BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234086.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,909,907 number of mapped reads = 778,267 (40.75%) number of supplementary alignments = 3,683 (0.19%) number of secondary alignments = 0 number of mapped bases = 46,264,194 bp number of sequenced bases = 46,231,205 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 68,104 duplication rate = 7.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4022 >>>>>>> ACTG content number of A's = 12,309,403 bp (26.63%) number of C's = 7,362,248 bp (15.92%) number of T's = 15,539,072 bp (33.61%) number of G's = 11,014,638 bp (23.83%) number of N's = 5,844 bp (0.01%) GC percentage = 39.75% >>>>>>> Mismatches and indels general error rate = 0.0112 number of mismatches = 508,000 number of insertions = 4,216 mapped reads with insertion percentage = 0.54% number of deletions = 18,675 mapped reads with deletion percentage = 2.36% homopolymer indels = 45.59% >>>>>>> Coverage mean coverageData = 0.0149X std coverageData = 0.1843X There is a 1.18% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 4030028 0.016168577569963205 0.2100990623353263 chr2 243199373 3241037 0.013326666759128528 0.18656167269781923 chr3 198022430 3965385 0.020024928489161556 0.17813765082114671 chr4 191154276 2355413 0.01232205237198042 0.14409729807952373 chr5 180915260 2766074 0.01528933490740361 0.16674034552449324 chr6 171115067 3046069 0.017801290403024535 0.1835190490761406 chr7 159138663 2836946 0.017826880950985495 0.2234720531889633 chr8 146364022 2345518 0.01602523603785635 0.3112363611213244 chr9 141213431 1879536 0.013309895430555753 0.15949561204810286 chr10 135534747 2286228 0.01686820575981154 0.17484514351665295 chr11 135006516 2160191 0.01600064251713599 0.17693186734743746 chr12 133851895 1749683 0.013071783555996723 0.1457789531704994 chr13 115169878 1847132 0.016038325576762356 0.16393593940806425 chr14 107349540 1957342 0.01823335246709022 0.1718934363779592 chr15 102531392 1044677 0.010188850259635606 0.13157959491347057 chr16 90354753 1149452 0.012721544377416426 0.1427071756896701 chr17 81195210 1109191 0.013660793536958645 0.15110313947426898 chr18 78077248 1077572 0.013801357342922742 0.29610155682643585 chr19 59128983 1025161 0.017337707296606133 0.1826156429296138 chr20 63025520 1026668 0.016289718831355934 0.16030537314066612 chr21 48129895 735820 0.01528821120428374 0.15554084939814136 chr22 51304566 406808 0.00792927475499939 0.11004779062658637 chrMT 16571 33439 2.0179228773157925 2.256715131655871 chrX 155270560 2021191 0.01301721974854731 0.1453354167023716 chrY 59373566 167633 0.0028233608202006934 0.06903320601873705