BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080768.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 = 4,392,789 number of mapped reads = 3,283,540 (74.75%) number of supplementary alignments = 24,082 (0.55%) number of secondary alignments = 0 number of mapped bases = 210,340,173 bp number of sequenced bases = 210,266,046 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 423,379 duplication rate = 9.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5311 >>>>>>> ACTG content number of A's = 65,542,698 bp (31.17%) number of C's = 42,255,996 bp (20.1%) number of T's = 54,461,594 bp (25.9%) number of G's = 47,935,732 bp (22.8%) number of N's = 70,026 bp (0.03%) GC percentage = 42.89% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,629,486 number of insertions = 16,362 mapped reads with insertion percentage = 0.49% number of deletions = 38,669 mapped reads with deletion percentage = 1.16% homopolymer indels = 42.61% >>>>>>> Coverage mean coverageData = 0.0679X std coverageData = 0.5406X There is a 4.47% of reference with a coverageData >= 1X There is a 1.28% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 26057142 0.10454193412019623 0.8276920370812038 chr2 243199373 15459667 0.06356787358987147 0.5230317221171438 chr3 198022430 12378012 0.06250813102333912 0.3616746691593632 chr4 191154276 12417903 0.06496272675584824 0.48836928396021445 chr5 180915260 15557687 0.08599433237417341 0.4332642759833638 chr6 171115067 13781751 0.08054083863929995 0.5123199659391824 chr7 159138663 14070876 0.08841896579211553 0.7178676305399678 chr8 146364022 9581566 0.06546394304469168 0.8102286122924244 chr9 141213431 7211537 0.05106835057353716 0.38977718396386635 chr10 135534747 9375373 0.06917320618896348 0.7347606719772004 chr11 135006516 8359947 0.06192254453851694 0.4542447569136151 chr12 133851895 7985512 0.059659312257028564 0.3592011083374259 chr13 115169878 8195749 0.07116226171568923 0.3907440893372747 chr14 107349540 5598209 0.05214935247975911 0.36533826170553196 chr15 102531392 5293351 0.05162663743022235 0.33132095649417587 chr16 90354753 5290464 0.05855213836952219 0.39472242341351166 chr17 81195210 5653255 0.06962547421208715 0.41667271693335584 chr18 78077248 2921462 0.03741758418534424 0.5933022934428475 chr19 59128983 3858539 0.06525630586272725 0.7623368857071521 chr20 63025520 4023961 0.06384653391197724 0.3905963698409588 chr21 48129895 3446345 0.0716050803767596 0.4989185149961269 chr22 51304566 2236255 0.04358783582732188 0.3127199354118858 chrMT 16571 60153 3.6300162935248323 3.648710862122691 chrX 155270560 10751053 0.06924076914516183 0.40490177620571793 chrY 59373566 774404 0.013042908691049482 0.45902387036289866