BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708547.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,770,166 number of mapped reads = 3,102,314 (82.29%) number of supplementary alignments = 80 (0%) number of secondary alignments = 0 number of mapped bases = 154,693,638 bp number of sequenced bases = 154,679,302 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,398 duplication rate = 0.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4037 >>>>>>> ACTG content number of A's = 48,003,552 bp (31.03%) number of C's = 29,302,606 bp (18.94%) number of T's = 47,673,061 bp (30.82%) number of G's = 29,693,533 bp (19.2%) number of N's = 6,550 bp (0%) GC percentage = 38.14% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 246,981 number of insertions = 10,704 mapped reads with insertion percentage = 0.34% number of deletions = 8,322 mapped reads with deletion percentage = 0.27% homopolymer indels = 48.1% >>>>>>> Coverage mean coverageData = 0.05X std coverageData = 0.2307X There is a 4.73% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 11138922 0.04468964592870563 0.21891398474971957 chr2 243199373 13386312 0.05504254322234622 0.24137960077643886 chr3 198022430 11913818 0.06016398243370713 0.2522875917821743 chr4 191154276 12243068 0.0640480990338924 0.26003106181790014 chr5 180915260 10881809 0.06014865191581959 0.25218215302639835 chr6 171115067 10726114 0.06268363264586163 0.258019592661237 chr7 159138663 8766073 0.055084495714281576 0.2422078713269316 chr8 146364022 8047542 0.05498306134276632 0.24103266246112828 chr9 141213431 6222358 0.044063499880546066 0.21684417003728532 chr10 135534747 6413036 0.0473165453284094 0.22318069699900003 chr11 135006516 7208586 0.0533943561657424 0.23915610510165222 chr12 133851895 7121839 0.05320685971610637 0.23801779797975284 chr13 115169878 6047609 0.05251033607936964 0.23641084056337436 chr14 107349540 4949970 0.04611077047931458 0.22244832978559584 chr15 102531392 3916578 0.03819881817268218 0.2018925290060095 chr16 90354753 2793357 0.030915440607756407 0.18049221745361554 chr17 81195210 2389434 0.02942826307118363 0.17682222405001458 chr18 78077248 4414490 0.056540030714197304 0.24465055999568874 chr19 59128983 1322486 0.022366121196435933 0.15295126522347924 chr20 63025520 2396163 0.03801893264823519 0.20069932945814337 chr21 48129895 1766408 0.03670084881755923 0.19861422991066585 chr22 51304566 812596 0.015838668238612526 0.1289392235959516 chrMT 16571 250 0.01508659706716553 0.12189746369838267 chrX 155270560 9583350 0.06172032869592278 0.2565724081302083 chrY 59373566 231470 0.003898536261069446 0.06448929515368397