BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818911.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 = 1,656,723 number of mapped reads = 1,633,263 (98.58%) number of supplementary alignments = 24,402 (1.47%) number of secondary alignments = 0 number of mapped bases = 151,140,917 bp number of sequenced bases = 151,042,397 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 382,853 duplication rate = 19.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.217 >>>>>>> ACTG content number of A's = 44,798,915 bp (29.66%) number of C's = 31,704,534 bp (20.99%) number of T's = 41,940,264 bp (27.77%) number of G's = 32,596,422 bp (21.58%) number of N's = 2,262 bp (0%) GC percentage = 42.57% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 919,237 number of insertions = 22,469 mapped reads with insertion percentage = 1.33% number of deletions = 49,762 mapped reads with deletion percentage = 2.97% homopolymer indels = 40.18% >>>>>>> Coverage mean coverageData = 0.0488X std coverageData = 0.6269X There is a 3.34% of reference with a coverageData >= 1X There is a 0.91% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% 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 14372404 0.057662460146889666 0.9066356712789799 chr2 243199373 11621166 0.04778452286552565 0.9675072244642973 chr3 198022430 9211020 0.04651503367573057 0.29335936076342634 chr4 191154276 7567205 0.039586898908816455 0.36222719191449537 chr5 180915260 6678057 0.03691262417553942 0.2839617151576391 chr6 171115067 7510818 0.04389337614553837 0.3096731741834844 chr7 159138663 13569532 0.08526860628457084 1.374676247413968 chr8 146364022 13174992 0.09001523612134682 0.5077170440801205 chr9 141213431 5521656 0.03910149311505646 0.484071937576219 chr10 135534747 6990687 0.051578559408090384 0.7969228424304382 chr11 135006516 6604415 0.04891923142435584 0.36146458774045004 chr12 133851895 5868046 0.043839842536409365 0.290638534100361 chr13 115169878 4630797 0.04020840414539642 0.2727518201175133 chr14 107349540 4448341 0.04143791393982685 0.30870750622877413 chr15 102531392 4243171 0.04138411580328491 0.2848464556404383 chr16 90354753 3810227 0.04216963550329223 0.6685463598776503 chr17 81195210 3733858 0.04598618563829073 0.37728244867949534 chr18 78077248 2896028 0.03709182987597104 0.5636982303793105 chr19 59128983 2635361 0.04456969943149538 0.8130894520722938 chr20 63025520 6224888 0.09876773725944665 0.4645300660326526 chr21 48129895 1478602 0.0307210726306384 0.2951285317478063 chr22 51304566 1372776 0.026757384518173295 0.25378361565143226 chrMT 16571 206614 12.468408665741356 8.092248331318421 chrX 155270560 6209034 0.039988482040639255 0.32953874479426526 chrY 59373566 561222 0.00945238829010203 0.811214502971353