BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818756.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 = 938,630 number of mapped reads = 757,962 (80.75%) number of supplementary alignments = 6,824 (0.73%) number of secondary alignments = 0 number of mapped bases = 51,445,500 bp number of sequenced bases = 51,423,836 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 259,087 duplication rate = 30.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6556 >>>>>>> ACTG content number of A's = 15,276,790 bp (29.71%) number of C's = 10,455,025 bp (20.33%) number of T's = 14,716,348 bp (28.62%) number of G's = 10,972,352 bp (21.34%) number of N's = 3,321 bp (0.01%) GC percentage = 41.67% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 261,892 number of insertions = 5,626 mapped reads with insertion percentage = 0.74% number of deletions = 13,379 mapped reads with deletion percentage = 1.75% homopolymer indels = 42.6% >>>>>>> Coverage mean coverageData = 0.0166X std coverageData = 0.2382X There is a 0.98% of reference with a coverageData >= 1X There is a 0.38% 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 4271485 0.017137309359000555 0.2810717809319076 chr2 243199373 4642517 0.019089346089720387 0.3480662112697451 chr3 198022430 3390648 0.017122545158141933 0.20188317077835785 chr4 191154276 3525254 0.018441931165588992 0.22267453953861646 chr5 180915260 3070992 0.01697475381568144 0.20408758577291716 chr6 171115067 2916688 0.017045185156021356 0.2092671520321403 chr7 159138663 2802973 0.017613400459447117 0.22831143389294598 chr8 146364022 2675692 0.018281077299173974 0.22741493395392923 chr9 141213431 2199997 0.015579233394591198 0.21632727398898718 chr10 135534747 2494285 0.018403288125073934 0.26438488012516065 chr11 135006516 2470925 0.018302264758835788 0.2258293406182036 chr12 133851895 2462575 0.01839775970299113 0.2183385754672178 chr13 115169878 1670189 0.014501960312921405 0.18655788934964337 chr14 107349540 1655340 0.015420094021828132 0.20387427130475722 chr15 102531392 1532391 0.01494557881355985 0.188801533658426 chr16 90354753 1455154 0.01610489710485955 0.25685075540851127 chr17 81195210 1401447 0.017260217690181476 0.21251817768182077 chr18 78077248 1389937 0.01780207468377984 0.2910850065529599 chr19 59128983 866512 0.014654606861748324 0.24206051335834358 chr20 63025520 1115334 0.01769654578018555 0.21245338429790758 chr21 48129895 694992 0.014439923461291573 0.19914594555688916 chr22 51304566 604707 0.011786611741340916 0.17708067807094907 chrMT 16571 63842 3.8526341198479273 3.8406014749378605 chrX 155270560 1618303 0.010422471587659632 0.16445261478809559 chrY 59373566 453321 0.007635064398860597 0.31413308199396617