BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013256.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 = 2,048,002 number of mapped reads = 427,276 (20.86%) number of supplementary alignments = 3,129 (0.15%) number of secondary alignments = 0 number of mapped bases = 27,373,970 bp number of sequenced bases = 27,356,194 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,092 duplication rate = 3.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9734 >>>>>>> ACTG content number of A's = 7,464,654 bp (27.29%) number of C's = 4,852,828 bp (17.74%) number of T's = 8,924,683 bp (32.62%) number of G's = 6,113,666 bp (22.35%) number of N's = 363 bp (0%) GC percentage = 40.09% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 233,784 number of insertions = 2,085 mapped reads with insertion percentage = 0.48% number of deletions = 10,368 mapped reads with deletion percentage = 2.39% homopolymer indels = 44.37% >>>>>>> Coverage mean coverageData = 0.0088X std coverageData = 0.1812X There is a 0.73% of reference with a coverageData >= 1X There is a 0.11% 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 3058255 0.012269798918575213 0.27019813563041867 chr2 243199373 2681695 0.01102673484277445 0.23738640525740212 chr3 198022430 1669751 0.008432130642978172 0.10883027736880398 chr4 191154276 1438109 0.007523289722276472 0.17751132091829985 chr5 180915260 826136 0.004566425187129046 0.08570789802137091 chr6 171115067 1308328 0.007645895963094822 0.11644771592714966 chr7 159138663 2509834 0.01577136537838074 0.2775469212972716 chr8 146364022 1618292 0.011056624284347692 0.18373683332244928 chr9 141213431 740422 0.005243283126517902 0.09744026189680385 chr10 135534747 1040352 0.007675906164490793 0.11952293412193706 chr11 135006516 795954 0.005895670991169048 0.10512210236829447 chr12 133851895 1843590 0.013773357485898873 0.1618117761907147 chr13 115169878 836766 0.007265493499958383 0.10155201311611199 chr14 107349540 608336 0.005666871045744584 0.08818239376813064 chr15 102531392 1354988 0.013215347744425433 0.1347797597626621 chr16 90354753 713149 0.007892766858651033 0.3934472615572553 chr17 81195210 1017069 0.012526219219089403 0.1352982153032698 chr18 78077248 407259 0.00521610341594007 0.14294379384054962 chr19 59128983 544381 0.009206669426396188 0.23726465935256205 chr20 63025520 482915 0.007662213655674717 0.10258349778825511 chr21 48129895 479068 0.009953647312133135 0.32095603595101296 chr22 51304566 194305 0.003787284741868784 0.07619912991162876 chrMT 16571 2765 0.16685776356285076 0.4367990973390017 chrX 155270560 1140694 0.007346492470948775 0.11048784392144334 chrY 59373566 61557 0.0010367745134257221 0.04003736030266497