BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818949.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 = 2,065,102 number of mapped reads = 2,037,188 (98.65%) number of supplementary alignments = 25,565 (1.24%) number of secondary alignments = 0 number of mapped bases = 188,825,050 bp number of sequenced bases = 188,718,021 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 851,489 duplication rate = 35.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.19 >>>>>>> ACTG content number of A's = 53,940,184 bp (28.58%) number of C's = 41,810,796 bp (22.16%) number of T's = 51,869,159 bp (27.49%) number of G's = 41,089,661 bp (21.77%) number of N's = 8,221 bp (0%) GC percentage = 43.93% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 1,252,702 number of insertions = 24,812 mapped reads with insertion percentage = 1.18% number of deletions = 58,738 mapped reads with deletion percentage = 2.82% homopolymer indels = 42.41% >>>>>>> Coverage mean coverageData = 0.061X std coverageData = 0.6938X There is a 3.02% of reference with a coverageData >= 1X There is a 1.36% of reference with a coverageData >= 2X There is a 0.7% of reference with a coverageData >= 3X There is a 0.38% of reference with a coverageData >= 4X There is a 0.21% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.04% 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 0.01% 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% 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 21780720 0.08738481738827844 1.2059612959261354 chr2 243199373 16418984 0.06751244379236125 1.0476848434553996 chr3 198022430 12260958 0.06191701616831992 0.44081966545752277 chr4 191154276 12222937 0.06394278619223773 0.49701793448414305 chr5 180915260 9782507 0.05407231540335514 0.421370111879719 chr6 171115067 9889422 0.057793987247189635 0.4605319568034086 chr7 159138663 9836612 0.06181157874877961 0.5699218961186084 chr8 146364022 12138253 0.08293194484639128 0.5721700615838108 chr9 141213431 6944662 0.04917848076363218 0.7889643464940901 chr10 135534747 9108499 0.06720416130632538 0.8268702454345034 chr11 135006516 8212723 0.06083204902495225 0.5322191179544533 chr12 133851895 8399604 0.06275297036325111 0.459959678359783 chr13 115169878 2847296 0.024722575463698937 0.27331947907235177 chr14 107349540 5909374 0.055047967601910545 0.4493490967016306 chr15 102531392 5345672 0.052136929926787694 0.40501578798850185 chr16 90354753 5733633 0.06345690524990977 0.7906089043889816 chr17 81195210 4206855 0.05181161548815503 0.45597626715732037 chr18 78077248 4559197 0.058393413148988035 0.9224114591644303 chr19 59128983 3003305 0.05079243456631074 1.0803175938212013 chr20 63025520 4164120 0.06607037910992246 0.4886747203392001 chr21 48129895 2423582 0.05035502362928487 0.45718655561570787 chr22 51304566 2378283 0.046356166427760054 0.4267026603134921 chrMT 16571 8687 0.5242290748898678 1.421937786317364 chrX 155270560 10658279 0.06864327017304504 0.5519421427763236 chrY 59373566 590886 0.009952004567150305 0.5998884033670577