BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038464.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 19,178,672 number of mapped reads = 18,548,637 (96.71%) number of supplementary alignments = 184,767 (0.96%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,340,983 number of mapped paired reads (second in pair) = 9,207,654 number of mapped paired reads (both in pair) = 18,394,202 number of mapped paired reads (singletons) = 154,435 number of mapped bases = 2,733,113,189 bp number of sequenced bases = 2,732,190,366 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,861,644 duplication rate = 7.91% >>>>>>> Insert size mean insert size = 100,091.1294 std insert size = 3,186,100.5453 median insert size = 281 >>>>>>> Mapping quality mean mapping quality = 54.355 >>>>>>> ACTG content number of A's = 783,785,310 bp (28.69%) number of C's = 585,004,320 bp (21.41%) number of T's = 778,545,360 bp (28.5%) number of G's = 584,602,890 bp (21.4%) number of N's = 252,486 bp (0.01%) GC percentage = 42.81% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 24,728,334 number of insertions = 314,008 mapped reads with insertion percentage = 1.6% number of deletions = 340,213 mapped reads with deletion percentage = 1.76% homopolymer indels = 44.58% >>>>>>> Coverage mean coverageData = 0.8829X std coverageData = 7.9784X There is a 47.87% of reference with a coverageData >= 1X There is a 22.49% of reference with a coverageData >= 2X There is a 9.01% of reference with a coverageData >= 3X There is a 3.68% of reference with a coverageData >= 4X There is a 1.42% of reference with a coverageData >= 5X There is a 0.58% of reference with a coverageData >= 6X There is a 0.24% of reference with a coverageData >= 7X There is a 0.12% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% 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 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 233223936 0.9357005212837564 20.45460101589855 chr2 243199373 232150078 0.9545669264533836 7.01385955614367 chr3 198022430 185515410 0.9368403872228009 1.2898802745535558 chr4 191154276 152046435 0.7954121570369684 4.884677881099998 chr5 180915260 170518904 0.9425346651244345 1.249285016168214 chr6 171115067 155628980 0.9094989864334974 3.7359366630367594 chr7 159138663 143150936 0.8995358720589477 6.55162230488611 chr8 146364022 147859732 1.0102191097208302 4.848190271140331 chr9 141213431 116506322 0.8250371170430665 8.944019487738702 chr10 135534747 137390855 1.0136947022153662 15.769759118774317 chr11 135006516 126219956 0.9349175116851397 3.4931648633543397 chr12 133851895 119436559 0.892303833277818 1.4049295300911844 chr13 115169878 87530119 0.7600087845886231 1.1327993604429012 chr14 107349540 85383908 0.7953821506827137 1.2085155210819627 chr15 102531392 77978619 0.7605340908665319 1.1471379421059595 chr16 90354753 85238231 0.9433729623498611 4.421082280898023 chr17 81195210 79766966 0.9824097505259238 4.581750137440545 chr18 78077248 84285768 1.0795176592289728 7.414468850884563 chr19 59128983 56068795 0.9482455499023211 8.322723452448876 chr20 63025520 66866897 1.0609495486907525 2.035116806983855 chr21 48129895 34917299 0.725480473206933 2.783349521572591 chr22 51304566 30124908 0.5871779131705354 1.0371562749787588 chrMT 16571 3738602 225.61112787399674 28.724179620009693 chrX 155270560 115196755 0.7419098314580691 1.8138213611656275 chrY 59373566 6368219 0.10725680515803952 5.271167233943714