BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124965.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 4,702,220 number of mapped reads = 4,469,341 (95.05%) number of supplementary alignments = 14,739 (0.31%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,280,464 number of mapped paired reads (second in pair) = 2,188,877 number of mapped paired reads (both in pair) = 4,344,764 number of mapped paired reads (singletons) = 124,577 number of mapped bases = 272,330,240 bp number of sequenced bases = 272,199,399 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 391,214 duplication rate = 4.89% >>>>>>> Insert size mean insert size = 88,177.9158 std insert size = 2,796,243.3813 median insert size = 178 >>>>>>> Mapping quality mean mapping quality = 51.0894 >>>>>>> ACTG content number of A's = 75,479,991 bp (27.73%) number of C's = 48,291,936 bp (17.74%) number of T's = 82,373,902 bp (30.26%) number of G's = 66,053,567 bp (24.27%) number of N's = 3 bp (0%) GC percentage = 42.01% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 2,210,342 number of insertions = 36,626 mapped reads with insertion percentage = 0.81% number of deletions = 78,461 mapped reads with deletion percentage = 1.73% homopolymer indels = 45.85% >>>>>>> Coverage mean coverageData = 0.088X std coverageData = 1.2932X There is a 6.69% of reference with a coverageData >= 1X There is a 1.12% 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 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% 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 22519272 0.09034790729769135 0.74276314982779 chr2 243199373 23054949 0.09479855443541789 1.3963149678249247 chr3 198022430 18853531 0.09520906798285426 0.45133536972029625 chr4 191154276 17233778 0.0901563823767144 1.07677913473743 chr5 180915260 16069982 0.0888260172193324 0.3870537329486044 chr6 171115067 15593430 0.09112832828449875 0.49211108309216417 chr7 159138663 15739382 0.09890357065523417 0.7320483480820859 chr8 146364022 15981130 0.10918755703502053 0.4755649950886877 chr9 141213431 10590657 0.07499751918073572 0.7681094533807268 chr10 135534747 16455345 0.12141052655670652 4.506404902330281 chr11 135006516 10810937 0.08007714975771985 0.46486023316463354 chr12 133851895 11917758 0.0890369015694548 0.36728037489496196 chr13 115169878 7388462 0.06415272924053979 0.2983442194919308 chr14 107349540 8893762 0.08284862701787078 0.41965089741794437 chr15 102531392 7162900 0.06986055548724043 0.3325945057368909 chr16 90354753 10302023 0.1140174994446612 2.4266971856626367 chr17 81195210 5907775 0.07276014188521712 0.7264569122642155 chr18 78077248 5930353 0.07595494400622317 1.0624804376597206 chr19 59128983 3792427 0.06413820782271869 0.6207714461467347 chr20 63025520 5711037 0.09061467481743903 0.6241260934660416 chr21 48129895 3213017 0.06675719944953132 0.6059435949656696 chr22 51304566 2424809 0.04726302528316875 0.3335189654332556 chrMT 16571 91260 5.507211393398105 4.100012265710532 chrX 155270560 10227729 0.0658703684716536 0.46033855870087476 chrY 59373566 6464535 0.10887900854733906 2.6764268992192783