BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818956.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 3,445,617 number of mapped reads = 3,396,450 (98.57%) number of supplementary alignments = 45,946 (1.33%) number of secondary alignments = 0 number of mapped bases = 314,741,234 bp number of sequenced bases = 314,562,138 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,749,520 duplication rate = 42.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3177 >>>>>>> ACTG content number of A's = 90,016,087 bp (28.62%) number of C's = 68,216,826 bp (21.69%) number of T's = 88,180,126 bp (28.03%) number of G's = 68,135,032 bp (21.66%) number of N's = 14,067 bp (0%) GC percentage = 43.35% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 2,070,190 number of insertions = 43,748 mapped reads with insertion percentage = 1.25% number of deletions = 96,624 mapped reads with deletion percentage = 2.78% homopolymer indels = 41.66% >>>>>>> Coverage mean coverageData = 0.1017X std coverageData = 1.106X There is a 3.97% of reference with a coverageData >= 1X There is a 2.15% of reference with a coverageData >= 2X There is a 1.31% of reference with a coverageData >= 3X There is a 0.83% of reference with a coverageData >= 4X There is a 0.54% of reference with a coverageData >= 5X There is a 0.36% of reference with a coverageData >= 6X There is a 0.24% of reference with a coverageData >= 7X There is a 0.16% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% 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% 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 36610946 0.14688407135402884 1.8709281302730905 chr2 243199373 28082866 0.1154726085580821 1.6998746719420579 chr3 198022430 21295371 0.1075401963302844 0.6863874750631307 chr4 191154276 20444794 0.10695441623288615 0.7953200479726771 chr5 180915260 16059390 0.08876747047208731 0.6537023642899814 chr6 171115067 16852522 0.09848648804257547 0.7190062610440041 chr7 159138663 15735454 0.09887888777851551 0.8566715533312343 chr8 146364022 20828208 0.1423041517675703 0.93294380492853 chr9 141213431 11911696 0.08435242962123057 1.2957719813243675 chr10 135534747 15523094 0.11453220922011977 1.4235605148764237 chr11 135006516 11890090 0.08807048987176293 0.729787584841767 chr12 133851895 14311629 0.10692137754194664 0.7150156354288241 chr13 115169878 4842813 0.04204930216215042 0.4174477885269827 chr14 107349540 7885926 0.07346026820422333 0.6848546275281632 chr15 102531392 9058863 0.08835209220606309 0.6298782046309371 chr16 90354753 9855166 0.10907191567443054 1.2855674411907414 chr17 81195210 6738469 0.08299096707798403 0.6754962276739098 chr18 78077248 7840174 0.10041560378767449 1.5732929042668191 chr19 59128983 4981972 0.0842560069061225 1.694737710251528 chr20 63025520 7020663 0.11139397183870914 0.7611472724931545 chr21 48129895 4238211 0.08805776534521839 0.7351758512783243 chr22 51304566 3914928 0.07630759414279033 0.6445663742339018 chrMT 16571 53622 3.2358940317422 4.142482846803117 chrX 155270560 17833312 0.11485314408603924 0.8923628980206524 chrY 59373566 931055 0.015681305044066243 1.0459899524353362