BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240052.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 = 2,069,819 number of mapped reads = 1,664,885 (80.44%) number of supplementary alignments = 8,205 (0.4%) number of secondary alignments = 0 number of mapped bases = 103,176,776 bp number of sequenced bases = 103,121,252 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 154,289 duplication rate = 7.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5954 >>>>>>> ACTG content number of A's = 28,043,229 bp (27.19%) number of C's = 18,079,366 bp (17.53%) number of T's = 33,488,486 bp (32.47%) number of G's = 23,444,727 bp (22.74%) number of N's = 65,444 bp (0.06%) GC percentage = 40.27% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 1,000,853 number of insertions = 7,224 mapped reads with insertion percentage = 0.43% number of deletions = 31,975 mapped reads with deletion percentage = 1.9% homopolymer indels = 49.59% >>>>>>> Coverage mean coverageData = 0.0333X std coverageData = 0.3231X There is a 2.46% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.05% 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 7157659 0.028716714812116757 0.44094268917202917 chr2 243199373 11657974 0.047935871939933004 0.4088050237221725 chr3 198022430 6572928 0.03319284588114589 0.24214189830785637 chr4 191154276 6226665 0.03257402936672994 0.24157322473521708 chr5 180915260 6221375 0.034388337390665664 0.24250493815418256 chr6 171115067 5561681 0.03250257909784181 0.27709812959031516 chr7 159138663 5258691 0.03304471019716937 0.4727033178014572 chr8 146364022 6261047 0.04277722704285893 0.4780114582285201 chr9 141213431 3566699 0.02525750542807787 0.28474630541211104 chr10 135534747 5205414 0.038406490698654566 0.29954534479198897 chr11 135006516 5359517 0.03969820982566501 0.3623516118946189 chr12 133851895 5696518 0.04255836646914861 0.2726354132497525 chr13 115169878 2225794 0.019326181799029084 0.17809386832000978 chr14 107349540 3878871 0.03613309381670383 0.2542224370623603 chr15 102531392 2520528 0.02458298820326169 0.21742806196645859 chr16 90354753 2869470 0.0317578202001172 0.237267035041419 chr17 81195210 2510359 0.03091757506384921 0.25255387491285763 chr18 78077248 2719487 0.03483072302958219 0.4545187310495082 chr19 59128983 1739943 0.029426229096482178 0.3316830401844067 chr20 63025520 2078047 0.03297151693472739 0.2393462734311532 chr21 48129895 1554629 0.03230069377878344 0.24048181646732927 chr22 51304566 1010186 0.01968998236921057 0.17667764567043126 chrMT 16571 23594 1.4238126848108141 2.010315214490332 chrX 155270560 5089973 0.03278131411389255 0.25648199513421494 chrY 59373566 209727 0.003532329521861631 0.08207745765439116