BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008666.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 = 2,030,374 number of mapped reads = 1,796,574 (88.48%) number of supplementary alignments = 15,914 (0.78%) number of secondary alignments = 0 number of mapped bases = 118,228,525 bp number of sequenced bases = 118,173,502 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 97,256 duplication rate = 4.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1102 >>>>>>> ACTG content number of A's = 31,850,628 bp (26.95%) number of C's = 21,923,568 bp (18.55%) number of T's = 37,069,215 bp (31.37%) number of G's = 27,279,013 bp (23.08%) number of N's = 51,078 bp (0.04%) GC percentage = 41.64% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 977,144 number of insertions = 9,161 mapped reads with insertion percentage = 0.51% number of deletions = 33,738 mapped reads with deletion percentage = 1.86% homopolymer indels = 46.87% >>>>>>> Coverage mean coverageData = 0.0382X std coverageData = 0.327X There is a 3.13% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 10629377 0.04264533808322989 0.5759569228512447 chr2 243199373 11517970 0.0473601961136635 0.4019302517758182 chr3 198022430 8487297 0.04286028102978031 0.24328947394492095 chr4 191154276 6422948 0.03360085965327817 0.24497105513553 chr5 180915260 5702356 0.03151948597370946 0.20902362453741452 chr6 171115067 5413904 0.0316389672453566 0.22873558692237458 chr7 159138663 6640166 0.041725661601166024 0.4146049988136846 chr8 146364022 8602841 0.058777019669492274 0.3825881028223514 chr9 141213431 4170222 0.029531341108764646 0.27062418814481143 chr10 135534747 6450800 0.04759517498490627 0.3329190739025642 chr11 135006516 4701075 0.034821097079492075 0.3164073131310366 chr12 133851895 4969134 0.03712412140298798 0.22906606000364257 chr13 115169878 2593528 0.02251915209982249 0.17711559636673288 chr14 107349540 3864245 0.035996847308334995 0.22637071217639984 chr15 102531392 3434092 0.033493078880661255 0.21709919887256696 chr16 90354753 3796652 0.04201939437541266 0.24905253265893945 chr17 81195210 3094035 0.03810612719641959 0.27007078670181267 chr18 78077248 1892073 0.02423334644171885 0.4672787225533203 chr19 59128983 2550660 0.043137220878634086 0.40496818197196266 chr20 63025520 2972298 0.0471602296974305 0.2591417241719341 chr21 48129895 1589165 0.03301825196169657 0.23020226539682312 chr22 51304566 1428695 0.027847326493318354 0.1921270540365229 chrMT 16571 53471 3.2267817271136323 2.9470922376092834 chrX 155270560 6910375 0.044505378224951334 0.2707392885036332 chrY 59373566 341146 0.005745755611175519 0.1563501512677189