BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975214.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 48,339,192 number of mapped reads = 48,206,116 (99.72%) number of supplementary alignments = 127,197 (0.26%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 24,128,241 number of mapped paired reads (second in pair) = 24,077,875 number of mapped paired reads (both in pair) = 48,126,850 number of mapped paired reads (singletons) = 79,266 number of mapped bases = 4,747,985,805 bp number of sequenced bases = 4,746,186,609 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,326,591 duplication rate = 36.93% >>>>>>> Insert size mean insert size = 75,523.7459 std insert size = 2,737,694.1665 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 55.7043 >>>>>>> ACTG content number of A's = 1,287,686,161 bp (27.13%) number of C's = 1,057,884,349 bp (22.29%) number of T's = 1,305,891,868 bp (27.51%) number of G's = 1,094,364,160 bp (23.06%) number of N's = 360,071 bp (0.01%) GC percentage = 45.35% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 27,943,897 number of insertions = 406,960 mapped reads with insertion percentage = 0.83% number of deletions = 1,137,744 mapped reads with deletion percentage = 2.32% homopolymer indels = 48.9% >>>>>>> Coverage mean coverageData = 1.5337X std coverageData = 23.5702X There is a 13.97% of reference with a coverageData >= 1X There is a 6.57% of reference with a coverageData >= 2X There is a 3.7% of reference with a coverageData >= 3X There is a 2.67% of reference with a coverageData >= 4X There is a 2.13% of reference with a coverageData >= 5X There is a 1.85% of reference with a coverageData >= 6X There is a 1.68% of reference with a coverageData >= 7X There is a 1.56% of reference with a coverageData >= 8X There is a 1.47% of reference with a coverageData >= 9X There is a 1.39% of reference with a coverageData >= 10X There is a 1.33% of reference with a coverageData >= 11X There is a 1.28% of reference with a coverageData >= 12X There is a 1.24% of reference with a coverageData >= 13X There is a 1.2% of reference with a coverageData >= 14X There is a 1.16% of reference with a coverageData >= 15X There is a 1.12% of reference with a coverageData >= 16X There is a 1.09% of reference with a coverageData >= 17X There is a 1.06% of reference with a coverageData >= 18X There is a 1.04% of reference with a coverageData >= 19X There is a 1.01% of reference with a coverageData >= 20X There is a 0.99% of reference with a coverageData >= 21X There is a 0.96% of reference with a coverageData >= 22X There is a 0.94% of reference with a coverageData >= 23X There is a 0.92% of reference with a coverageData >= 24X There is a 0.9% of reference with a coverageData >= 25X There is a 0.88% of reference with a coverageData >= 26X There is a 0.86% of reference with a coverageData >= 27X There is a 0.85% of reference with a coverageData >= 28X There is a 0.83% of reference with a coverageData >= 29X There is a 0.81% of reference with a coverageData >= 30X There is a 0.8% of reference with a coverageData >= 31X There is a 0.78% of reference with a coverageData >= 32X There is a 0.77% of reference with a coverageData >= 33X There is a 0.76% of reference with a coverageData >= 34X There is a 0.74% of reference with a coverageData >= 35X There is a 0.73% of reference with a coverageData >= 36X There is a 0.72% of reference with a coverageData >= 37X There is a 0.71% of reference with a coverageData >= 38X There is a 0.7% of reference with a coverageData >= 39X There is a 0.69% of reference with a coverageData >= 40X There is a 0.67% of reference with a coverageData >= 41X There is a 0.66% of reference with a coverageData >= 42X There is a 0.65% of reference with a coverageData >= 43X There is a 0.64% of reference with a coverageData >= 44X There is a 0.63% of reference with a coverageData >= 45X There is a 0.63% of reference with a coverageData >= 46X There is a 0.62% of reference with a coverageData >= 47X There is a 0.61% of reference with a coverageData >= 48X There is a 0.6% of reference with a coverageData >= 49X There is a 0.59% of reference with a coverageData >= 50X There is a 0.58% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 642172532 2.576412967091464 32.890059717730296 chr2 243199373 382540532 1.5729503217099166 21.88471747519582 chr3 198022430 360080072 1.8183802309667647 25.665109786962073 chr4 191154276 145229590 0.7597506738483841 13.06365650974202 chr5 180915260 230205443 1.2724490073418904 18.862672967067898 chr6 171115067 281731855 1.6464468029574508 25.868519274218322 chr7 159138663 224359788 1.409838337023103 22.748399261778818 chr8 146364022 180837818 1.235534631591362 17.879200364793647 chr9 141213431 188812043 1.3370685894601626 20.888229057776 chr10 135534747 159977290 1.180341525262153 18.24956910390928 chr11 135006516 208421496 1.5437884198122704 21.31971277693736 chr12 133851895 265837072 1.9860538545233148 28.48905151858275 chr13 115169878 35632451 0.3093903685475815 6.747969931200848 chr14 107349540 152035654 1.416267400866366 20.673106623851954 chr15 102531392 109094024 1.0640060753295928 15.548358294978213 chr16 90354753 118130417 1.3074067835700907 18.784761615112085 chr17 81195210 270557557 3.332186184382059 40.277619772861534 chr18 78077248 119801761 1.5344004056085583 23.392069650415678 chr19 59128983 238857949 4.039608612919996 47.94984902211512 chr20 63025520 145690458 2.311610566640307 33.35033458837547 chr21 48129895 60725164 1.2616932573819244 22.520375969578268 chr22 51304566 41550636 0.8098818339092859 12.113311162439343 chrMT 16571 200510 12.100054311749442 20.73834177417844 chrX 155270560 183528286 1.1819902369129087 20.270530228590918 chrY 59373566 1975407 0.033270816174322426 2.32234392347751