BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472632.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 = 15,157,804 number of mapped reads = 15,040,408 (99.23%) number of supplementary alignments = 68,160 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,543,755 number of mapped paired reads (second in pair) = 7,496,653 number of mapped paired reads (both in pair) = 14,959,320 number of mapped paired reads (singletons) = 81,088 number of mapped bases = 1,478,802,877 bp number of sequenced bases = 1,478,589,558 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,799,077 duplication rate = 48.26% >>>>>>> Insert size mean insert size = 21,459.6433 std insert size = 1,413,547.0136 median insert size = 213 >>>>>>> Mapping quality mean mapping quality = 54.8442 >>>>>>> ACTG content number of A's = 395,790,665 bp (26.77%) number of C's = 345,154,879 bp (23.34%) number of T's = 397,925,828 bp (26.91%) number of G's = 339,452,241 bp (22.96%) number of N's = 265,945 bp (0.02%) GC percentage = 46.3% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 9,076,404 number of insertions = 90,481 mapped reads with insertion percentage = 0.59% number of deletions = 90,968 mapped reads with deletion percentage = 0.6% homopolymer indels = 47.86% >>>>>>> Coverage mean coverageData = 0.4777X std coverageData = 18.4469X There is a 3.24% of reference with a coverageData >= 1X There is a 1.44% of reference with a coverageData >= 2X There is a 0.69% of reference with a coverageData >= 3X There is a 0.55% of reference with a coverageData >= 4X There is a 0.44% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 225091359 0.903072409998128 30.54342340380802 chr2 243199373 84919580 0.3491768048267131 13.020786222352823 chr3 198022430 109680795 0.5538806639227688 19.33416217125401 chr4 191154276 29755390 0.15566164996486923 7.144358629921452 chr5 180915260 58864319 0.3253695625233604 13.083608615383358 chr6 171115067 168847156 0.9867462810858146 33.224899671231405 chr7 159138663 73272706 0.4604330878411364 17.58752383397726 chr8 146364022 90920873 0.6211968744614028 21.974460083678355 chr9 141213431 50777827 0.359582134931627 9.560622797660342 chr10 135534747 26393945 0.1947393239314491 8.080977337775499 chr11 135006516 59850325 0.4433143434350976 14.854445752313158 chr12 133851895 50180420 0.37489510327814185 11.419480526137178 chr13 115169878 45779092 0.39749188585577905 14.263219650405338 chr14 107349540 25866270 0.240953710654 8.578736181899135 chr15 102531392 20578621 0.20070556537455378 7.836839914721836 chr16 90354753 101790913 1.1265695452678621 35.67792271395222 chr17 81195210 55250189 0.6804611873040294 16.272454164006618 chr18 78077248 22607170 0.28954875561187815 15.903001870049318 chr19 59128983 46062811 0.7790225480455161 22.59434211952227 chr20 63025520 48388824 0.7677655654407929 20.67082004495213 chr21 48129895 8640130 0.1795169093969559 11.689945254697223 chr22 51304566 16722823 0.32595194353656554 9.908707745991293 chrMT 16571 1158 0.06988111761511073 0.2806663354117372 chrX 155270560 56279764 0.362462555683447 12.33102856898446 chrY 59373566 2280417 0.03840795077054998 3.354210650086699