BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094046.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 480,802 number of mapped reads = 452,375 (94.09%) number of supplementary alignments = 18,237 (3.79%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 227,229 number of mapped paired reads (second in pair) = 225,146 number of mapped paired reads (both in pair) = 449,184 number of mapped paired reads (singletons) = 3,191 number of mapped bases = 58,397,582 bp number of sequenced bases = 56,788,956 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 431,975 duplication rate = 52.93% >>>>>>> Insert size mean insert size = 607,659.5136 std insert size = 6,839,688.5069 median insert size = 159 >>>>>>> Mapping quality mean mapping quality = 41.3436 >>>>>>> ACTG content number of A's = 15,563,216 bp (27.41%) number of C's = 12,857,430 bp (22.64%) number of T's = 14,939,651 bp (26.31%) number of G's = 13,427,948 bp (23.65%) number of N's = 711 bp (0%) GC percentage = 46.29% >>>>>>> Mismatches and indels general error rate = 0.0469 number of mismatches = 2,598,968 number of insertions = 42,815 mapped reads with insertion percentage = 9.28% number of deletions = 208,023 mapped reads with deletion percentage = 42.76% homopolymer indels = 29.07% >>>>>>> Coverage mean coverageData = 0.0189X std coverageData = 4.337X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% 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% 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 1129896 0.004533172256369223 1.7442279503440086 chr2 243199373 2202060 0.00905454637006815 3.2755265007079735 chr3 198022430 1783813 0.009008136098521769 2.6476385403147957 chr4 191154276 1182776 0.006187546649492685 2.899544706537494 chr5 180915260 434109 0.0023995156627472994 0.908846768557104 chr6 171115067 1857955 0.010857927548834726 4.753209589054808 chr7 159138663 1732793 0.01088857331923167 3.687633597014036 chr8 146364022 1176755 0.008039919810347929 2.639638501231137 chr9 141213431 725236 0.005135743780632311 2.1388549909057732 chr10 135534747 1399971 0.010329240515718085 3.249583561279356 chr11 135006516 2300754 0.017041799671358084 4.547441563055194 chr12 133851895 1866751 0.013946392017834338 3.7960579061071646 chr13 115169878 1413815 0.012275909504740466 3.240787587239356 chr14 107349540 349859 0.0032590638022296134 1.374665704935147 chr15 102531392 650513 0.006344525196731943 2.6195028553660955 chr16 90354753 382783 0.004236445646639087 1.2265327162960247 chr17 81195210 1044323 0.012861879413822564 4.021885195274549 chr18 78077248 192938 0.0024711168098547737 0.7130183314434408 chr19 59128983 253729 0.004291110503287364 1.012390105933233 chr20 63025520 228813 0.003630481747711086 0.8679678740333271 chr21 48129895 505680 0.010506567695607896 3.6961719358518175 chr22 51304566 175326 0.0034173566539867036 1.3957849255947614 chrMT 16571 2169618 130.92861022267817 558.9071927510897 chrX 155270560 32798314 0.2112333078466388 13.327496381397292 chrY 59373566 439002 0.007393896469011142 2.4364340878374007