BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013292.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 = 2,336,721 number of mapped reads = 2,064,758 (88.36%) number of supplementary alignments = 18,677 (0.8%) number of secondary alignments = 0 number of mapped bases = 138,491,315 bp number of sequenced bases = 138,436,834 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,013 duplication rate = 3.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.7766 >>>>>>> ACTG content number of A's = 39,291,456 bp (28.38%) number of C's = 25,492,900 bp (18.41%) number of T's = 44,029,342 bp (31.8%) number of G's = 29,593,250 bp (21.38%) number of N's = 29,886 bp (0.02%) GC percentage = 39.79% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,075,628 number of insertions = 9,550 mapped reads with insertion percentage = 0.46% number of deletions = 31,746 mapped reads with deletion percentage = 1.52% homopolymer indels = 47.38% >>>>>>> Coverage mean coverageData = 0.0447X std coverageData = 0.3096X There is a 3.57% of reference with a coverageData >= 1X There is a 0.66% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 4327871 0.01736353146337798 0.2655711303631634 chr2 243199373 26959341 0.11085283924642356 0.503381937442865 chr3 198022430 9835055 0.049666368602789085 0.26760600128217044 chr4 191154276 5282818 0.027636410288828694 0.19966973408783828 chr5 180915260 8274848 0.045738806112872954 0.25499942069097814 chr6 171115067 7602718 0.04443044165128954 0.3157154882095159 chr7 159138663 3403972 0.02138997485482205 0.19453937596892698 chr8 146364022 15744567 0.10757129234942724 0.6000063049522028 chr9 141213431 4481160 0.031733242144651244 0.2579751975572093 chr10 135534747 4182258 0.03085745974794198 0.27084442428612 chr11 135006516 3192477 0.02364683642380639 0.2264934976815336 chr12 133851895 4784924 0.03574789882504092 0.22408846109287028 chr13 115169878 3264495 0.0283450417478084 0.19872138875439313 chr14 107349540 5129289 0.0477811921690582 0.2656267603701667 chr15 102531392 1007142 0.009822767255515267 0.11959555514848239 chr16 90354753 3210034 0.03552700763843602 0.2323383157228097 chr17 81195210 7211570 0.088817677791584 0.374889592334746 chr18 78077248 5584617 0.0715268166214055 0.4606540055255854 chr19 59128983 1637848 0.02769958008579312 0.2608496670536911 chr20 63025520 4279406 0.0678995746484916 0.3154363386314461 chr21 48129895 2389744 0.04965196786737224 0.2660244151973563 chr22 51304566 254748 0.004965406003044641 0.0784117464971094 chrMT 16571 19199 1.158590308370044 1.2681084824766147 chrX 155270560 6221585 0.04006931513610822 0.2749306096744027 chrY 59373566 209629 0.0035306789556820623 0.07177746653273812