BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506345.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 10,296,961 number of mapped reads = 6,890,422 (66.92%) number of supplementary alignments = 96,109 (0.93%) number of secondary alignments = 0 number of mapped bases = 512,358,233 bp number of sequenced bases = 512,144,590 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,184,552 duplication rate = 12.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3876 >>>>>>> ACTG content number of A's = 144,551,182 bp (28.22%) number of C's = 95,647,152 bp (18.68%) number of T's = 140,552,005 bp (27.44%) number of G's = 131,266,514 bp (25.63%) number of N's = 127,737 bp (0.02%) GC percentage = 44.31% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 3,882,557 number of insertions = 43,831 mapped reads with insertion percentage = 0.62% number of deletions = 103,535 mapped reads with deletion percentage = 1.47% homopolymer indels = 41.67% >>>>>>> Coverage mean coverageData = 0.1655X std coverageData = 1.0518X There is a 9.17% of reference with a coverageData >= 1X There is a 3.58% of reference with a coverageData >= 2X There is a 1.59% of reference with a coverageData >= 3X There is a 0.78% of reference with a coverageData >= 4X There is a 0.41% of reference with a coverageData >= 5X There is a 0.24% of reference with a coverageData >= 6X There is a 0.14% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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% 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 38614070 0.15492065714853323 1.3844749277515613 chr2 243199373 37186339 0.15290474864834458 1.1994509425410058 chr3 198022430 32668308 0.1649727659639365 0.6851698502039911 chr4 191154276 31603320 0.16532886766289234 1.1937707839644696 chr5 180915260 37903261 0.20950836872467254 0.7840060731640686 chr6 171115067 18403813 0.1075522648160492 0.5868542938639079 chr7 159138663 26477859 0.1663823140200694 1.3701646114993007 chr8 146364022 31298444 0.21383973719989738 1.2498914531209606 chr9 141213431 14322895 0.10142728562412735 0.8690447379111609 chr10 135534747 31311604 0.23102270593385177 1.5287382121462207 chr11 135006516 22798410 0.1688689603692906 0.9636643062209541 chr12 133851895 22267867 0.1663619853869084 0.799185736445643 chr13 115169878 10295092 0.0893904914963963 0.4843967462920994 chr14 107349540 14373779 0.1338969780401481 0.6935546228050491 chr15 102531392 19302114 0.18825565149842108 0.800674156677883 chr16 90354753 19125932 0.21167599229671957 0.983389706933724 chr17 81195210 13626914 0.16782903819079967 0.8240579193312736 chr18 78077248 9258322 0.11857900012049605 1.3876936809224383 chr19 59128983 13648201 0.2308208311311561 1.2133099295122323 chr20 63025520 14753793 0.23409236448981302 0.9236204048626866 chr21 48129895 8620811 0.17911551645811818 1.0391256218504794 chr22 51304566 6473051 0.12616910159614253 0.6447023676110336 chrMT 16571 66870 4.035362983525436 3.484591444909626 chrX 155270560 35863581 0.23097476430818567 0.890431331346718 chrY 59373566 2093583 0.035261196876738045 1.4155635542227722