BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777272.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 50,384,732 number of mapped reads = 50,210,168 (99.65%) number of supplementary alignments = 1,605,032 (3.19%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 25,106,223 number of mapped paired reads (second in pair) = 25,103,945 number of mapped paired reads (both in pair) = 50,150,964 number of mapped paired reads (singletons) = 59,204 number of mapped bases = 5,037,915,400 bp number of sequenced bases = 5,037,176,266 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,411,989 duplication rate = 35.75% >>>>>>> Insert size mean insert size = 436,677.8779 std insert size = 6,499,023.9605 median insert size = 232 >>>>>>> Mapping quality mean mapping quality = 54.6865 >>>>>>> ACTG content number of A's = 1,408,654,630 bp (27.97%) number of C's = 1,111,256,969 bp (22.06%) number of T's = 1,399,852,938 bp (27.79%) number of G's = 1,117,201,366 bp (22.18%) number of N's = 210,363 bp (0%) GC percentage = 44.24% >>>>>>> Mismatches and indels general error rate = 0.0025 number of mismatches = 11,515,790 number of insertions = 856,881 mapped reads with insertion percentage = 1.68% number of deletions = 338,484 mapped reads with deletion percentage = 0.67% homopolymer indels = 52.25% >>>>>>> Coverage mean coverageData = 1.6274X std coverageData = 13.9563X There is a 22.35% of reference with a coverageData >= 1X There is a 11.02% of reference with a coverageData >= 2X There is a 6.37% of reference with a coverageData >= 3X There is a 4.55% of reference with a coverageData >= 4X There is a 3.6% of reference with a coverageData >= 5X There is a 3.09% of reference with a coverageData >= 6X There is a 2.76% of reference with a coverageData >= 7X There is a 2.53% of reference with a coverageData >= 8X There is a 2.36% of reference with a coverageData >= 9X There is a 2.22% of reference with a coverageData >= 10X There is a 2.1% of reference with a coverageData >= 11X There is a 2% of reference with a coverageData >= 12X There is a 1.92% of reference with a coverageData >= 13X There is a 1.84% of reference with a coverageData >= 14X There is a 1.77% of reference with a coverageData >= 15X There is a 1.7% of reference with a coverageData >= 16X There is a 1.64% of reference with a coverageData >= 17X There is a 1.58% of reference with a coverageData >= 18X There is a 1.53% of reference with a coverageData >= 19X There is a 1.48% of reference with a coverageData >= 20X There is a 1.44% of reference with a coverageData >= 21X There is a 1.39% of reference with a coverageData >= 22X There is a 1.35% of reference with a coverageData >= 23X There is a 1.31% of reference with a coverageData >= 24X There is a 1.28% of reference with a coverageData >= 25X There is a 1.24% of reference with a coverageData >= 26X There is a 1.21% of reference with a coverageData >= 27X There is a 1.18% of reference with a coverageData >= 28X There is a 1.15% of reference with a coverageData >= 29X There is a 1.12% of reference with a coverageData >= 30X There is a 1.09% of reference with a coverageData >= 31X There is a 1.06% of reference with a coverageData >= 32X There is a 1.04% of reference with a coverageData >= 33X There is a 1.02% of reference with a coverageData >= 34X There is a 0.99% of reference with a coverageData >= 35X There is a 0.97% of reference with a coverageData >= 36X There is a 0.95% of reference with a coverageData >= 37X There is a 0.93% of reference with a coverageData >= 38X There is a 0.91% of reference with a coverageData >= 39X There is a 0.89% of reference with a coverageData >= 40X There is a 0.87% of reference with a coverageData >= 41X There is a 0.85% of reference with a coverageData >= 42X There is a 0.83% of reference with a coverageData >= 43X There is a 0.81% of reference with a coverageData >= 44X There is a 0.8% of reference with a coverageData >= 45X There is a 0.78% of reference with a coverageData >= 46X There is a 0.77% of reference with a coverageData >= 47X There is a 0.75% of reference with a coverageData >= 48X There is a 0.74% of reference with a coverageData >= 49X There is a 0.72% of reference with a coverageData >= 50X There is a 0.71% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 500849737 2.0094222232649925 16.13936279605939 chr2 243199373 450534103 1.8525298706259412 14.627801094364168 chr3 198022430 314029352 1.5858271812945635 13.764261521597408 chr4 191154276 238451474 1.2474294532652777 11.545150870132822 chr5 180915260 268746283 1.485481561920205 12.451738206177483 chr6 171115067 236977191 1.384899618453821 12.155444720948799 chr7 159138663 328883456 2.066647097569244 16.955922908982828 chr8 146364022 182291708 1.2454680153569433 12.331416926372334 chr9 141213431 173722041 1.2302090514322253 11.432629074606412 chr10 135534747 211311251 1.559092820677195 12.734864178038492 chr11 135006516 343824433 2.5467247299382203 19.372205875955164 chr12 133851895 284679783 2.126826691545906 16.1695453333924 chr13 115169878 160184376 1.3908530492669273 13.987962194306286 chr14 107349540 112967563 1.0523339270946108 9.632321313757803 chr15 102531392 233451042 2.276873818313127 17.87639186822846 chr16 90354753 144346269 1.5975503690436739 12.638926925121662 chr17 81195210 206814018 2.5471209200641267 17.123027509290008 chr18 78077248 80090892 1.0257904069569665 9.50788132738145 chr19 59128983 217272151 3.6745457130558123 22.383837681555434 chr20 63025520 126270593 2.003483557136855 14.851956908714941 chr21 48129895 33379991 0.693539659706301 8.375215572362979 chr22 51304566 48519771 0.945720328284231 8.928767887053553 chrMT 16571 1661979 100.2944300283628 28.971786771107936 chrX 155270560 137283323 0.8841555218194614 9.068179159329825 chrY 59373566 1372620 0.023118368871426723 0.6395184614645111