BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238062.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,029,345 number of mapped reads = 2,780,755 (91.79%) number of supplementary alignments = 19,744 (0.65%) number of secondary alignments = 0 number of mapped bases = 188,121,095 bp number of sequenced bases = 188,042,413 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 123,179 duplication rate = 3.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6361 >>>>>>> ACTG content number of A's = 51,256,206 bp (27.26%) number of C's = 36,258,763 bp (19.28%) number of T's = 58,011,701 bp (30.85%) number of G's = 42,488,531 bp (22.6%) number of N's = 27,212 bp (0.01%) GC percentage = 41.88% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 1,348,908 number of insertions = 12,520 mapped reads with insertion percentage = 0.45% number of deletions = 44,072 mapped reads with deletion percentage = 1.57% homopolymer indels = 47.27% >>>>>>> Coverage mean coverageData = 0.0608X std coverageData = 0.589X There is a 4.91% of reference with a coverageData >= 1X There is a 0.83% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% 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 19928760 0.07995470550903863 1.4847134171055179 chr2 243199373 8017103 0.03296514666590033 0.5514942761386692 chr3 198022430 8569666 0.04327623895939465 0.2593713945754575 chr4 191154276 15751427 0.08240164609239503 0.35218508645301816 chr5 180915260 13763704 0.07607818157517503 0.3274316011124509 chr6 171115067 14540872 0.0849771575053645 0.4563769538459352 chr7 159138663 9960738 0.0625915651936827 0.5218870932805492 chr8 146364022 6715621 0.045883003952979645 0.48123196286879427 chr9 141213431 5602047 0.039670780324004735 0.39852226365405896 chr10 135534747 9026384 0.06659830190998918 0.61768111256917 chr11 135006516 5698383 0.042208207194977164 0.2936183664711264 chr12 133851895 2753495 0.02057120670573995 0.17807987407565168 chr13 115169878 8027356 0.06970013461332311 0.3115268375267435 chr14 107349540 4367054 0.04068069597689939 0.256060934211742 chr15 102531392 7124014 0.0694812960307805 0.31547756711701797 chr16 90354753 6968865 0.07712781861071548 0.3614515628093226 chr17 81195210 6515894 0.0802497339436649 0.3886897874188166 chr18 78077248 6689519 0.08567821191648559 0.767425134001132 chr19 59128983 5035447 0.08516038572826459 0.9359829604342036 chr20 63025520 5157434 0.08183088374360101 0.3557510953571104 chr21 48129895 1941955 0.04034820769918571 0.257645620123168 chr22 51304566 1465968 0.028573831030945667 0.1973669994415947 chrMT 16571 2893 0.17458210126123952 0.4584796147411243 chrX 155270560 13999539 0.09016222392705997 0.39724954067242235 chrY 59373566 496957 0.00837000425408169 0.16514359757295027