BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819007.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 617,856 number of mapped reads = 605,280 (97.96%) number of supplementary alignments = 10,603 (1.72%) number of secondary alignments = 0 number of mapped bases = 55,794,920 bp number of sequenced bases = 55,759,661 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 199,368 duplication rate = 28.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.6602 >>>>>>> ACTG content number of A's = 16,504,537 bp (29.6%) number of C's = 12,149,059 bp (21.79%) number of T's = 15,728,866 bp (28.21%) number of G's = 11,374,455 bp (20.4%) number of N's = 2,744 bp (0%) GC percentage = 42.19% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 389,361 number of insertions = 10,359 mapped reads with insertion percentage = 1.66% number of deletions = 19,087 mapped reads with deletion percentage = 3.09% homopolymer indels = 41.29% >>>>>>> Coverage mean coverageData = 0.018X std coverageData = 0.3015X There is a 1.09% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 5804894 0.02328938630808868 0.5441416322781375 chr2 243199373 4779470 0.019652476653383478 0.4609134550628206 chr3 198022430 3088887 0.015598672332220143 0.18773553593941264 chr4 191154276 3341955 0.017483025072376618 0.22346830840393722 chr5 180915260 3151526 0.01741990144999377 0.2020495404333185 chr6 171115067 2558930 0.014954439985112474 0.2064901341867888 chr7 159138663 2848095 0.01789693935030735 0.2786031360960526 chr8 146364022 5173122 0.035344218676909546 0.3064814067842924 chr9 141213431 2550597 0.018062000065701966 0.2675562161281526 chr10 135534747 3115581 0.022987322948262116 0.35646220733162753 chr11 135006516 1033217 0.007653089870121528 0.1587879183210801 chr12 133851895 2754884 0.020581583846833097 0.2182696801826422 chr13 115169878 1226265 0.010647445506541215 0.15607240561042532 chr14 107349540 1030720 0.00960153159482565 0.15306736929941103 chr15 102531392 1537397 0.014994402884923283 0.18497337260323315 chr16 90354753 1784865 0.01975396911327952 0.33085479060856604 chr17 81195210 1588391 0.019562619519057835 0.22565276602135761 chr18 78077248 1428095 0.018290795802638947 0.2918136689678322 chr19 59128983 1189155 0.020111203333228307 0.44550754497266315 chr20 63025520 1507627 0.023920897439640324 0.2419760734832179 chr21 48129895 843088 0.01751692996629226 0.2158323040397428 chr22 51304566 452601 0.008821846383029535 0.14571827432709253 chrMT 16571 7847 0.47353810874419167 1.1593029161977884 chrX 155270560 2760858 0.017780949588898243 0.22411974952251495 chrY 59373566 236853 0.003989199503361479 0.29801659993389384