BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013228.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,164,874 number of mapped reads = 1,878,908 (86.79%) number of supplementary alignments = 12,903 (0.6%) number of secondary alignments = 0 number of mapped bases = 126,572,159 bp number of sequenced bases = 126,518,695 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 95,708 duplication rate = 4.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9504 >>>>>>> ACTG content number of A's = 35,236,252 bp (27.85%) number of C's = 23,288,452 bp (18.41%) number of T's = 40,400,750 bp (31.93%) number of G's = 27,565,957 bp (21.79%) number of N's = 27,284 bp (0.02%) GC percentage = 40.2% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,026,200 number of insertions = 9,127 mapped reads with insertion percentage = 0.48% number of deletions = 30,743 mapped reads with deletion percentage = 1.62% homopolymer indels = 46.6% >>>>>>> Coverage mean coverageData = 0.0409X std coverageData = 0.383X There is a 3.38% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.09% 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% 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 9261315 0.03715663761575944 0.6607465624173113 chr2 243199373 10958968 0.04506166222722951 0.448504718755979 chr3 198022430 9795593 0.049467088147539647 0.2589508083978515 chr4 191154276 8273509 0.04328184110304705 0.25409403019044113 chr5 180915260 7743921 0.042804133824863644 0.24389256830760153 chr6 171115067 7425526 0.0433949279288188 0.2938257020888402 chr7 159138663 8528364 0.05359077322397763 0.6074026768925408 chr8 146364022 6295089 0.04300981152321709 0.39572331820671364 chr9 141213431 4708539 0.033343421844909356 0.3591182843356186 chr10 135534747 5648833 0.04167811668250652 0.3730409002022925 chr11 135006516 5518560 0.04087624926192451 0.30744555566979553 chr12 133851895 6303866 0.04709582931194213 0.2593148038298131 chr13 115169878 2271425 0.019722387827831162 0.16364330473967315 chr14 107349540 3226288 0.03005404587667539 0.22035986868097798 chr15 102531392 4626990 0.04512754493765188 0.24898002990065393 chr16 90354753 3247374 0.03594026758061084 0.26018596450331316 chr17 81195210 3161437 0.038936250057115436 0.25896893470019805 chr18 78077248 3091268 0.039592430306969836 0.7201877834540783 chr19 59128983 2369463 0.04007278461055216 0.5028334491102341 chr20 63025520 2702390 0.042877710489338285 0.24368389004913105 chr21 48129895 1797682 0.03735063207596859 0.23820677580327754 chr22 51304566 1366886 0.026642579921638942 0.18666882295462414 chrMT 16571 42778 2.5814977973568283 2.149946300101031 chrX 155270560 7885240 0.05078387042591976 0.29211002244764706 chrY 59373566 320855 0.005404004199444581 0.13430166899572568