BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617387.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 29,297,022 (91.55%) number of supplementary alignments = 86,551 (0.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,795,178 number of mapped paired reads (second in pair) = 14,501,844 number of mapped paired reads (both in pair) = 28,573,800 number of mapped paired reads (singletons) = 723,222 number of mapped bases = 2,861,547,200 bp number of sequenced bases = 2,860,720,057 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,535,661 duplication rate = 1.51% >>>>>>> Insert size mean insert size = 58,038.7013 std insert size = 2,293,761.9764 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 53.3104 >>>>>>> ACTG content number of A's = 870,432,146 bp (30.43%) number of C's = 564,859,047 bp (19.75%) number of T's = 856,978,555 bp (29.96%) number of G's = 567,734,173 bp (19.85%) number of N's = 716,136 bp (0.03%) GC percentage = 39.59% >>>>>>> Mismatches and indels general error rate = 0.0134 number of mismatches = 37,567,270 number of insertions = 290,820 mapped reads with insertion percentage = 0.96% number of deletions = 347,395 mapped reads with deletion percentage = 1.15% homopolymer indels = 41.06% >>>>>>> Coverage mean coverageData = 0.9244X std coverageData = 9.5189X There is a 51.68% of reference with a coverageData >= 1X There is a 22.95% of reference with a coverageData >= 2X There is a 8.71% of reference with a coverageData >= 3X There is a 3.04% of reference with a coverageData >= 4X There is a 1.04% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.17% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% 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 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% 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 185599554 0.7446302571097706 19.543303421713922 chr2 243199373 282978120 1.1635643484985465 8.484395739694483 chr3 198022430 228397220 1.1533906537759384 1.465368718713446 chr4 191154276 157544699 0.8241756464814839 8.6168995171356 chr5 180915260 180281935 0.9964993279173907 1.4499641538754744 chr6 171115067 134657418 0.7869407432134541 3.616812881849275 chr7 159138663 232576283 1.4614693790659785 10.771205028893261 chr8 146364022 120749886 0.8249970474301396 7.415198457436279 chr9 141213431 120211392 0.851274493854625 14.281301957270824 chr10 135534747 120752646 0.8909349718268187 19.821666483342767 chr11 135006516 153273524 1.135304639666429 5.294263357186721 chr12 133851895 126283656 0.9434581109217767 1.3551686701500347 chr13 115169878 125464464 1.089386097986489 1.3037054127620626 chr14 107349540 82617145 0.769608747275489 1.3601410181046911 chr15 102531392 64063237 0.6248158320136724 1.0697661541702859 chr16 90354753 71856152 0.795266985014059 7.922602350755835 chr17 81195210 87824082 1.081641170704528 6.930923096119183 chr18 78077248 51672308 0.6618100576495729 14.566559691953882 chr19 59128983 52173336 0.8823648463563123 9.362886254294159 chr20 63025520 81163739 1.287791659632479 2.350067099957592 chr21 48129895 45457480 0.9444749463924657 3.0507611812529314 chr22 51304566 24884844 0.485041506831965 0.9038396525140141 chrMT 16571 1905516 114.99100838814797 20.244247588998725 chrX 155270560 119556479 0.7699880711449743 2.9330851283560926 chrY 59373566 9602085 0.16172323218719928 7.745684234597033