BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013367.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 = 2,130,794 number of mapped reads = 1,913,647 (89.81%) number of supplementary alignments = 11,674 (0.55%) number of secondary alignments = 0 number of mapped bases = 129,837,817 bp number of sequenced bases = 129,784,269 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 88,223 duplication rate = 3.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3739 >>>>>>> ACTG content number of A's = 37,186,303 bp (28.65%) number of C's = 23,835,032 bp (18.37%) number of T's = 41,252,958 bp (31.79%) number of G's = 27,481,694 bp (21.17%) number of N's = 28,282 bp (0.02%) GC percentage = 39.54% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,040,833 number of insertions = 9,785 mapped reads with insertion percentage = 0.51% number of deletions = 31,028 mapped reads with deletion percentage = 1.6% homopolymer indels = 46.53% >>>>>>> Coverage mean coverageData = 0.0419X std coverageData = 0.501X There is a 3.59% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% 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 9943268 0.039892650859232964 0.9624001292003319 chr2 243199373 6056565 0.024903703185122934 0.45612172875767354 chr3 198022430 11872093 0.05995327398012437 0.2742851689685223 chr4 191154276 7877612 0.04121075481460849 0.24824261313342905 chr5 180915260 7725639 0.04270308098940907 0.234009540100905 chr6 171115067 11230963 0.06563398067102998 0.3931203743810997 chr7 159138663 10008848 0.06289388016286149 1.046764458092739 chr8 146364022 9043641 0.06178868875303249 0.573008525410355 chr9 141213431 4299595 0.03044749334077153 0.4030645805734204 chr10 135534747 5193336 0.03831737701919346 0.46880329831487955 chr11 135006516 4603250 0.034096502423631166 0.3215892569872221 chr12 133851895 6596437 0.04928161084308892 0.2580083636443661 chr13 115169878 3392139 0.029453352377433274 0.19223166908845432 chr14 107349540 6077224 0.056611551386247204 0.2824557207403132 chr15 102531392 2670722 0.026047846887712205 0.18212270233312186 chr16 90354753 3690755 0.040847380768115206 0.2633108873003148 chr17 81195210 3406411 0.04195334921850685 0.2568741483584213 chr18 78077248 3276582 0.04196590023254918 0.8652891104682875 chr19 59128983 1871811 0.03165640444044167 0.718513754246535 chr20 63025520 2062940 0.03273182038006192 0.21628750136957983 chr21 48129895 2295427 0.04769233342395615 0.261529378909688 chr22 51304566 1377865 0.026856576469236677 0.18092448198710867 chrMT 16571 28442 1.7163719751372881 1.6863611924769346 chrX 155270560 4991161 0.032144928182135754 0.2333826238216753 chrY 59373566 245091 0.004127948117517482 0.1139025051010866