BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927016.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 10,528,924 number of mapped reads = 10,308,180 (97.9%) number of supplementary alignments = 288,535 (2.74%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,172,656 number of mapped paired reads (second in pair) = 5,135,524 number of mapped paired reads (both in pair) = 10,163,092 number of mapped paired reads (singletons) = 145,088 number of mapped bases = 937,343,811 bp number of sequenced bases = 936,634,094 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 573,851 duplication rate = 4.29% >>>>>>> Insert size mean insert size = 324,976.1462 std insert size = 5,612,209.2391 median insert size = 187 >>>>>>> Mapping quality mean mapping quality = 52.43 >>>>>>> ACTG content number of A's = 266,334,448 bp (28.44%) number of C's = 182,253,062 bp (19.46%) number of T's = 271,694,566 bp (29.01%) number of G's = 216,179,011 bp (23.08%) number of N's = 173,007 bp (0.02%) GC percentage = 42.54% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 8,850,866 number of insertions = 161,656 mapped reads with insertion percentage = 1.54% number of deletions = 482,876 mapped reads with deletion percentage = 4.57% homopolymer indels = 51.8% >>>>>>> Coverage mean coverageData = 0.3028X std coverageData = 1.5837X There is a 18.83% of reference with a coverageData >= 1X There is a 6.68% of reference with a coverageData >= 2X There is a 2.4% of reference with a coverageData >= 3X There is a 0.98% of reference with a coverageData >= 4X There is a 0.42% of reference with a coverageData >= 5X There is a 0.19% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% 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 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 75928637 0.3046276743278405 1.9250367379906776 chr2 243199373 82280303 0.3383244865520274 2.2641882532918816 chr3 198022430 63773184 0.32205030510937577 0.8219087854657405 chr4 191154276 57534252 0.30098333766805196 1.0658237790654885 chr5 180915260 57065089 0.31542440919577486 0.7783026806130563 chr6 171115067 54060952 0.3159333245622374 0.8721400253939957 chr7 159138663 48225082 0.3030381246824978 1.1017955044617445 chr8 146364022 47818332 0.3267082398159296 0.9061676962628805 chr9 141213431 39639954 0.28070951692973173 1.725881319994895 chr10 135534747 47560907 0.35091301716156964 4.367641322380034 chr11 135006516 44467944 0.32937627988266877 1.5369126636318766 chr12 133851895 42017764 0.31391235813284524 0.7877782343082241 chr13 115169878 28581786 0.2481706718487624 0.6894566218471284 chr14 107349540 28327147 0.2638776747436459 0.7372352728842899 chr15 102531392 27112367 0.26442991235308694 0.724420396812208 chr16 90354753 29180202 0.3229514887833294 2.1203133441602215 chr17 81195210 23739750 0.2923787006647313 0.8572055141129207 chr18 78077248 25115972 0.32168106129970153 1.7189784424332462 chr19 59128983 15405909 0.26054750510422275 1.3119511579065206 chr20 63025520 21319436 0.3382667211631098 0.8485892488140976 chr21 48129895 12062768 0.25062942688738465 1.0713687936656173 chr22 51304566 11539476 0.22492103334428362 0.6941292018142599 chrMT 16571 63056 3.8052018586687586 3.5712509848912517 chrX 155270560 52730797 0.3396058918058903 0.9077838814727035 chrY 59373566 1792745 0.03019432924072642 0.9662202849844511