BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818745.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 = 2,258,692 number of mapped reads = 2,206,765 (97.7%) number of supplementary alignments = 17,585 (0.78%) number of secondary alignments = 0 number of mapped bases = 149,935,594 bp number of sequenced bases = 149,874,361 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,082,269 duplication rate = 42.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.804 >>>>>>> ACTG content number of A's = 42,545,012 bp (28.39%) number of C's = 31,385,846 bp (20.94%) number of T's = 43,567,062 bp (29.07%) number of G's = 32,367,124 bp (21.6%) number of N's = 9,317 bp (0.01%) GC percentage = 42.54% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 750,457 number of insertions = 17,187 mapped reads with insertion percentage = 0.77% number of deletions = 38,840 mapped reads with deletion percentage = 1.74% homopolymer indels = 41.71% >>>>>>> Coverage mean coverageData = 0.0484X std coverageData = 0.5811X There is a 2.09% of reference with a coverageData >= 1X There is a 1.1% of reference with a coverageData >= 2X There is a 0.64% of reference with a coverageData >= 3X There is a 0.38% of reference with a coverageData >= 4X There is a 0.22% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.08% 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 0.01% 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% 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 12257641 0.049177975769215836 0.84805484543502 chr2 243199373 13179970 0.05419409531125724 0.9088820386112284 chr3 198022430 10295726 0.05199272627853319 0.4386425059731972 chr4 191154276 10097902 0.052825927890830966 0.5115056198627271 chr5 180915260 9478834 0.052393778169956474 0.4550910350674342 chr6 171115067 8874412 0.051862247758696786 0.47977798342540223 chr7 159138663 8108070 0.05094971798273811 0.5146113980043362 chr8 146364022 7842971 0.05358537496325429 0.5030256755794981 chr9 141213431 6330727 0.044830912719626505 0.4813477436258469 chr10 135534747 7309325 0.05392952849205525 0.6003029180715781 chr11 135006516 6990013 0.05177537504930503 0.49069351873418454 chr12 133851895 6944177 0.051879556878892154 0.4952230398504553 chr13 115169878 4814952 0.04180738994965333 0.3909334327007736 chr14 107349540 4655060 0.043363576592875944 0.4440211519826859 chr15 102531392 4227723 0.0412334497516624 0.39118698598373125 chr16 90354753 4333938 0.047965799873306056 0.6042849252209311 chr17 81195210 3993611 0.04918530292612089 0.44828651129816394 chr18 78077248 4000649 0.051239626171250295 0.6536203361476591 chr19 59128983 2967085 0.050179875408985136 0.7098886159781352 chr20 63025520 3159752 0.050134485205358084 0.4498730962061939 chr21 48129895 2062763 0.04285824849607505 0.41637662429812294 chr22 51304566 1737139 0.03385934499475154 0.3759923288972917 chrMT 16571 68598 4.139641542453684 4.421125773353229 chrX 155270560 4774365 0.03074868152726441 0.38090217547349287 chrY 59373566 1430191 0.024088009131875286 0.9661325544279752