BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472396.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 16,433,458 number of mapped reads = 16,286,831 (99.11%) number of supplementary alignments = 65,531 (0.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,169,798 number of mapped paired reads (second in pair) = 8,117,033 number of mapped paired reads (both in pair) = 16,196,328 number of mapped paired reads (singletons) = 90,503 number of mapped bases = 1,598,293,658 bp number of sequenced bases = 1,598,098,228 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,716,146 duplication rate = 46.11% >>>>>>> Insert size mean insert size = 19,380.512 std insert size = 1,350,756.822 median insert size = 220 >>>>>>> Mapping quality mean mapping quality = 54.7636 >>>>>>> ACTG content number of A's = 430,276,971 bp (26.92%) number of C's = 370,080,580 bp (23.16%) number of T's = 430,628,910 bp (26.95%) number of G's = 366,918,944 bp (22.96%) number of N's = 192,823 bp (0.01%) GC percentage = 46.12% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 8,913,024 number of insertions = 91,621 mapped reads with insertion percentage = 0.56% number of deletions = 80,522 mapped reads with deletion percentage = 0.49% homopolymer indels = 45.27% >>>>>>> Coverage mean coverageData = 0.5163X std coverageData = 15.0292X There is a 4.64% of reference with a coverageData >= 1X There is a 1.93% of reference with a coverageData >= 2X There is a 0.83% of reference with a coverageData >= 3X There is a 0.64% of reference with a coverageData >= 4X There is a 0.5% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.43% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.39% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.37% of reference with a coverageData >= 11X There is a 0.36% of reference with a coverageData >= 12X There is a 0.35% of reference with a coverageData >= 13X There is a 0.34% of reference with a coverageData >= 14X There is a 0.33% of reference with a coverageData >= 15X There is a 0.32% of reference with a coverageData >= 16X There is a 0.31% of reference with a coverageData >= 17X There is a 0.3% of reference with a coverageData >= 18X There is a 0.3% of reference with a coverageData >= 19X There is a 0.29% of reference with a coverageData >= 20X There is a 0.29% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.27% of reference with a coverageData >= 24X There is a 0.26% of reference with a coverageData >= 25X There is a 0.26% of reference with a coverageData >= 26X There is a 0.26% of reference with a coverageData >= 27X There is a 0.25% of reference with a coverageData >= 28X There is a 0.25% of reference with a coverageData >= 29X There is a 0.24% of reference with a coverageData >= 30X There is a 0.24% of reference with a coverageData >= 31X There is a 0.24% of reference with a coverageData >= 32X There is a 0.23% of reference with a coverageData >= 33X There is a 0.23% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.22% of reference with a coverageData >= 36X There is a 0.22% of reference with a coverageData >= 37X There is a 0.22% of reference with a coverageData >= 38X There is a 0.21% of reference with a coverageData >= 39X There is a 0.21% of reference with a coverageData >= 40X There is a 0.21% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.2% of reference with a coverageData >= 43X There is a 0.2% of reference with a coverageData >= 44X There is a 0.2% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.19% of reference with a coverageData >= 47X There is a 0.19% of reference with a coverageData >= 48X There is a 0.19% of reference with a coverageData >= 49X There is a 0.19% of reference with a coverageData >= 50X There is a 0.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 156161109 0.6265224470594197 18.0877588568583 chr2 243199373 119448752 0.4911556741554593 13.830961199902248 chr3 198022430 86243306 0.43552291525763015 9.218277179176775 chr4 191154276 40026961 0.2093961057925798 8.89646797757224 chr5 180915260 56628688 0.31301222461831024 9.554839081940978 chr6 171115067 113807088 0.6650909823154264 14.506412371781387 chr7 159138663 136985181 0.8607913276235079 21.429987837152044 chr8 146364022 79022271 0.539902292381662 11.99167992312764 chr9 141213431 56594994 0.40077628310015356 10.080044847911527 chr10 135534747 38824545 0.28645455028591305 8.926930232990122 chr11 135006516 43040189 0.3188008273615475 9.68145253209728 chr12 133851895 51915049 0.3878544192444941 10.085715990584545 chr13 115169878 56071456 0.48685869060311066 17.040319541095705 chr14 107349540 52904325 0.4928230246724858 16.215029834804813 chr15 102531392 53406869 0.5208830969543454 17.110963048648916 chr16 90354753 118984160 1.3168555726116589 29.50929229362072 chr17 81195210 73444586 0.9045433345144375 19.915666631824156 chr18 78077248 19443818 0.2490330857972863 8.890542947606942 chr19 59128983 31665006 0.5355242791847105 9.791959762359896 chr20 63025520 68161558 1.081491402212945 31.60985921640667 chr21 48129895 11593653 0.2408825741257071 10.498110079044567 chr22 51304566 10276045 0.20029494061015934 4.888438090843833 chrMT 16571 28091 1.6951903928549876 1.8573239486067878 chrX 155270560 123222683 0.7935997847885652 19.16212900602626 chrY 59373566 393275 0.0066237389211219015 0.5003460397309157