BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237315.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 = 2,751,345 number of mapped reads = 2,296,697 (83.48%) number of supplementary alignments = 13,445 (0.49%) number of secondary alignments = 0 number of mapped bases = 155,149,377 bp number of sequenced bases = 155,086,067 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 103,928 duplication rate = 3.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8615 >>>>>>> ACTG content number of A's = 43,571,731 bp (28.1%) number of C's = 28,315,403 bp (18.26%) number of T's = 49,276,963 bp (31.77%) number of G's = 33,919,245 bp (21.87%) number of N's = 2,725 bp (0%) GC percentage = 40.13% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,193,829 number of insertions = 12,826 mapped reads with insertion percentage = 0.55% number of deletions = 38,595 mapped reads with deletion percentage = 1.66% homopolymer indels = 47.5% >>>>>>> Coverage mean coverageData = 0.0501X std coverageData = 0.3832X There is a 3.97% of reference with a coverageData >= 1X There is a 0.75% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.04% 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% 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 15156132 0.06080679734795927 0.5373309899784918 chr2 243199373 15436648 0.06347322285242898 0.4966239924285731 chr3 198022430 20532895 0.1036897436315674 0.39196567633424323 chr4 191154276 6180578 0.032332930914922356 0.24938035882712606 chr5 180915260 8861852 0.048983441197829304 0.2673867564133958 chr6 171115067 12971341 0.07580478579364376 0.4034145545636431 chr7 159138663 11471632 0.07208576334463737 0.3793087067230428 chr8 146364022 7166606 0.048964259809695584 0.5948376683250803 chr9 141213431 10283587 0.07282300930709629 0.45582389671822476 chr10 135534747 6509211 0.04802614196048191 0.3617439199907323 chr11 135006516 1343927 0.009954534342623878 0.2226136654353565 chr12 133851895 7213992 0.05389532961038766 0.28854191302554555 chr13 115169878 4094476 0.03555162227401161 0.22800831427112325 chr14 107349540 5905909 0.055015689866952384 0.3108298900878887 chr15 102531392 4337396 0.04230310264392002 0.2555965995579248 chr16 90354753 4650827 0.05147296457110563 0.29383082516614195 chr17 81195210 795857 0.009801772789306168 0.11827977880707083 chr18 78077248 2066587 0.02646849181979365 0.7300352999043024 chr19 59128983 1852466 0.03132923831955642 0.39538787651306206 chr20 63025520 2960334 0.0469704018308774 0.2644827845254003 chr21 48129895 871402 0.018105212986647905 0.20935594355780937 chr22 51304566 2037234 0.03970862944245547 0.23638229690808357 chrMT 16571 34100 2.0578118399613783 1.9804186807774553 chrX 155270560 2155937 0.013885033969092402 0.17005591199079098 chrY 59373566 258451 0.004352964078324014 0.1436190070862637