BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084409.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 = 2,404,164 number of mapped reads = 2,222,373 (92.44%) number of supplementary alignments = 15,748 (0.66%) number of secondary alignments = 0 number of mapped bases = 149,783,196 bp number of sequenced bases = 149,732,066 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 76,574 duplication rate = 2.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1981 >>>>>>> ACTG content number of A's = 42,565,962 bp (28.43%) number of C's = 28,479,437 bp (19.02%) number of T's = 46,446,880 bp (31.02%) number of G's = 32,046,336 bp (21.4%) number of N's = 193,451 bp (0.13%) GC percentage = 40.42% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 1,485,414 number of insertions = 10,685 mapped reads with insertion percentage = 0.48% number of deletions = 29,897 mapped reads with deletion percentage = 1.33% homopolymer indels = 46.56% >>>>>>> Coverage mean coverageData = 0.0484X std coverageData = 0.3335X There is a 4.08% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 14942954 0.059951521645356304 0.5310063010706344 chr2 243199373 14302358 0.05880918944638891 0.372701216753421 chr3 198022430 10558645 0.05332044960765303 0.2676046432451392 chr4 191154276 7156672 0.03743924619295464 0.2283051794372399 chr5 180915260 8027501 0.04437160801139716 0.24064544438665886 chr6 171115067 7125391 0.04164093276485115 0.26193364465931696 chr7 159138663 8381057 0.05266512136023161 0.4753029890787658 chr8 146364022 6617479 0.0452124703159633 0.34527547366272837 chr9 141213431 5441891 0.038536638912200924 0.27295800762851563 chr10 135534747 11042397 0.08147281228185714 0.45623096061692026 chr11 135006516 8498572 0.06294934683004486 0.34644706345833665 chr12 133851895 7716397 0.05764876918627114 0.2763423541716794 chr13 115169878 3711618 0.032227332914253844 0.2055393322350003 chr14 107349540 4354905 0.04056752362422792 0.23873427171427913 chr15 102531392 3174736 0.030963551143439075 0.20327673861056766 chr16 90354753 3157656 0.03494731483577848 0.22700575577577903 chr17 81195210 3779614 0.04654971641800052 0.2595988041093909 chr18 78077248 4001337 0.051248437957239476 0.45799459230042927 chr19 59128983 2936652 0.04966518703695614 0.40225342229784145 chr20 63025520 3145466 0.04990781511997045 0.25897122279052265 chr21 48129895 1478326 0.03071533814898204 0.20892519658127148 chr22 51304566 1190501 0.0232045818300071 0.17163482308172312 chrMT 16571 55128 3.3267756924748055 2.9829688784628186 chrX 155270560 8707726 0.056080985345837615 0.3070944440746523 chrY 59373566 278217 0.004685873171235832 0.1005269103608116