BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238052.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 = 2,129,798 number of mapped reads = 1,889,518 (88.72%) number of supplementary alignments = 24,877 (1.17%) number of secondary alignments = 0 number of mapped bases = 126,290,382 bp number of sequenced bases = 126,233,250 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 135,213 duplication rate = 5.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.4962 >>>>>>> ACTG content number of A's = 34,561,676 bp (27.38%) number of C's = 24,234,122 bp (19.2%) number of T's = 39,129,478 bp (31%) number of G's = 28,300,263 bp (22.42%) number of N's = 7,711 bp (0.01%) GC percentage = 41.62% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 944,440 number of insertions = 8,609 mapped reads with insertion percentage = 0.45% number of deletions = 32,068 mapped reads with deletion percentage = 1.68% homopolymer indels = 45.39% >>>>>>> Coverage mean coverageData = 0.0408X std coverageData = 0.3874X There is a 2.84% of reference with a coverageData >= 1X There is a 0.8% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.08% 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 5134868 0.020601224500058517 0.5736577704383349 chr2 243199373 4566044 0.01877490037772425 0.4156192789064728 chr3 198022430 15012259 0.07581090182561642 0.37293538602058074 chr4 191154276 3967167 0.020753744478098936 0.19684984686516394 chr5 180915260 3802488 0.02101806116299974 0.2015383604155419 chr6 171115067 17067191 0.09974101813021527 0.4913518354512317 chr7 159138663 6550820 0.04116422669706607 0.36702387033737127 chr8 146364022 4261589 0.029116369868545974 0.5462949254065028 chr9 141213431 2031681 0.014387307111035351 0.28932710687780333 chr10 135534747 10642753 0.07852416620514295 0.4536879022916622 chr11 135006516 12441729 0.09215650746812842 0.49872982533423454 chr12 133851895 2285174 0.017072406782137825 0.18456664236572493 chr13 115169878 6013423 0.05221350499303299 0.3132402748547893 chr14 107349540 3152257 0.02936442019220576 0.23759064307180172 chr15 102531392 4803307 0.04684718412873981 0.2931638778847313 chr16 90354753 3620362 0.040068307197962234 0.2941177279403257 chr17 81195210 5291401 0.06516888126774967 0.38117816603992477 chr18 78077248 4544530 0.05820556072877978 0.6734653373122638 chr19 59128983 1945266 0.03289868861772914 0.3678853863603573 chr20 63025520 3156010 0.05007511243064714 0.3187131685257728 chr21 48129895 1984953 0.041241581765345633 0.2900251375587104 chr22 51304566 2247883 0.04381448232112518 0.2862256556329133 chrMT 16571 165051 9.960231730130952 6.252811087353835 chrX 155270560 1322507 0.008517435629780688 0.15812264661615688 chrY 59373566 279669 0.00471032849871271 0.1669268742308154