BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081696.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 = 1,798,984 number of mapped reads = 1,566,659 (87.09%) number of supplementary alignments = 15,968 (0.89%) number of secondary alignments = 0 number of mapped bases = 105,617,643 bp number of sequenced bases = 105,578,805 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,427 duplication rate = 4.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6118 >>>>>>> ACTG content number of A's = 29,910,899 bp (28.33%) number of C's = 18,633,506 bp (17.65%) number of T's = 34,427,877 bp (32.61%) number of G's = 22,530,435 bp (21.34%) number of N's = 76,088 bp (0.07%) GC percentage = 38.99% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 893,149 number of insertions = 8,594 mapped reads with insertion percentage = 0.54% number of deletions = 24,119 mapped reads with deletion percentage = 1.52% homopolymer indels = 49.31% >>>>>>> Coverage mean coverageData = 0.0341X std coverageData = 0.2795X There is a 2.79% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.09% 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 6952965 0.027895477139051942 0.29696787000155966 chr2 243199373 8676202 0.035675264672660155 0.3098100123112892 chr3 198022430 7280104 0.03676403728607916 0.2269051528811684 chr4 191154276 7099899 0.037142245251160375 0.2305292911562628 chr5 180915260 6127881 0.03387155400821357 0.2185297974095246 chr6 171115067 6251372 0.03653314760412068 0.2619369167117865 chr7 159138663 6673035 0.04193220474649834 0.3391536410934722 chr8 146364022 4839141 0.03306236692511771 0.5138011102908975 chr9 141213431 4416773 0.03127728693172252 0.27796739326271 chr10 135534747 4910104 0.0362276398391034 0.262613314742105 chr11 135006516 5137744 0.038055526149567476 0.2525206598326272 chr12 133851895 4875814 0.03642693291716191 0.22961278048650707 chr13 115169878 4348194 0.037754611496592885 0.22997369125600206 chr14 107349540 3463416 0.032262979422175445 0.21970934885833812 chr15 102531392 3123126 0.030460193108467697 0.2069032233348752 chr16 90354753 3049806 0.03375368642754189 0.22586771508086434 chr17 81195210 2098457 0.025844591078710184 0.1967198605925103 chr18 78077248 3346317 0.042859054151088934 0.4575889443440594 chr19 59128983 1568515 0.026527007914206813 0.31177565103534605 chr20 63025520 2359569 0.037438310703346835 0.23392331470759564 chr21 48129895 1360974 0.0282771030354419 0.20620179516889484 chr22 51304566 926903 0.0180666765605229 0.15830832618210242 chrMT 16571 11291 0.681371069941464 0.9880708423924233 chrX 155270560 6473335 0.041690678516262195 0.2530592844551278 chrY 59373566 246706 0.004155148774456296 0.08985904976241599