BamQC report ----------------------------------- >>>>>>> Input bam file = SRR960903.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 = 142,486,778 number of mapped reads = 136,728,382 (95.96%) number of supplementary alignments = 282,491 (0.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 68,598,505 number of mapped paired reads (second in pair) = 68,129,877 number of mapped paired reads (both in pair) = 135,620,768 number of mapped paired reads (singletons) = 1,107,614 number of mapped bases = 13,456,573,687 bp number of sequenced bases = 13,452,646,769 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,950,426 duplication rate = 4.73% >>>>>>> Insert size mean insert size = 21,835.7755 std insert size = 1,437,475.9752 median insert size = 150 >>>>>>> Mapping quality mean mapping quality = 53.6103 >>>>>>> ACTG content number of A's = 3,977,097,440 bp (29.56%) number of C's = 2,739,189,823 bp (20.36%) number of T's = 3,968,443,752 bp (29.5%) number of G's = 2,762,908,390 bp (20.54%) number of N's = 5,007,364 bp (0.04%) GC percentage = 40.9% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 131,650,776 number of insertions = 1,495,683 mapped reads with insertion percentage = 1.06% number of deletions = 1,638,805 mapped reads with deletion percentage = 1.16% homopolymer indels = 41.06% >>>>>>> Coverage mean coverageData = 4.3469X std coverageData = 46.2506X There is a 87.73% of reference with a coverageData >= 1X There is a 80.19% of reference with a coverageData >= 2X There is a 68.59% of reference with a coverageData >= 3X There is a 55.15% of reference with a coverageData >= 4X There is a 41.57% of reference with a coverageData >= 5X There is a 29.58% of reference with a coverageData >= 6X There is a 19.95% of reference with a coverageData >= 7X There is a 12.84% of reference with a coverageData >= 8X There is a 7.93% of reference with a coverageData >= 9X There is a 4.75% of reference with a coverageData >= 10X There is a 2.78% of reference with a coverageData >= 11X There is a 1.62% of reference with a coverageData >= 12X There is a 0.96% of reference with a coverageData >= 13X There is a 0.59% of reference with a coverageData >= 14X There is a 0.39% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.22% of reference with a coverageData >= 17X There is a 0.18% of reference with a coverageData >= 18X There is a 0.15% of reference with a coverageData >= 19X There is a 0.14% of reference with a coverageData >= 20X There is a 0.13% of reference with a coverageData >= 21X There is a 0.12% of reference with a coverageData >= 22X There is a 0.11% of reference with a coverageData >= 23X There is a 0.1% of reference with a coverageData >= 24X There is a 0.09% of reference with a coverageData >= 25X There is a 0.09% of reference with a coverageData >= 26X There is a 0.08% of reference with a coverageData >= 27X There is a 0.08% of reference with a coverageData >= 28X There is a 0.07% of reference with a coverageData >= 29X There is a 0.07% of reference with a coverageData >= 30X There is a 0.07% of reference with a coverageData >= 31X There is a 0.06% of reference with a coverageData >= 32X There is a 0.06% of reference with a coverageData >= 33X There is a 0.06% of reference with a coverageData >= 34X There is a 0.06% of reference with a coverageData >= 35X There is a 0.05% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.05% of reference with a coverageData >= 38X There is a 0.05% of reference with a coverageData >= 39X There is a 0.05% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1096090377 4.397543214145092 114.99409308220507 chr2 243199373 1160160701 4.770409917956491 31.94395083301798 chr3 198022430 892307558 4.506093365281902 8.179368899368578 chr4 191154276 909953345 4.760308605390549 35.72323664540294 chr5 180915260 814513489 4.50218234216395 4.885323738427249 chr6 171115067 776069009 4.535363382115264 14.147221870250606 chr7 159138663 719379732 4.520458563862636 29.659013990575502 chr8 146364022 680921118 4.652243828063156 51.43157646218502 chr9 141213431 560653487 3.9702561082876033 40.6425759585269 chr10 135534747 690953954 5.097983869774738 96.61056728040168 chr11 135006516 605955535 4.488342881168787 19.178876001360052 chr12 133851895 594973840 4.445016187480947 4.429452465068991 chr13 115169878 432200181 3.7527189270791794 3.1617965077060552 chr14 107349540 397429469 3.7022000187425115 5.851473732843592 chr15 102531392 372041445 3.6285613385605844 3.2305258072066816 chr16 90354753 416098327 4.605162575122086 38.62686935302212 chr17 81195210 352926528 4.3466422218749114 17.909958003204515 chr18 78077248 369341859 4.730467177839055 49.081436767726736 chr19 59128983 253902901 4.294051548290624 56.14438566620051 chr20 63025520 274360534 4.3531657334997 14.146096947380428 chr21 48129895 184329139 3.8298263272753865 18.985855617020025 chr22 51304566 152968669 2.981580021552078 3.9323164040083207 chrMT 16571 10291928 621.0806831211152 92.4164295602407 chrX 155270560 696435822 4.485305018543116 14.799679422463333 chrY 59373566 42314740 0.7126865177678565 39.090430079233556