BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094031.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 374,366 number of mapped reads = 334,972 (89.48%) number of supplementary alignments = 15,784 (4.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 168,444 number of mapped paired reads (second in pair) = 166,528 number of mapped paired reads (both in pair) = 329,276 number of mapped paired reads (singletons) = 5,696 number of mapped bases = 43,455,295 bp number of sequenced bases = 42,744,642 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 313,137 duplication rate = 43.84% >>>>>>> Insert size mean insert size = 362,512.8084 std insert size = 5,781,272.1926 median insert size = 175 >>>>>>> Mapping quality mean mapping quality = 42.8478 >>>>>>> ACTG content number of A's = 12,120,911 bp (28.36%) number of C's = 9,245,408 bp (21.63%) number of T's = 11,741,652 bp (27.47%) number of G's = 9,636,231 bp (22.54%) number of N's = 440 bp (0%) GC percentage = 44.17% >>>>>>> Mismatches and indels general error rate = 0.0331 number of mismatches = 1,358,265 number of insertions = 24,203 mapped reads with insertion percentage = 7.06% number of deletions = 99,619 mapped reads with deletion percentage = 28.48% homopolymer indels = 31.45% >>>>>>> Coverage mean coverageData = 0.014X std coverageData = 6.7975X There is a 0.03% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 0.01% 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% 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 1201409 0.004820084279749899 1.3005410242353073 chr2 243199373 3508746 0.014427446735234798 5.051008079800618 chr3 198022430 427068 0.002156664777823401 0.5095249342617102 chr4 191154276 936207 0.00489765136093529 1.9749753785306283 chr5 180915260 376238 0.0020796366210346215 0.5608015104571632 chr6 171115067 481129 0.0028117278532813245 0.7426016625932413 chr7 159138663 889926 0.005592141992546463 1.498287525808637 chr8 146364022 1100014 0.007515603800502284 2.6743021324321106 chr9 141213431 664303 0.004704247997486868 1.0862807016522988 chr10 135534747 1004965 0.007414814446069686 1.9671069532934025 chr11 135006516 1482059 0.010977684958554149 2.9036983619637846 chr12 133851895 1027024 0.007672838699818183 2.560914524899318 chr13 115169878 1057092 0.009178545799970371 4.029735812997465 chr14 107349540 121789 0.0011345088204383548 0.21057836718977094 chr15 102531392 331163 0.003229869345770708 0.7187272061007317 chr16 90354753 484666 0.005364034363527063 1.7916396585516556 chr17 81195210 563820 0.006944005687034987 1.6169326334976912 chr18 78077248 215977 0.002766196370035993 0.7957138915689139 chr19 59128983 153009 0.0025877157400119666 0.26218694424309263 chr20 63025520 137713 0.002185035522118659 0.5663655120995227 chr21 48129895 308892 0.006417882274623703 1.7364428518879182 chr22 51304566 282508 0.00550648844783133 1.1937596249965707 chrMT 16571 9396754 567.0601653491038 2540.9010673107255 chrX 155270560 17215354 0.11087326535049528 10.251904908195732 chrY 59373566 87470 0.0014732145278253963 0.16944186506362902