BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714155.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 = 1,119,608 number of mapped reads = 379,859 (33.93%) number of supplementary alignments = 29,548 (2.64%) number of secondary alignments = 0 number of mapped bases = 45,672,519 bp number of sequenced bases = 45,041,075 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 336,591 duplication rate = 41.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.6078 >>>>>>> ACTG content number of A's = 11,262,035 bp (25%) number of C's = 7,414,050 bp (16.46%) number of T's = 10,255,493 bp (22.77%) number of G's = 16,109,001 bp (35.77%) number of N's = 496 bp (0%) GC percentage = 52.23% >>>>>>> Mismatches and indels general error rate = 0.0378 number of mismatches = 1,473,347 number of insertions = 54,735 mapped reads with insertion percentage = 12.82% number of deletions = 112,860 mapped reads with deletion percentage = 28.31% homopolymer indels = 31.12% >>>>>>> Coverage mean coverageData = 0.0148X std coverageData = 11.16X There is a 0.06% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% 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 2136245 0.00857067072262179 0.8451032344505446 chr2 243199373 11315983 0.04652965532110973 37.52554204675192 chr3 198022430 1922064 0.009706294382914097 1.002641983753546 chr4 191154276 2096190 0.01096595924435402 2.4750448547061 chr5 180915260 1733742 0.009583171701491627 0.8533294314661456 chr6 171115067 1684470 0.009844077611236887 1.3440036130575912 chr7 159138663 2734631 0.017183951080448626 7.608572228752873 chr8 146364022 1247994 0.0085266446148904 0.7925514433096881 chr9 141213431 1016841 0.007200738575638743 0.6592257384353414 chr10 135534747 1498860 0.011058861533124048 1.4484029325124033 chr11 135006516 1593791 0.01180528945728812 1.4724276625272308 chr12 133851895 1332727 0.009956728666411485 1.6219542133677374 chr13 115169878 821717 0.007134825652936786 0.852063304415039 chr14 107349540 977048 0.00910155739838289 1.0500150286067451 chr15 102531392 917946 0.00895282880778601 1.0910579527583963 chr16 90354753 1684797 0.018646467884207485 4.398268534510336 chr17 81195210 809652 0.009971671974245772 1.1364616031996218 chr18 78077248 794443 0.010175089675291835 0.9527269189253725 chr19 59128983 942466 0.015939154576698877 3.923687258129046 chr20 63025520 954099 0.0151382963599507 2.6308775862240386 chr21 48129895 316497 0.006575892176785343 1.4606217461050093 chr22 51304566 393479 0.0076694733174431295 0.8716260920874953 chrMT 16571 526918 31.79759821374691 257.5017140966721 chrX 155270560 5802683 0.03737143087524126 12.895379191295362 chrY 59373566 417236 0.00702730235202649 1.5168426101649553