BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068107.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 = 4,702,961 number of mapped reads = 4,511,257 (95.92%) number of supplementary alignments = 29,331 (0.62%) number of secondary alignments = 0 number of mapped bases = 299,393,222 bp number of sequenced bases = 299,255,851 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 511,657 duplication rate = 9.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6974 >>>>>>> ACTG content number of A's = 82,815,108 bp (27.67%) number of C's = 53,734,969 bp (17.96%) number of T's = 97,236,238 bp (32.49%) number of G's = 65,433,290 bp (21.87%) number of N's = 36,246 bp (0.01%) GC percentage = 39.82% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 1,639,052 number of insertions = 19,405 mapped reads with insertion percentage = 0.43% number of deletions = 78,354 mapped reads with deletion percentage = 1.72% homopolymer indels = 45.64% >>>>>>> Coverage mean coverageData = 0.0967X std coverageData = 0.9667X There is a 6.96% of reference with a coverageData >= 1X There is a 1.79% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 33890133 0.1359680985508959 2.5555182818099715 chr2 243199373 33065679 0.13596120167628886 0.971948005668603 chr3 198022430 16213183 0.08187548753946712 0.379256952247285 chr4 191154276 18246360 0.09545358012289508 0.42066250182814174 chr5 180915260 14445951 0.07984926755211252 0.37110226991177936 chr6 171115067 22716350 0.13275482047410822 0.649428292568853 chr7 159138663 19910724 0.12511556666779336 0.7530423445427079 chr8 146364022 10371806 0.07086308409863183 1.159081809259816 chr9 141213431 7646285 0.054147009571632036 0.5856809026594494 chr10 135534747 14554575 0.1073862999869694 0.7848182922113409 chr11 135006516 14511595 0.107488108203607 0.612743333055864 chr12 133851895 13757817 0.10278387915240199 0.43724408984548396 chr13 115169878 10053737 0.08729484805045987 0.3973010304430855 chr14 107349540 4562871 0.0425048025357165 0.32551287214823577 chr15 102531392 4444843 0.043351045112115516 0.3004349576001331 chr16 90354753 4765873 0.052746234611476386 0.344252658896233 chr17 81195210 6976777 0.08592596780031729 0.4383263547138162 chr18 78077248 8172731 0.10467493680105118 1.0231345681495996 chr19 59128983 5226659 0.08839419747841765 1.4644325938202056 chr20 63025520 5518658 0.08756227636043304 0.40987015290447193 chr21 48129895 4070609 0.08457548058228674 0.4032472948935679 chr22 51304566 3541281 0.0690246751137121 0.3354098546783945 chrMT 16571 297946 17.979964999094804 10.997629184495002 chrX 155270560 21638266 0.13935845919535553 0.5737388339438945 chrY 59373566 792513 0.013347909741516957 0.6034905128987972