BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714258.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 12,310 number of mapped reads = 2,617 (21.26%) number of supplementary alignments = 186 (1.51%) number of secondary alignments = 0 number of mapped bases = 280,230 bp number of sequenced bases = 275,631 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,660 duplication rate = 44.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 19.0701 >>>>>>> ACTG content number of A's = 56,080 bp (20.35%) number of C's = 45,030 bp (16.34%) number of T's = 52,472 bp (19.04%) number of G's = 122,048 bp (44.28%) number of N's = 1 bp (0%) GC percentage = 60.62% >>>>>>> Mismatches and indels general error rate = 0.0367 number of mismatches = 9,015 number of insertions = 187 mapped reads with insertion percentage = 5.24% number of deletions = 597 mapped reads with deletion percentage = 22.01% homopolymer indels = 35.84% >>>>>>> Coverage mean coverageData = 0.0001X std coverageData = 0.095X There is a 0% 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 5966 2.3935747786963387E-5 0.016400661981960284 chr2 243199373 90633 3.726695463149899E-4 0.32748849024710813 chr3 198022430 4123 2.0820873675775013E-5 0.007020464203413427 chr4 191154276 4033 2.109814169158319E-5 0.008534401659339611 chr5 180915260 5089 2.8129191534202257E-5 0.012033364433687226 chr6 171115067 3337 1.950149720012674E-5 0.008961155770583486 chr7 159138663 10178 6.395680225112863E-5 0.03939137604157812 chr8 146364022 8229 5.6222833231516415E-5 0.02157894652398456 chr9 141213431 2290 1.621658778335327E-5 0.008533381419947183 chr10 135534747 3185 2.349950894880115E-5 0.020851401679379676 chr11 135006516 2774 2.054715640539898E-5 0.007253914493519649 chr12 133851895 5785 4.321941052833058E-5 0.016760239757184107 chr13 115169878 1612 1.3996715356423318E-5 0.006037408983562699 chr14 107349540 2153 2.0055977883091068E-5 0.008332847964848414 chr15 102531392 1409 1.3742132750913984E-5 0.005357538191475653 chr16 90354753 1696 1.8770456934346332E-5 0.006777146920692415 chr17 81195210 2897 3.567944463718981E-5 0.008873269863137476 chr18 78077248 1606 2.056937252706448E-5 0.0075426753195662315 chr19 59128983 2185 3.695311316279531E-5 0.012102686681211306 chr20 63025520 3877 6.151476417806628E-5 0.020649332220226645 chr21 48129895 31 6.440903309678943E-7 8.025521267279402E-4 chr22 51304566 693 1.3507569677131661E-5 0.005074250007145333 chrMT 16571 754 0.045501176754571236 0.3123747828099847 chrX 155270560 115362 7.429740705514297E-4 0.08867546525952673 chrY 59373566 333 5.608556508126865E-6 0.00435290645259728