BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080657.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 = 1,431,136 number of mapped reads = 1,288,838 (90.06%) number of supplementary alignments = 11,092 (0.78%) number of secondary alignments = 0 number of mapped bases = 84,869,660 bp number of sequenced bases = 84,838,701 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,819 duplication rate = 3.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0755 >>>>>>> ACTG content number of A's = 22,675,532 bp (26.73%) number of C's = 15,695,156 bp (18.5%) number of T's = 26,816,640 bp (31.61%) number of G's = 19,647,729 bp (23.16%) number of N's = 3,644 bp (0%) GC percentage = 41.66% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 579,759 number of insertions = 6,101 mapped reads with insertion percentage = 0.47% number of deletions = 19,658 mapped reads with deletion percentage = 1.51% homopolymer indels = 47.89% >>>>>>> Coverage mean coverageData = 0.0274X std coverageData = 0.2218X There is a 2.4% of reference with a coverageData >= 1X There is a 0.27% 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 10298500 0.041317850919215963 0.25193228171236043 chr2 243199373 5656036 0.023256786932588022 0.33845318402388863 chr3 198022430 5262469 0.02657511575835121 0.1807072913423605 chr4 191154276 3599910 0.018832484814517044 0.15613218061259027 chr5 180915260 3858996 0.021330406290768395 0.1619300051306365 chr6 171115067 5030429 0.029397931393148446 0.2261301819902928 chr7 159138663 5347852 0.03360498259307356 0.35889340270382786 chr8 146364022 11581670 0.0791292138719719 0.3418677169566029 chr9 141213431 2659518 0.018833321881400928 0.17033984778813002 chr10 135534747 2894161 0.021353645939959587 0.16823295120037926 chr11 135006516 3558606 0.026358772194373197 0.18677030130610955 chr12 133851895 2745588 0.020512133952231306 0.15896192044394628 chr13 115169878 1743272 0.015136527278426048 0.13700410810242042 chr14 107349540 1721809 0.0160392769265709 0.14100466468691167 chr15 102531392 1571036 0.01532248777037963 0.15039840135244323 chr16 90354753 2055831 0.022752881633133343 0.1705327634155224 chr17 81195210 1447936 0.017832776096028326 0.14962335389322493 chr18 78077248 2720584 0.03484477321741668 0.23510203255558987 chr19 59128983 1361145 0.023019929160628384 0.18248104072618423 chr20 63025520 2114391 0.03354817223245441 0.2047020496945829 chr21 48129895 1231973 0.02559683539720999 0.17972028031255827 chr22 51304566 880160 0.017155588062083987 0.14411593911594128 chrMT 16571 10180 0.6143262325749804 0.9598360027695987 chrX 155270560 5345700 0.034428290849211854 0.20939574592633564 chrY 59373566 171908 0.002895362559156376 0.0664115729153814