BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006156.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 10,951,026 number of mapped reads = 9,568,704 (87.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,857,535 number of mapped paired reads (second in pair) = 4,711,169 number of mapped paired reads (both in pair) = 8,786,260 number of mapped paired reads (singletons) = 782,444 number of mapped bases = 369,134,986 bp number of sequenced bases = 369,096,306 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 915,128 duplication rate = 8.59% >>>>>>> Insert size mean insert size = 66,346.0368 std insert size = 2,528,666.1305 median insert size = 92 >>>>>>> Mapping quality mean mapping quality = 46.463 >>>>>>> ACTG content number of A's = 99,563,598 bp (26.97%) number of C's = 81,294,207 bp (22.03%) number of T's = 102,677,148 bp (27.82%) number of G's = 85,546,985 bp (23.18%) number of N's = 14,368 bp (0%) GC percentage = 45.2% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 1,846,971 number of insertions = 12,452 mapped reads with insertion percentage = 0.13% number of deletions = 30,820 mapped reads with deletion percentage = 0.32% homopolymer indels = 44.68% >>>>>>> Coverage mean coverageData = 0.1192X std coverageData = 0.7623X There is a 5.46% of reference with a coverageData >= 1X There is a 2.89% of reference with a coverageData >= 2X There is a 1.54% of reference with a coverageData >= 3X There is a 0.85% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.26% of reference with a coverageData >= 6X There is a 0.15% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% 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% 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 31902134 0.1279921946513425 0.8714114611066865 chr2 243199373 32570191 0.13392382800263222 0.7683865542403553 chr3 198022430 25725415 0.12991162162791356 0.6577218716937012 chr4 191154276 23733435 0.12415853569501108 0.6830536627389742 chr5 180915260 22902232 0.12659093544679426 0.6500502966487167 chr6 171115067 21095133 0.12328039470656316 0.7257149622008902 chr7 159138663 20582640 0.12933777129948615 0.9145838201246319 chr8 146364022 18453642 0.12608045165635035 1.005917490416492 chr9 141213431 15609153 0.11053589513025854 0.6523152625675784 chr10 135534747 17850914 0.1317072883162574 0.6978868096569312 chr11 135006516 17394395 0.12884115163745133 1.3020714977016594 chr12 133851895 17110224 0.12782952381809762 0.6579955022241553 chr13 115169878 11437516 0.09930996019636315 0.5801911022148071 chr14 107349540 11479531 0.10693600550128114 0.6127615110199657 chr15 102531392 10891504 0.10622604245926945 0.6086942889266438 chr16 90354753 11316585 0.1252461505815859 0.676956162579027 chr17 81195210 10535110 0.12975038798470995 0.7526483219638809 chr18 78077248 9677536 0.12394822112582657 0.9028713406979362 chr19 59128983 7413752 0.12538270783382152 0.8472733620465127 chr20 63025520 8395862 0.13321368867722155 0.683093322760558 chr21 48129895 4816751 0.10007815308967534 0.6264578450747835 chr22 51304566 4793874 0.09343951959363617 0.635778277506751 chrMT 16571 28732 1.7338724277352 2.5898173616906144 chrX 155270560 11051141 0.07117344717504723 0.513746201851319 chrY 59373566 2367584 0.03987606201722834 0.37781878917663747