BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063584.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 = 3,103,042 number of mapped reads = 2,683,573 (86.48%) number of supplementary alignments = 25,301 (0.82%) number of secondary alignments = 0 number of mapped bases = 175,036,554 bp number of sequenced bases = 174,967,906 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 195,350 duplication rate = 5.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1422 >>>>>>> ACTG content number of A's = 46,339,074 bp (26.48%) number of C's = 33,045,415 bp (18.89%) number of T's = 54,580,344 bp (31.19%) number of G's = 40,998,636 bp (23.43%) number of N's = 4,437 bp (0%) GC percentage = 42.32% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,416,025 number of insertions = 12,460 mapped reads with insertion percentage = 0.46% number of deletions = 43,132 mapped reads with deletion percentage = 1.59% homopolymer indels = 46.11% >>>>>>> Coverage mean coverageData = 0.0565X std coverageData = 0.5299X There is a 4.37% of reference with a coverageData >= 1X There is a 0.9% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 18582916 0.07455514423773492 1.037452947966804 chr2 243199373 17321175 0.07122212029716048 0.7536144768321 chr3 198022430 12082189 0.06101424469945147 0.30571360381781154 chr4 191154276 9014648 0.047159018299962066 0.29656585823017223 chr5 180915260 8199516 0.04532241227191117 0.26527682668866 chr6 171115067 11800416 0.06896187581190615 0.3807941218754675 chr7 159138663 13312524 0.08365361219605069 0.8455783707471491 chr8 146364022 6525892 0.04458672227523237 0.546784606597572 chr9 141213431 5294365 0.037491936584983905 0.4255814213924461 chr10 135534747 6754015 0.04983235037137746 0.35962517096736063 chr11 135006516 8758005 0.06487098000514287 0.4479453224784203 chr12 133851895 6927282 0.051753335281506475 0.2938516804797632 chr13 115169878 4459739 0.0387231373119975 0.250058986371911 chr14 107349540 3623860 0.03375757362351064 0.2715395138096982 chr15 102531392 3103564 0.03026940276008347 0.2345783963380939 chr16 90354753 4230507 0.04682107868747093 0.2882969874902812 chr17 81195210 5433971 0.06692477302540384 0.34819950623588286 chr18 78077248 4794313 0.06140473854816195 0.6909715146868003 chr19 59128983 4293654 0.07261504903610468 0.7166897378602363 chr20 63025520 2767608 0.04391249766761147 0.2800599641523493 chr21 48129895 2981794 0.061953054333486496 0.3215204015506037 chr22 51304566 2035007 0.039665221999928814 0.242957348338719 chrMT 16571 185732 11.208255385915153 7.827040009763737 chrX 155270560 12159626 0.07831250173890016 0.4093342449023681 chrY 59373566 394236 0.006639924575188898 0.17892837106094855