BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714148.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 659,640 number of mapped reads = 633,866 (96.09%) number of supplementary alignments = 18,240 (2.77%) number of secondary alignments = 0 number of mapped bases = 82,542,461 bp number of sequenced bases = 81,451,638 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 637,251 duplication rate = 23.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 18.0818 >>>>>>> ACTG content number of A's = 24,042,138 bp (29.52%) number of C's = 17,920,482 bp (22%) number of T's = 22,512,294 bp (27.64%) number of G's = 16,976,157 bp (20.84%) number of N's = 567 bp (0%) GC percentage = 42.84% >>>>>>> Mismatches and indels general error rate = 0.0448 number of mismatches = 2,773,973 number of insertions = 254,600 mapped reads with insertion percentage = 39.58% number of deletions = 169,424 mapped reads with deletion percentage = 25.89% homopolymer indels = 48.95% >>>>>>> Coverage mean coverageData = 0.0267X std coverageData = 77.4934X There is a 0.01% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% 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 79198 3.177444440549659E-4 0.13804689054690816 chr2 243199373 568962 0.0023394879393870806 1.539565857505754 chr3 198022430 3236689 0.01634506252650268 18.53266652029187 chr4 191154276 106190 5.555198775673739E-4 0.1945715033407568 chr5 180915260 23683632 0.13091008464404827 130.54816570525813 chr6 171115067 369512 0.0021594357906542503 1.5687038807280353 chr7 159138663 813982 0.005114922952444309 5.319426203560314 chr8 146364022 211389 0.0014442688654729644 0.8851812870161192 chr9 141213431 85817 6.077113160716278E-4 0.2302432306741586 chr10 135534747 1645296 0.012139292959317658 11.466218262846377 chr11 135006516 332016 0.0024592590775396354 1.713902390206888 chr12 133851895 69884 5.220994443149273E-4 0.15837680613279184 chr13 115169878 50323 4.3694584794124727E-4 0.20465195248783621 chr14 107349540 50511655 0.4705344335895617 378.9379740145665 chr15 102531392 161567 0.0015757808106223702 0.9203143213443575 chr16 90354753 25227 2.7919947941200174E-4 0.061203045355778835 chr17 81195210 15036 1.8518333778556642E-4 0.020989485275789446 chr18 78077248 127697 0.001635521272471079 1.2273632284633051 chr19 59128983 25676 4.342371320677036E-4 0.24524512777485852 chr20 63025520 18294 2.902633726782421E-4 0.03741996162967753 chr21 48129895 17280 3.590284167459746E-4 0.27300056667961137 chr22 51304566 10217 1.9914406838564817E-4 0.0728698436734529 chrMT 16571 65933 3.9788184177176995 33.563835718475175 chrX 155270560 304527 0.00196126683641767 0.9877615146686382 chrY 59373566 6462 1.0883631277932674E-4 0.020956066035079053