BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472541.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 8,420,880 number of mapped reads = 8,304,399 (98.62%) number of supplementary alignments = 33,390 (0.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,162,049 number of mapped paired reads (second in pair) = 4,142,350 number of mapped paired reads (both in pair) = 8,250,178 number of mapped paired reads (singletons) = 54,221 number of mapped bases = 816,393,642 bp number of sequenced bases = 816,293,730 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,639,109 duplication rate = 43.52% >>>>>>> Insert size mean insert size = 29,031.7009 std insert size = 1,660,761.3497 median insert size = 222 >>>>>>> Mapping quality mean mapping quality = 55.1196 >>>>>>> ACTG content number of A's = 222,934,995 bp (27.31%) number of C's = 186,605,577 bp (22.86%) number of T's = 221,533,463 bp (27.14%) number of G's = 185,092,507 bp (22.67%) number of N's = 127,188 bp (0.02%) GC percentage = 45.53% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 4,539,791 number of insertions = 43,252 mapped reads with insertion percentage = 0.52% number of deletions = 42,200 mapped reads with deletion percentage = 0.5% homopolymer indels = 42.52% >>>>>>> Coverage mean coverageData = 0.2637X std coverageData = 9.8464X There is a 2.82% of reference with a coverageData >= 1X There is a 1.29% of reference with a coverageData >= 2X There is a 0.59% of reference with a coverageData >= 3X There is a 0.45% of reference with a coverageData >= 4X There is a 0.35% of reference with a coverageData >= 5X There is a 0.32% of reference with a coverageData >= 6X There is a 0.29% of reference with a coverageData >= 7X There is a 0.27% of reference with a coverageData >= 8X There is a 0.25% of reference with a coverageData >= 9X There is a 0.24% of reference with a coverageData >= 10X There is a 0.23% of reference with a coverageData >= 11X There is a 0.22% of reference with a coverageData >= 12X There is a 0.21% of reference with a coverageData >= 13X There is a 0.2% of reference with a coverageData >= 14X There is a 0.2% of reference with a coverageData >= 15X There is a 0.19% of reference with a coverageData >= 16X There is a 0.18% of reference with a coverageData >= 17X There is a 0.18% of reference with a coverageData >= 18X There is a 0.17% of reference with a coverageData >= 19X There is a 0.17% of reference with a coverageData >= 20X There is a 0.16% of reference with a coverageData >= 21X There is a 0.16% of reference with a coverageData >= 22X There is a 0.16% of reference with a coverageData >= 23X There is a 0.15% of reference with a coverageData >= 24X There is a 0.15% of reference with a coverageData >= 25X There is a 0.15% of reference with a coverageData >= 26X There is a 0.14% of reference with a coverageData >= 27X There is a 0.14% of reference with a coverageData >= 28X There is a 0.14% of reference with a coverageData >= 29X There is a 0.13% of reference with a coverageData >= 30X There is a 0.13% of reference with a coverageData >= 31X There is a 0.13% of reference with a coverageData >= 32X There is a 0.13% of reference with a coverageData >= 33X There is a 0.12% of reference with a coverageData >= 34X There is a 0.12% of reference with a coverageData >= 35X There is a 0.12% of reference with a coverageData >= 36X There is a 0.12% of reference with a coverageData >= 37X There is a 0.11% of reference with a coverageData >= 38X There is a 0.11% of reference with a coverageData >= 39X There is a 0.11% of reference with a coverageData >= 40X There is a 0.11% of reference with a coverageData >= 41X There is a 0.11% of reference with a coverageData >= 42X There is a 0.11% of reference with a coverageData >= 43X There is a 0.1% of reference with a coverageData >= 44X There is a 0.1% of reference with a coverageData >= 45X There is a 0.1% of reference with a coverageData >= 46X There is a 0.1% of reference with a coverageData >= 47X There is a 0.1% of reference with a coverageData >= 48X There is a 0.1% of reference with a coverageData >= 49X There is a 0.09% of reference with a coverageData >= 50X There is a 0.09% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 101735844 0.4081668627016179 15.735531629249257 chr2 243199373 51797505 0.21298371110520914 7.748025556282165 chr3 198022430 75682702 0.3821925728312697 10.456088684088357 chr4 191154276 30303782 0.15853049502277416 6.532744752725771 chr5 180915260 42846299 0.2368307626454507 7.8504320319924625 chr6 171115067 66704355 0.3898216338833564 13.287474510945977 chr7 159138663 28426748 0.17862879745319968 5.378499171090257 chr8 146364022 31666109 0.21635172747575904 7.189447154173809 chr9 141213431 47824802 0.33867034928143624 9.742446860631274 chr10 135534747 24195455 0.17851846508408653 7.490572950623944 chr11 135006516 51921391 0.38458433369245676 14.831653249104516 chr12 133851895 45149800 0.3373116234178082 10.682531117712877 chr13 115169878 21600410 0.1875525994739701 9.51175506406474 chr14 107349540 17014393 0.15849525764153252 7.02269342884196 chr15 102531392 18332651 0.17880037169494392 5.541963695844212 chr16 90354753 26025377 0.28803550600154926 10.83125923084511 chr17 81195210 40539033 0.49927862739686246 14.084295238596807 chr18 78077248 13446275 0.17221758379598626 6.661886402022284 chr19 59128983 13070454 0.2210498699089751 5.769588521863466 chr20 63025520 15267517 0.24224341187506268 11.557200348994957 chr21 48129895 2404465 0.04995782766615219 1.514501374732775 chr22 51304566 9733418 0.18971835762142497 7.071076182627605 chrMT 16571 1175 0.070907006215678 0.3134084663776821 chrX 155270560 37960523 0.24447984859460803 8.75565996022574 chrY 59373566 2743159 0.04620168847530566 2.7989174243249555