BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549042.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 2,951,858 number of mapped reads = 2,467,842 (83.6%) number of secondary alignments = 0 number of mapped bases = 97,656,394 bp number of sequenced bases = 97,647,595 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 64,323 duplication rate = 1.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.6227 >>>>>>> ACTG content number of A's = 27,551,123 bp (28.21%) number of C's = 21,203,403 bp (21.71%) number of T's = 28,136,201 bp (28.81%) number of G's = 20,756,234 bp (21.26%) number of N's = 634 bp (0%) GC percentage = 42.97% >>>>>>> Mismatches and indels general error rate = 0.0027 number of mismatches = 264,695 number of insertions = 3,133 mapped reads with insertion percentage = 0.13% number of deletions = 6,768 mapped reads with deletion percentage = 0.27% homopolymer indels = 39.78% >>>>>>> Coverage mean coverageData = 0.0315X std coverageData = 0.2642X There is a 2.81% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 8284880 0.03323915489863514 0.34707601499332 chr2 243199373 8448627 0.03473950979306184 0.26556660144931243 chr3 198022430 6720958 0.033940387460147825 0.2020706554961415 chr4 191154276 6368813 0.03331765908286561 0.20939644991365863 chr5 180915260 5807528 0.03210081891378317 0.19721442744181858 chr6 171115067 5786931 0.0338189447689022 0.20473378416267915 chr7 159138663 5355374 0.03365224954793041 0.2893576268823833 chr8 146364022 5024519 0.034328921351997284 0.5353449119471324 chr9 141213431 4381178 0.03102522167314241 0.2520896627756537 chr10 135534747 4512155 0.03329149978049541 0.245727975724832 chr11 135006516 4349194 0.03221469695581212 0.22332905322417837 chr12 133851895 4227642 0.03158447626012317 0.19672449288504887 chr13 115169878 3331024 0.028922701472341578 0.18732932946736133 chr14 107349540 3194342 0.0297564572703339 0.21127377215678572 chr15 102531392 2880057 0.028089514282611125 0.18398965647812043 chr16 90354753 2906157 0.03216385307367284 0.21321662785262355 chr17 81195210 2680202 0.03300936102018826 0.20095579300911615 chr18 78077248 2694755 0.03451395981579679 0.4058872500501577 chr19 59128983 2123972 0.0359209966455875 0.36622486050609543 chr20 63025520 1864780 0.029587697174097097 0.19389124551238202 chr21 48129895 1332593 0.02768742794888707 0.21003011244307154 chr22 51304566 1163827 0.02268466709181401 0.20331729156065245 chrMT 16571 1511 0.09118339267394847 0.3525771187046358 chrX 155270560 3263649 0.021019110126220965 0.17530964133663102 chrY 59373566 951726 0.01602945661037102 0.18445481950815998