BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006160.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 10,061,324 number of mapped reads = 8,707,180 (86.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,374,401 number of mapped paired reads (second in pair) = 4,332,779 number of mapped paired reads (both in pair) = 8,151,938 number of mapped paired reads (singletons) = 555,242 number of mapped bases = 336,211,734 bp number of sequenced bases = 336,171,825 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 563,684 duplication rate = 5.76% >>>>>>> Insert size mean insert size = 54,254.4009 std insert size = 2,281,652.5778 median insert size = 74 >>>>>>> Mapping quality mean mapping quality = 46.7677 >>>>>>> ACTG content number of A's = 89,400,822 bp (26.59%) number of C's = 77,092,431 bp (22.93%) number of T's = 90,836,826 bp (27.02%) number of G's = 78,796,524 bp (23.44%) number of N's = 45,222 bp (0.01%) GC percentage = 46.37% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 1,260,297 number of insertions = 11,252 mapped reads with insertion percentage = 0.13% number of deletions = 30,104 mapped reads with deletion percentage = 0.35% homopolymer indels = 39.03% >>>>>>> Coverage mean coverageData = 0.1086X std coverageData = 0.6448X There is a 7.63% of reference with a coverageData >= 1X There is a 2.21% of reference with a coverageData >= 2X There is a 0.54% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 29476082 0.11825881067714572 0.7009545433899793 chr2 243199373 28545988 0.11737689800705202 0.5498379078076431 chr3 198022430 21283723 0.10748137471093552 0.43146718013803786 chr4 191154276 19730949 0.10322002422796966 0.4877078093934517 chr5 180915260 19742618 0.10912632798360956 0.4396928599691077 chr6 171115067 18330924 0.10712629998853344 0.4779001471879035 chr7 159138663 18024084 0.11326024524913848 0.6256128958027946 chr8 146364022 16410088 0.11211831825720121 1.053270130060032 chr9 141213431 13514110 0.09569989132266038 0.47092693611193226 chr10 135534747 16576596 0.12230513847493292 0.6275413847311968 chr11 135006516 15184324 0.11247104547161264 0.5181666345277331 chr12 133851895 14960789 0.11177121549156999 0.45447759050307207 chr13 115169878 10208482 0.08863847194489517 0.40091374446703554 chr14 107349540 10748119 0.10012263676211375 1.7228468569974342 chr15 102531392 10172466 0.09921318536278138 0.4206494535486174 chr16 90354753 11290650 0.12495911532180272 0.529151116219785 chr17 81195210 9971255 0.1228059512377639 0.49942232677180176 chr18 78077248 8640438 0.11066524783250557 0.6695376664375466 chr19 59128983 8267937 0.1398288382534839 0.6757795529420986 chr20 63025520 7756153 0.12306368912148603 0.5068038038223455 chr21 48129895 4392698 0.09126755834393571 0.5012258247867628 chr22 51304566 5172810 0.1008255288622849 0.7535121531146856 chrMT 16571 1357 0.0818900488805745 0.570315265235157 chrX 155270560 16902140 0.10885605101185955 0.4596218432376673 chrY 59373566 906954 0.015275383661476558 0.35571815771118753