BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082918.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,983,166 number of mapped reads = 1,766,643 (89.08%) number of supplementary alignments = 16,017 (0.81%) number of secondary alignments = 0 number of mapped bases = 116,906,861 bp number of sequenced bases = 116,861,049 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 87,914 duplication rate = 4.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8901 >>>>>>> ACTG content number of A's = 31,137,544 bp (26.64%) number of C's = 21,913,747 bp (18.75%) number of T's = 36,701,907 bp (31.41%) number of G's = 27,102,325 bp (23.19%) number of N's = 5,526 bp (0%) GC percentage = 41.94% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 887,260 number of insertions = 9,606 mapped reads with insertion percentage = 0.54% number of deletions = 27,810 mapped reads with deletion percentage = 1.56% homopolymer indels = 47.39% >>>>>>> Coverage mean coverageData = 0.0378X std coverageData = 0.3281X There is a 3.17% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.08% 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 10959442 0.0439695674820405 0.4670193501697083 chr2 243199373 11516310 0.04735337043817132 0.5396364592613936 chr3 198022430 7348661 0.0371102455413763 0.22150590902245865 chr4 191154276 7568185 0.03959202565785136 0.23755725399293676 chr5 180915260 6426732 0.0355234378791485 0.21842131778878687 chr6 171115067 6580088 0.03845417072477902 0.27722215092211194 chr7 159138663 6038159 0.037942753107081215 0.38794516356034725 chr8 146364022 10446408 0.07137278586126855 0.3755696792748331 chr9 141213431 3143694 0.022262004242358503 0.29005483694209294 chr10 135534747 4567709 0.03370138729074398 0.25485126114400564 chr11 135006516 4980620 0.03689170084205417 0.297287676606525 chr12 133851895 3702989 0.02766482312409548 0.19470556603331363 chr13 115169878 2351028 0.02041356681822655 0.16747741327126492 chr14 107349540 2635534 0.024550957554173032 0.19457038769183113 chr15 102531392 2586788 0.025229229307644627 0.19626549978859073 chr16 90354753 5214156 0.0577076006173134 0.29325875531302825 chr17 81195210 3276149 0.040349042757571535 0.25641143097385793 chr18 78077248 4046241 0.05182356068697503 0.6457864000043743 chr19 59128983 1497999 0.025334428633754787 0.3473891193101705 chr20 63025520 2366012 0.0375405391339889 0.23823557964588427 chr21 48129895 2741482 0.05696006608782338 0.2821121622876566 chr22 51304566 1610609 0.031393092770729214 0.2047337383477608 chrMT 16571 51606 3.1142357129925773 2.5940619150855158 chrX 155270560 5029099 0.03238926297425603 0.23698941551968886 chrY 59373566 221161 0.0037249068044860234 0.08359919482659915