BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818749.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 = 2,301,271 number of mapped reads = 2,250,647 (97.8%) number of supplementary alignments = 17,739 (0.77%) number of secondary alignments = 0 number of mapped bases = 152,972,235 bp number of sequenced bases = 152,908,837 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,227,302 duplication rate = 46.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7347 >>>>>>> ACTG content number of A's = 43,022,076 bp (28.14%) number of C's = 32,353,327 bp (21.16%) number of T's = 44,464,197 bp (29.08%) number of G's = 33,059,975 bp (21.62%) number of N's = 9,262 bp (0.01%) GC percentage = 42.78% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 745,348 number of insertions = 17,917 mapped reads with insertion percentage = 0.79% number of deletions = 39,337 mapped reads with deletion percentage = 1.73% homopolymer indels = 40.87% >>>>>>> Coverage mean coverageData = 0.0494X std coverageData = 0.592X There is a 1.93% of reference with a coverageData >= 1X There is a 1.07% of reference with a coverageData >= 2X There is a 0.67% of reference with a coverageData >= 3X There is a 0.43% of reference with a coverageData >= 4X There is a 0.28% of reference with a coverageData >= 5X There is a 0.18% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.07% 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 13047435 0.05234664992068365 0.863673289421705 chr2 243199373 13610382 0.05596388605820953 0.8362428159030463 chr3 198022430 9892121 0.04995454807821518 0.45917889882709595 chr4 191154276 9951217 0.05205856341921433 0.5176448840420623 chr5 180915260 9606830 0.053101269622031884 0.48179901279193726 chr6 171115067 8980453 0.05248195356169308 0.5077393248560653 chr7 159138663 8132113 0.051100800061390485 0.5282450195990074 chr8 146364022 7793633 0.05324828392595005 0.5290501522052863 chr9 141213431 6599006 0.04673072492658294 0.5139697565692102 chr10 135534747 7304240 0.05389201043773668 0.610947397411977 chr11 135006516 7236016 0.053597531544329315 0.5255036512350196 chr12 133851895 7075620 0.05286156015945833 0.49447151283721136 chr13 115169878 4824393 0.04188936450900816 0.42266477361113397 chr14 107349540 4821452 0.0449135785770484 0.4761975644014613 chr15 102531392 4583224 0.04470069030175656 0.4388949797899907 chr16 90354753 4593162 0.05083475796785145 0.6382402484062647 chr17 81195210 4154654 0.0511687081048254 0.4959967878365025 chr18 78077248 3945018 0.0505271138654887 0.6637540082504756 chr19 59128983 3111837 0.05262794727925559 0.7581024348332115 chr20 63025520 3424119 0.05432908764576635 0.5145382596163454 chr21 48129895 2054068 0.04267759154679228 0.44653992626104755 chr22 51304566 2011139 0.03920000024949046 0.45028551255355576 chrMT 16571 138828 8.377768390561824 9.055705131829551 chrX 155270560 4727545 0.03044714336059585 0.4048858671544127 chrY 59373566 1353730 0.022800213819058803 0.935129496905544