BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975251.sorted.bam outfile = /mainsd/zhouyj/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 = 3,258,236 number of mapped reads = 3,230,369 (99.14%) number of supplementary alignments = 8,561 (0.26%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,614,800 number of mapped paired reads (second in pair) = 1,615,569 number of mapped paired reads (both in pair) = 3,222,080 number of mapped paired reads (singletons) = 8,289 number of mapped bases = 299,024,229 bp number of sequenced bases = 298,877,953 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 118,130 duplication rate = 2.1% >>>>>>> Insert size mean insert size = 41,974.9901 std insert size = 1,947,922.7415 median insert size = 171 >>>>>>> Mapping quality mean mapping quality = 52.8707 >>>>>>> ACTG content number of A's = 88,000,594 bp (29.44%) number of C's = 57,519,429 bp (19.25%) number of T's = 90,905,118 bp (30.42%) number of G's = 62,448,934 bp (20.89%) number of N's = 3,878 bp (0%) GC percentage = 40.14% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 2,254,566 number of insertions = 46,335 mapped reads with insertion percentage = 1.41% number of deletions = 91,746 mapped reads with deletion percentage = 2.79% homopolymer indels = 46.36% >>>>>>> Coverage mean coverageData = 0.0966X std coverageData = 0.9937X There is a 7% of reference with a coverageData >= 1X There is a 1.82% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% 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 27134828 0.10886563849323369 1.0102066231742326 chr2 243199373 22902101 0.09417006597299081 0.9551165020085982 chr3 198022430 22329575 0.11276285721774043 0.45288871359179544 chr4 191154276 17564985 0.0918890509150839 0.488755556791804 chr5 180915260 17207453 0.09511333095947794 0.378129147626615 chr6 171115067 25107103 0.14672643058369605 1.4367842270163154 chr7 159138663 16747863 0.10524069188642109 1.3006584617808137 chr8 146364022 14302354 0.09771768911898308 0.4388712581793505 chr9 141213431 10894048 0.07714597629173106 0.8926400497246202 chr10 135534747 14176948 0.10460009933836377 2.7458687951123726 chr11 135006516 13938826 0.10324557964298553 0.7383002409512796 chr12 133851895 10942162 0.08174827857311993 0.34961651474714533 chr13 115169878 13582177 0.11793167828136451 0.4310336448700304 chr14 107349540 8490487 0.07909197375228623 0.354437562675007 chr15 102531392 4620883 0.04506798269158386 0.256894801603929 chr16 90354753 11249806 0.12450707490728241 1.6835415430251364 chr17 81195210 7502929 0.0924060544950866 1.1194886528014614 chr18 78077248 6636314 0.08499677140259862 1.1129712747500005 chr19 59128983 3061560 0.05177765360855268 0.5631868018378189 chr20 63025520 5345121 0.08480883616668296 0.3644140548815188 chr21 48129895 2532957 0.05262751975669176 0.30235380055941713 chr22 51304566 1588625 0.03096459289802783 0.21354954895696457 chrMT 16571 16739 1.0101381932291353 1.2142998015253301 chrX 155270560 20663747 0.13308219536272684 0.5956689233517358 chrY 59373566 484638 0.00816252134830507 0.32193832440402537