> Coverage mean coverageData = 0.0547X std coverageData = 0.4325X There is a 4.63% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% 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 19021164 0.07631340665747027 0.7984508505088189 chr2 243199373 17980665 0.0739338460383284 0.5420610714482792 chr3 198022430 12796325 0.06462058363792425 0.2894981326994149 chr4 191154276 8637002 0.04518340986523367 0.2530458197863679 chr5 180915260 9139427 0.05051772304890146 0.2604120884648259 chr6 171115067 11656462 0.06812060565069936 0.36562346915333 chr7 159138663 8311213 0.05222623367144916 0.3764426279104251 chr8 146364022 11010534 0.07522705272474679 0.5110598963276545 chr9 141213431 5941959 0.04207786014348734 0.41525155385231866 chr10 135534747 6791513 0.05010901743152256 0.3736310710636899 chr11 135006516 6324138 0.046843205701271484 0.34524508905431833 chr12 133851895 6088604 0.045487618983653534 0.24997513385189687 chr13 115169878 2976961 0.02584843408447476 0.18069055489305294 chr14 107349540 3239455 0.030176701269516385 0.262323907290043 chr15 102531392 3560246 0.03472347278772925 0.20992672723357658 chr16 90354753 6200534 0.06862432571754139 0.34256473716475194 chr17 81195210 3585929 0.04416429245025661 0.27747165764808557 chr18 78077248 6029632 0.07722649240915869 0.9965775210316749 chr19 59128983 3100194 0.0524310387682467 0.5406622462876883 chr20 63025520 3475764 0.055148517616356044 0.2842521492442254 chr21 48129895 3957346 0.08222220306111201 0.34241897548195566 chr22 51304566 2468287 0.048110474221729115 0.2497842694005455 chrMT 16571 117299 7.078570997525798 6.29214067563625 chrX 155270560 6692166 0.043100031325964176 0.2754368473148329 chrY 59373566 304956 0.005136225100577587 0.11394900554997704