BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472665.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 15,846,230 number of mapped reads = 15,731,706 (99.28%) number of supplementary alignments = 94,092 (0.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,886,326 number of mapped paired reads (second in pair) = 7,845,380 number of mapped paired reads (both in pair) = 15,653,224 number of mapped paired reads (singletons) = 78,482 number of mapped bases = 1,547,773,331 bp number of sequenced bases = 1,547,555,703 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,793,206 duplication rate = 49.23% >>>>>>> Insert size mean insert size = 22,850.5603 std insert size = 1,512,335.1068 median insert size = 209 >>>>>>> Mapping quality mean mapping quality = 54.5417 >>>>>>> ACTG content number of A's = 419,129,437 bp (27.08%) number of C's = 356,550,057 bp (23.04%) number of T's = 420,652,318 bp (27.18%) number of G's = 350,937,930 bp (22.68%) number of N's = 285,961 bp (0.02%) GC percentage = 45.72% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 9,213,364 number of insertions = 96,801 mapped reads with insertion percentage = 0.61% number of deletions = 78,298 mapped reads with deletion percentage = 0.49% homopolymer indels = 45.81% >>>>>>> Coverage mean coverageData = 0.5X std coverageData = 22.5382X There is a 3.28% of reference with a coverageData >= 1X There is a 1.53% of reference with a coverageData >= 2X There is a 0.73% of reference with a coverageData >= 3X There is a 0.56% of reference with a coverageData >= 4X There is a 0.43% of reference with a coverageData >= 5X There is a 0.38% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.31% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.24% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.23% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.21% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.2% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.19% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 182017259 0.7302579960272195 28.94679161315992 chr2 243199373 111874711 0.4600123331732438 23.374426991269477 chr3 198022430 139136933 0.7026321866669346 17.241639174725158 chr4 191154276 51703818 0.2704821418695337 18.87630591424192 chr5 180915260 72365525 0.39999679960662243 32.521663522683596 chr6 171115067 103880620 0.6070804974760055 19.584844311915504 chr7 159138663 105198123 0.661046919817342 25.17097944029136 chr8 146364022 89735189 0.6130959492217288 24.880994333939242 chr9 141213431 96835597 0.68573928353883 19.795237952084225 chr10 135534747 27226867 0.20088477385064954 12.592365442914229 chr11 135006516 59946113 0.44402384993032484 23.754358711309496 chr12 133851895 32627017 0.24375461400826637 11.946201955365703 chr13 115169878 55910231 0.48545880199682073 22.08797426493677 chr14 107349540 21914050 0.2041373442308183 10.329414957986637 chr15 102531392 10872107 0.10603686137412432 4.340976197448794 chr16 90354753 100267191 1.1097057727555295 44.693802190782584 chr17 81195210 70408760 0.867154109214078 25.487305680429255 chr18 78077248 15309506 0.19608152684889713 12.534532383884248 chr19 59128983 52677025 0.8908833253567037 26.496029955498898 chr20 63025520 59758569 0.9481646323584478 26.948712914288436 chr21 48129895 9239050 0.1919607345912556 10.954460954810974 chr22 51304566 31922344 0.6222125336758526 33.25331590642923 chrMT 16571 3698 0.22316094381751253 0.6369409170451673 chrX 155270560 46017796 0.29637167535172154 10.830906064378782 chrY 59373566 925232 0.015583231096478188 0.5521176682398083