BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085115.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,209,741 number of mapped reads = 1,872,007 (84.72%) number of supplementary alignments = 12,208 (0.55%) number of secondary alignments = 0 number of mapped bases = 110,950,210 bp number of sequenced bases = 110,916,993 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 56,590 duplication rate = 2.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6365 >>>>>>> ACTG content number of A's = 33,058,061 bp (29.8%) number of C's = 22,183,120 bp (20%) number of T's = 32,076,651 bp (28.92%) number of G's = 23,596,850 bp (21.27%) number of N's = 2,311 bp (0%) GC percentage = 41.27% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 897,331 number of insertions = 7,645 mapped reads with insertion percentage = 0.41% number of deletions = 20,956 mapped reads with deletion percentage = 1.11% homopolymer indels = 45.32% >>>>>>> Coverage mean coverageData = 0.0358X std coverageData = 0.2649X There is a 3.15% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.05% 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 11464783 0.04599700876973943 0.3947456105268083 chr2 243199373 8945647 0.03678318282506427 0.25991907230379246 chr3 198022430 5861454 0.029599949864265375 0.19461561993733964 chr4 191154276 8156112 0.042667693188302 0.2320155275734803 chr5 180915260 5909804 0.03266614435951948 0.19963779701673295 chr6 171115067 8122616 0.04746873634453242 0.2736298205021769 chr7 159138663 10210401 0.06416040456491708 0.3082503779100753 chr8 146364022 7073056 0.04832510000305949 0.4481412877702674 chr9 141213431 2864830 0.020287234576150195 0.19143767170128614 chr10 135534747 6371492 0.04701002614480846 0.37616765057243107 chr11 135006516 5849916 0.04333061968653424 0.2640922484979428 chr12 133851895 4277916 0.03196007049433256 0.19886462467478078 chr13 115169878 2192555 0.01903757334882303 0.1505915891713809 chr14 107349540 3623823 0.03375722895505654 0.2081513024426536 chr15 102531392 1968276 0.01919681340130445 0.15257634026035907 chr16 90354753 2359146 0.026109816270539748 0.18857015863870857 chr17 81195210 1490753 0.018360110159207667 0.1568077868385512 chr18 78077248 3032648 0.03884163540190351 0.3255366879920621 chr19 59128983 1860955 0.03147280581504336 0.2693096506321636 chr20 63025520 2760974 0.043807238718538144 0.2339738823638415 chr21 48129895 1197116 0.024872607762805216 0.17986472211956128 chr22 51304566 678025 0.013215685325161897 0.12548035464840496 chrMT 16571 46637 2.8143745096855954 2.2782356522582017 chrX 155270560 4403858 0.028362479017271527 0.20009681601920967 chrY 59373566 227417 0.0038302735597858482 0.07828368368652314