BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927015.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 28,344,068 number of mapped reads = 27,655,683 (97.57%) number of supplementary alignments = 621,230 (2.19%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,850,942 number of mapped paired reads (second in pair) = 13,804,741 number of mapped paired reads (both in pair) = 27,287,764 number of mapped paired reads (singletons) = 367,919 number of mapped bases = 2,566,982,161 bp number of sequenced bases = 2,565,070,801 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,069,832 duplication rate = 5.79% >>>>>>> Insert size mean insert size = 236,814.058 std insert size = 4,785,286.1722 median insert size = 192 >>>>>>> Mapping quality mean mapping quality = 52.7356 >>>>>>> ACTG content number of A's = 732,215,630 bp (28.55%) number of C's = 507,569,657 bp (19.79%) number of T's = 742,487,104 bp (28.95%) number of G's = 582,664,371 bp (22.72%) number of N's = 134,039 bp (0.01%) GC percentage = 42.5% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 23,474,976 number of insertions = 427,406 mapped reads with insertion percentage = 1.52% number of deletions = 1,309,607 mapped reads with deletion percentage = 4.62% homopolymer indels = 52.54% >>>>>>> Coverage mean coverageData = 0.8292X std coverageData = 3.4994X There is a 34.9% of reference with a coverageData >= 1X There is a 18.78% of reference with a coverageData >= 2X There is a 10.5% of reference with a coverageData >= 3X There is a 6.24% of reference with a coverageData >= 4X There is a 3.83% of reference with a coverageData >= 5X There is a 2.42% of reference with a coverageData >= 6X There is a 1.56% of reference with a coverageData >= 7X There is a 1.03% of reference with a coverageData >= 8X There is a 0.69% of reference with a coverageData >= 9X There is a 0.47% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.23% of reference with a coverageData >= 12X There is a 0.16% of reference with a coverageData >= 13X There is a 0.12% of reference with a coverageData >= 14X There is a 0.09% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% 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 0.01% 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 207887425 0.8340497775530116 5.177797586053743 chr2 243199373 222381788 0.9144011567825876 6.6300080555756935 chr3 198022430 170222713 0.8596132922921913 1.677467322146141 chr4 191154276 152966866 0.8002272782011949 2.070129941976294 chr5 180915260 158325940 0.8751386698944025 1.6867329762961603 chr6 171115067 147807800 0.8637918483239118 2.013683502990937 chr7 159138663 133742465 0.8404146577503921 2.7589562960302296 chr8 146364022 128888110 0.8805996736001146 1.9933930423833255 chr9 141213431 113010824 0.8002838200284221 4.1973452906387445 chr10 135534747 126275910 0.9316866176022006 5.930680994509337 chr11 135006516 124064078 0.9189488157741956 4.217271941694625 chr12 133851895 118255916 0.8834833156452511 1.7515098185633458 chr13 115169878 77436643 0.6723688897195845 1.4654624331891108 chr14 107349540 78587059 0.7320670307483386 1.6109786615004822 chr15 102531392 76685427 0.7479214463410386 1.615438439173227 chr16 90354753 78292297 0.8664989322697833 3.5106077661556 chr17 81195210 65439544 0.8059532575874858 1.8874737200780347 chr18 78077248 69408308 0.8889697034403672 4.50649444744386 chr19 59128983 41623111 0.7039375427783021 2.9607642074207154 chr20 63025520 60119348 0.9538889643433327 1.8983326051529577 chr21 48129895 33425052 0.6944758969451315 2.566064585472704 chr22 51304566 33220912 0.6475234972263483 1.582985434625766 chrMT 16571 1173758 70.83205600144831 54.14800406569684 chrX 155270560 143240881 0.92252440514158 2.1540195862861045 chrY 59373566 4499986 0.07579106836870805 1.9131050618227083