BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089717.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 25,035,994 number of mapped reads = 21,548,477 (86.07%) number of supplementary alignments = 947 (0%) number of secondary alignments = 0 number of mapped bases = 1,020,826,312 bp number of sequenced bases = 1,020,637,379 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,977,479 duplication rate = 12.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.0523 >>>>>>> ACTG content number of A's = 303,449,020 bp (29.73%) number of C's = 207,059,299 bp (20.29%) number of T's = 292,994,245 bp (28.71%) number of G's = 217,126,563 bp (21.27%) number of N's = 8,252 bp (0%) GC percentage = 41.56% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 3,688,723 number of insertions = 36,443 mapped reads with insertion percentage = 0.17% number of deletions = 125,346 mapped reads with deletion percentage = 0.58% homopolymer indels = 47.63% >>>>>>> Coverage mean coverageData = 0.3298X std coverageData = 2.211X There is a 11.13% of reference with a coverageData >= 1X There is a 6.56% of reference with a coverageData >= 2X There is a 4.28% of reference with a coverageData >= 3X There is a 2.9% of reference with a coverageData >= 4X There is a 2.02% of reference with a coverageData >= 5X There is a 1.43% of reference with a coverageData >= 6X There is a 1.03% of reference with a coverageData >= 7X There is a 0.75% of reference with a coverageData >= 8X There is a 0.55% of reference with a coverageData >= 9X There is a 0.41% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.23% of reference with a coverageData >= 12X There is a 0.18% of reference with a coverageData >= 13X There is a 0.14% of reference with a coverageData >= 14X There is a 0.11% of reference with a coverageData >= 15X There is a 0.09% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% 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% 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 46983617 0.1884994982620324 2.5500557588298602 chr2 243199373 177515071 0.7299158250708154 2.8337347262093706 chr3 198022430 80406927 0.4060495924628336 1.4857371193789959 chr4 191154276 54936544 0.2873937489109582 1.2556212759112453 chr5 180915260 39424416 0.21791647647633483 1.0609085420057265 chr6 171115067 29459622 0.1721626418788709 0.9256654934074091 chr7 159138663 109639514 0.6889558573204804 4.906814144687817 chr8 146364022 141744972 0.9684413564420906 4.476734858204946 chr9 141213431 41592106 0.29453364106704555 1.96397076511059 chr10 135534747 26141338 0.19287554356817443 1.4935318956995813 chr11 135006516 23943108 0.1773477955686228 1.2074448791814407 chr12 133851895 8178300 0.061099620591848924 0.6757663191714018 chr13 115169878 24679091 0.2142842506093477 1.03138850668265 chr14 107349540 19996079 0.18627074694497991 0.9793266469213725 chr15 102531392 39294930 0.38324779595306774 1.4456061250401866 chr16 90354753 23622889 0.2614460027354621 1.199580092210567 chr17 81195210 10523969 0.1296131754570251 0.8428536741138947 chr18 78077248 32458173 0.41571871231936863 2.95131335763002 chr19 59128983 9396530 0.15891580614535514 1.9222620142074982 chr20 63025520 27808078 0.4412193346441251 1.6277332314914472 chr21 48129895 17770074 0.3692107369027088 1.5312709490553742 chr22 51304566 10250757 0.1998020410113205 1.0163950886440567 chrMT 16571 1809567 109.20083278015811 58.75689329266381 chrX 155270560 20765901 0.13374010501411215 0.9974481477892175 chrY 59373566 2484739 0.04184924651485478 1.6600223450449982