BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708641.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 6,445,670 number of mapped reads = 6,220,112 (96.5%) number of supplementary alignments = 169 (0%) number of secondary alignments = 0 number of mapped bases = 310,251,701 bp number of sequenced bases = 310,222,006 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,747 duplication rate = 0.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3703 >>>>>>> ACTG content number of A's = 95,822,179 bp (30.89%) number of C's = 58,979,674 bp (19.01%) number of T's = 95,851,783 bp (30.9%) number of G's = 59,559,428 bp (19.2%) number of N's = 8,942 bp (0%) GC percentage = 38.21% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 505,349 number of insertions = 20,828 mapped reads with insertion percentage = 0.33% number of deletions = 17,484 mapped reads with deletion percentage = 0.28% homopolymer indels = 49.2% >>>>>>> Coverage mean coverageData = 0.1002X std coverageData = 0.3358X There is a 9.02% of reference with a coverageData >= 1X There is a 0.89% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.01% 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 23946594 0.09607436043258645 0.33144701738147775 chr2 243199373 27744203 0.11408007618506484 0.35640444838431484 chr3 198022430 23375186 0.11804312269069721 0.36157725864996965 chr4 191154276 24182750 0.12650907165686423 0.37504797349548397 chr5 180915260 20758981 0.11474422334522803 0.3570443561003633 chr6 171115067 19681236 0.11501755131826001 0.3577328742687884 chr7 159138663 18508091 0.11630166202917012 0.3608156005731067 chr8 146364022 18350657 0.12537682928663985 0.37270119043902555 chr9 141213431 13478397 0.09544699044951326 0.3278416225733458 chr10 135534747 13371163 0.09865487113795254 0.3299120521508778 chr11 135006516 14485446 0.10729442125593405 0.3479827269757683 chr12 133851895 12543543 0.09371210620514563 0.3234990196299496 chr13 115169878 11985919 0.1040716479703139 0.3421381456550145 chr14 107349540 10314215 0.09608066322408089 0.32927247601174076 chr15 102531392 7755960 0.07564473522411555 0.2918614830983768 chr16 90354753 5839471 0.06462826587550961 0.2692640288183767 chr17 81195210 4642362 0.05717531859330126 0.25072025116888336 chr18 78077248 13731471 0.17587032524507012 0.447752069483142 chr19 59128983 2603014 0.044022641147066575 0.2190134329314153 chr20 63025520 3941033 0.0625307494487947 0.26263528945256476 chr21 48129895 4452661 0.09251341603799468 0.3279797268401528 chr22 51304566 1750540 0.03412054981617036 0.19221596131004068 chrMT 16571 233 0.014060708466598274 0.11774126270775087 chrX 155270560 11655225 0.07506397220438955 0.2873145325371295 chrY 59373566 1153350 0.019425311257201563 0.1474225536605342