BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617499.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,678,712 (95.87%) number of supplementary alignments = 139,852 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,409,182 number of mapped paired reads (second in pair) = 15,269,530 number of mapped paired reads (both in pair) = 30,213,984 number of mapped paired reads (singletons) = 464,728 number of mapped bases = 2,999,154,560 bp number of sequenced bases = 2,997,372,542 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,350,220 duplication rate = 9.99% >>>>>>> Insert size mean insert size = 30,450.6529 std insert size = 1,615,580.8819 median insert size = 220 >>>>>>> Mapping quality mean mapping quality = 52.8093 >>>>>>> ACTG content number of A's = 883,739,787 bp (29.48%) number of C's = 606,410,607 bp (20.23%) number of T's = 883,359,474 bp (29.47%) number of G's = 621,750,527 bp (20.74%) number of N's = 2,112,147 bp (0.07%) GC percentage = 40.97% >>>>>>> Mismatches and indels general error rate = 0.0122 number of mismatches = 35,648,600 number of insertions = 445,903 mapped reads with insertion percentage = 1.43% number of deletions = 1,047,583 mapped reads with deletion percentage = 3.34% homopolymer indels = 47.46% >>>>>>> Coverage mean coverageData = 0.9688X std coverageData = 9.8008X There is a 38.4% of reference with a coverageData >= 1X There is a 20.79% of reference with a coverageData >= 2X There is a 11.77% of reference with a coverageData >= 3X There is a 7.02% of reference with a coverageData >= 4X There is a 4.34% of reference with a coverageData >= 5X There is a 2.79% of reference with a coverageData >= 6X There is a 1.85% of reference with a coverageData >= 7X There is a 1.27% of reference with a coverageData >= 8X There is a 0.89% of reference with a coverageData >= 9X There is a 0.64% of reference with a coverageData >= 10X There is a 0.48% of reference with a coverageData >= 11X There is a 0.36% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.22% of reference with a coverageData >= 14X There is a 0.18% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 193183857 0.7750586787906137 9.52405525882196 chr2 243199373 309858982 1.2740944936564453 11.587453462592585 chr3 198022430 247832924 1.2515396563914503 2.2626287029792542 chr4 191154276 155142065 0.8116065632766698 6.266117196838158 chr5 180915260 191883764 1.0606278541677467 2.0914504274482097 chr6 171115067 141397542 0.826330167640936 5.472809067691267 chr7 159138663 231309561 1.4535095157862423 13.240377840399642 chr8 146364022 133194499 0.9100221296187119 3.862603926437289 chr9 141213431 124369345 0.8807189522928595 18.628869544809998 chr10 135534747 126796608 0.9355284220953317 18.728113199763573 chr11 135006516 169089404 1.25245365194077 12.825639207543336 chr12 133851895 130926752 0.9781464207137299 1.9891626671318865 chr13 115169878 127431260 1.1064634452421664 2.137799927358882 chr14 107349540 87450160 0.8146300394021251 2.2312928869205133 chr15 102531392 67711973 0.6604023575530897 1.4505410587499823 chr16 90354753 80826135 0.8945421498745063 14.99153174159438 chr17 81195210 83825116 1.032389915612017 13.913710044021105 chr18 78077248 53610297 0.6866314883434416 17.071108323277805 chr19 59128983 35861685 0.6064992695714047 5.894754335183198 chr20 63025520 88561305 1.4051657963313908 2.8098963854540533 chr21 48129895 43239730 0.898396516343948 3.8278790072548294 chr22 51304566 22429005 0.4371736620869183 1.2612018439188506 chrMT 16571 2127844 128.40770019914308 93.91481637780016 chrX 155270560 140735031 0.9063858016613066 4.133754745633684 chrY 59373566 10359716 0.1744836414238619 13.997435579331048