BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124780.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 584,793 number of mapped reads = 583,855 (99.84%) number of supplementary alignments = 270,614 (46.28%) number of secondary alignments = 0 number of mapped bases = 87,858,755 bp number of sequenced bases = 87,809,334 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 848,569 duplication rate = 7.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.7254 >>>>>>> ACTG content number of A's = 23,320,458 bp (26.56%) number of C's = 17,310,054 bp (19.71%) number of T's = 28,309,514 bp (32.24%) number of G's = 18,869,308 bp (21.49%) number of N's = 0 bp (0%) GC percentage = 41.2% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 725,378 number of insertions = 19,330 mapped reads with insertion percentage = 3.23% number of deletions = 46,135 mapped reads with deletion percentage = 7.55% homopolymer indels = 81.72% >>>>>>> Coverage mean coverageData = 0.0284X std coverageData = 60.1335X There is a 0.02% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% 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 78398 3.145348231649942E-4 0.07950335915273542 chr2 243199373 56862 2.338081685761583E-4 0.015759540137184776 chr3 198022430 39971 2.0185087113616372E-4 0.0142719562446479 chr4 191154276 28128 1.4714816005476121E-4 0.012339521468931858 chr5 180915260 46423 2.5660079752255283E-4 0.157222785598455 chr6 171115067 35498 2.0745104813008663E-4 0.014698289054777701 chr7 159138663 49004 3.079327114869628E-4 0.017606453307717245 chr8 146364022 82768230 0.5654957336441602 275.7430372758734 chr9 141213431 26143 1.8513111546733822E-4 0.013907721008202352 chr10 135534747 4484241 0.03308554521446814 21.968083408934802 chr11 135006516 26302 1.9482022630670656E-4 0.014015494937678253 chr12 133851895 35749 2.670787738940864E-4 0.016440187958367717 chr13 115169878 15224 1.3218734155470756E-4 0.011492739567117966 chr14 107349540 14811 1.3796985063932273E-4 0.011771391146447794 chr15 102531392 16982 1.6562732319093065E-4 0.012860604313383928 chr16 90354753 23718 2.6249864243444945E-4 0.01649856041871383 chr17 81195210 16700 2.0567715755646178E-4 0.014429020149150557 chr18 78077248 14967 1.916947687500461E-4 0.013952343039357704 chr19 59128983 10330 1.747028187513389E-4 0.013210607148799918 chr20 63025520 16864 2.675741509153752E-4 0.01635647749652264 chr21 48129895 6881 1.4296727636742195E-4 0.012174738504917229 chr22 51304566 8482 1.6532641558648017E-4 0.013091980346407461 chrMT 16571 1182 0.07132943093355863 0.25970843456003995 chrX 155270560 31932 2.0565392434985743E-4 0.020729933134030355 chrY 59373566 5733 9.655812150477874E-5 0.01006052892107832