BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124873.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 4,144,596 number of mapped reads = 4,081,894 (98.49%) number of supplementary alignments = 17,896 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,042,241 number of mapped paired reads (second in pair) = 2,039,653 number of mapped paired reads (both in pair) = 4,068,258 number of mapped paired reads (singletons) = 13,636 number of mapped bases = 374,657,938 bp number of sequenced bases = 374,383,522 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 181,751 duplication rate = 2.52% >>>>>>> Insert size mean insert size = 58,883.6525 std insert size = 2,289,030.0764 median insert size = 167 >>>>>>> Mapping quality mean mapping quality = 52.9009 >>>>>>> ACTG content number of A's = 107,564,679 bp (28.73%) number of C's = 73,875,916 bp (19.73%) number of T's = 111,028,163 bp (29.66%) number of G's = 81,671,237 bp (21.81%) number of N's = 243,527 bp (0.07%) GC percentage = 41.55% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 3,256,261 number of insertions = 58,653 mapped reads with insertion percentage = 1.4% number of deletions = 149,515 mapped reads with deletion percentage = 3.58% homopolymer indels = 46.69% >>>>>>> Coverage mean coverageData = 0.121X std coverageData = 1.1452X There is a 8.37% of reference with a coverageData >= 1X There is a 2.48% of reference with a coverageData >= 2X There is a 0.57% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 28699987 0.11514509727139255 1.1771240792873259 chr2 243199373 31058085 0.12770627085457165 1.4552599484404456 chr3 198022430 27366425 0.1381986121471189 0.5140460936443209 chr4 191154276 20183787 0.10558899032946562 0.6891238507125191 chr5 180915260 19654907 0.10864150984278496 0.43075709565648196 chr6 171115067 19554076 0.11427442564131421 0.7889134772323907 chr7 159138663 25713023 0.16157621608270015 1.3622532622522072 chr8 146364022 24240992 0.16562124809606557 0.6814339643698719 chr9 141213431 14028120 0.09933984253948196 1.3330846174777404 chr10 135534747 18094178 0.13350213432722163 3.0468466853821385 chr11 135006516 24062949 0.17823546383494557 1.5683237923639435 chr12 133851895 19214861 0.1435531487992755 0.49517629268803104 chr13 115169878 9674366 0.08400083570462756 0.36780326545129066 chr14 107349540 10569859 0.09846208004244825 0.4390346561935146 chr15 102531392 9825354 0.0958277636570076 0.3966960714760821 chr16 90354753 11281945 0.124862772852691 1.4177978146105379 chr17 81195210 9764755 0.12026269776258969 1.1026911869319438 chr18 78077248 8804197 0.1127626450153571 1.3926135046112376 chr19 59128983 5530440 0.09353179641192205 0.6939805861733728 chr20 63025520 11183281 0.17744051933248628 0.5707633825258055 chr21 48129895 2400033 0.04986574352593123 0.38405720181233133 chr22 51304566 4059337 0.07912233386790564 0.3838889049629649 chrMT 16571 188466 11.373242411441675 7.052102266784702 chrX 155270560 18578535 0.11965265662724472 0.6569336148129696 chrY 59373566 925980 0.015595829295481426 0.992302781940362