BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084404.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,536,056 number of mapped reads = 2,329,989 (91.87%) number of supplementary alignments = 17,446 (0.69%) number of secondary alignments = 0 number of mapped bases = 156,838,428 bp number of sequenced bases = 156,785,257 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,756 duplication rate = 2.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4129 >>>>>>> ACTG content number of A's = 44,708,854 bp (28.52%) number of C's = 29,765,665 bp (18.98%) number of T's = 48,682,182 bp (31.05%) number of G's = 33,425,769 bp (21.32%) number of N's = 202,787 bp (0.13%) GC percentage = 40.3% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 1,555,055 number of insertions = 11,150 mapped reads with insertion percentage = 0.47% number of deletions = 30,548 mapped reads with deletion percentage = 1.3% homopolymer indels = 47.36% >>>>>>> Coverage mean coverageData = 0.0507X std coverageData = 0.3243X There is a 4.24% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 14415664 0.05783602039651488 0.48639908240019747 chr2 243199373 15011686 0.06172584170272511 0.36800181220696304 chr3 198022430 10539268 0.05322259705630317 0.26689477111571597 chr4 191154276 7576066 0.039633254136569776 0.23564054452127656 chr5 180915260 7952488 0.04395697742689036 0.24203846116289734 chr6 171115067 7511041 0.04389467936216277 0.2692111015116731 chr7 159138663 8852104 0.05562509972827911 0.4395064624250283 chr8 146364022 7616049 0.052034980290443233 0.33698941198168536 chr9 141213431 5229383 0.03703176789182326 0.27143257666372583 chr10 135534747 9693528 0.07152061161113173 0.3975792463988282 chr11 135006516 8780114 0.06503474247124487 0.3486693989105043 chr12 133851895 7961225 0.05947786544224869 0.2821922247823995 chr13 115169878 3893399 0.033805705689815876 0.2108843474361437 chr14 107349540 6644589 0.061896762668941105 0.29551879487444654 chr15 102531392 3558025 0.03470181112921982 0.21804094735143645 chr16 90354753 3270932 0.036200995425221295 0.23515678214095975 chr17 81195210 4132064 0.050890489722238544 0.2748169867858351 chr18 78077248 4156833 0.05324000405342155 0.42606728195508087 chr19 59128983 3073698 0.051982933648630485 0.36219628517338776 chr20 63025520 3123825 0.04956444627509618 0.25978568025550436 chr21 48129895 1583046 0.03289111684120649 0.219086125073555 chr22 51304566 1329528 0.02591441861139611 0.18372115237188308 chrMT 16571 8545 0.5156598877557178 0.940916005369782 chrX 155270560 10607172 0.06831412213622466 0.33839887284223 chrY 59373566 318156 0.005358546259458291 0.11034411600703248