BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926957.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 = 9,992,208 number of mapped reads = 9,681,779 (96.89%) number of supplementary alignments = 228,189 (2.28%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,853,821 number of mapped paired reads (second in pair) = 4,827,958 number of mapped paired reads (both in pair) = 9,526,348 number of mapped paired reads (singletons) = 155,431 number of mapped bases = 882,950,301 bp number of sequenced bases = 882,282,895 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 595,086 duplication rate = 5.13% >>>>>>> Insert size mean insert size = 244,255.8363 std insert size = 4,837,467.9782 median insert size = 195 >>>>>>> Mapping quality mean mapping quality = 52.9858 >>>>>>> ACTG content number of A's = 250,299,518 bp (28.37%) number of C's = 173,480,313 bp (19.66%) number of T's = 252,633,873 bp (28.63%) number of G's = 205,820,396 bp (23.33%) number of N's = 48,795 bp (0.01%) GC percentage = 42.99% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 8,840,157 number of insertions = 148,972 mapped reads with insertion percentage = 1.52% number of deletions = 458,348 mapped reads with deletion percentage = 4.61% homopolymer indels = 52.57% >>>>>>> Coverage mean coverageData = 0.2852X std coverageData = 1.1819X There is a 17.04% of reference with a coverageData >= 1X There is a 6.49% of reference with a coverageData >= 2X There is a 2.54% of reference with a coverageData >= 3X There is a 1.11% of reference with a coverageData >= 4X There is a 0.51% of reference with a coverageData >= 5X There is a 0.24% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.04% 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% 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 71769125 0.28793960356873094 1.4479447705403092 chr2 243199373 75477435 0.310352095356759 1.9775660588762394 chr3 198022430 58859279 0.29723541419020055 0.7941793748626251 chr4 191154276 52815330 0.27629687969941097 1.201093855185528 chr5 180915260 52410661 0.289697292533532 0.7772889457552077 chr6 171115067 50449809 0.294829729985145 0.7983001757541004 chr7 159138663 45276017 0.2845067072104282 0.955566197576285 chr8 146364022 44193528 0.30194256345319614 0.8354080966349557 chr9 141213431 36872135 0.2611092637498483 1.2076281819773187 chr10 135534747 42423345 0.31300715085261493 2.220861508453311 chr11 135006516 41373370 0.30645461586461503 1.0476813765948028 chr12 133851895 39932318 0.29833210803627397 0.9033894109166294 chr13 115169878 26217975 0.22764611246701155 0.6886068495888061 chr14 107349540 26613726 0.24791653508715547 0.7273366782772944 chr15 102531392 26002186 0.2536021943406367 0.7442370797462307 chr16 90354753 26622052 0.29463919844925035 0.8888627190169881 chr17 81195210 23282151 0.2867429125437326 0.8233693369808555 chr18 78077248 23416031 0.29990850855808854 1.4331457448403317 chr19 59128983 14628747 0.24740400151986378 1.0045177895291277 chr20 63025520 21098495 0.334761141201215 0.897889048849974 chr21 48129895 11189681 0.23248920447468252 1.1169692458736222 chr22 51304566 22224410 0.43318581040135884 1.1219710907131397 chrMT 16571 157788 9.521935912135659 12.619162258750315 chrX 155270560 48082097 0.3096665394908088 0.8392236150455553 chrY 59373566 1562610 0.026318277733225592 0.8418502808605363