BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777296.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 1,845,642 number of mapped reads = 1,820,540 (98.64%) number of supplementary alignments = 54,331 (2.94%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 912,424 number of mapped paired reads (second in pair) = 908,116 number of mapped paired reads (both in pair) = 1,811,722 number of mapped paired reads (singletons) = 8,818 number of mapped bases = 178,744,464 bp number of sequenced bases = 178,678,434 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 119,191 duplication rate = 4.94% >>>>>>> Insert size mean insert size = 166,990.8673 std insert size = 3,931,586.9631 median insert size = 174 >>>>>>> Mapping quality mean mapping quality = 53.3075 >>>>>>> ACTG content number of A's = 52,125,337 bp (29.17%) number of C's = 37,337,788 bp (20.9%) number of T's = 51,142,879 bp (28.62%) number of G's = 38,069,354 bp (21.31%) number of N's = 3,076 bp (0%) GC percentage = 42.2% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 1,040,517 number of insertions = 36,155 mapped reads with insertion percentage = 1.93% number of deletions = 25,018 mapped reads with deletion percentage = 1.33% homopolymer indels = 44.16% >>>>>>> Coverage mean coverageData = 0.0577X std coverageData = 0.7736X There is a 4.25% of reference with a coverageData >= 1X There is a 1.08% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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% 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 13923552 0.055861654202257735 1.2787743418528181 chr2 243199373 15598060 0.06413692522143138 0.5352431152927869 chr3 198022430 11919842 0.06019440322997753 0.340343586011899 chr4 191154276 11600446 0.060686301362152105 0.6690764875441869 chr5 180915260 10714788 0.059225451739118085 0.3003689668160756 chr6 171115067 9989454 0.05837857632957593 0.40036544030172794 chr7 159138663 9543423 0.05996922947630897 0.48187635562370384 chr8 146364022 8955930 0.06118942263010509 0.3755024623974536 chr9 141213431 7512679 0.053200881437403785 0.6539191363240698 chr10 135534747 10172452 0.07505419993885405 2.2870033552221436 chr11 135006516 8530865 0.06318854269226531 0.38686514919157805 chr12 133851895 7671226 0.05731129917884241 0.2913767364564106 chr13 115169878 5474250 0.04753195970217143 0.2655044637516104 chr14 107349540 5522630 0.051445306612399086 0.2798970542764969 chr15 102531392 5162956 0.05035488058135405 0.27352001306122187 chr16 90354753 5846904 0.06471053050192058 0.5033546001361017 chr17 81195210 5036411 0.0620284250758142 0.39894029872928227 chr18 78077248 4928876 0.06312819837092619 0.7946414546073811 chr19 59128983 3504166 0.059263085921839716 0.7185579497896358 chr20 63025520 3948663 0.06265181152015882 0.33928606512577125 chr21 48129895 2514654 0.05224723635902385 0.3876870306921906 chr22 51304566 2218658 0.04324484491302392 0.25469348000041386 chrMT 16571 1644750 99.25472210488202 22.542514911130635 chrX 155270560 4985253 0.03210687847071589 0.245304321541965 chrY 59373566 1823576 0.030713600729321194 0.6642857905935992