BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472719.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 = 13,119,452 number of mapped reads = 13,006,171 (99.14%) number of supplementary alignments = 46,415 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,525,790 number of mapped paired reads (second in pair) = 6,480,381 number of mapped paired reads (both in pair) = 12,934,374 number of mapped paired reads (singletons) = 71,797 number of mapped bases = 1,282,314,007 bp number of sequenced bases = 1,282,117,989 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,715,916 duplication rate = 46.62% >>>>>>> Insert size mean insert size = 21,965.2769 std insert size = 1,489,748.9921 median insert size = 249 >>>>>>> Mapping quality mean mapping quality = 55.2155 >>>>>>> ACTG content number of A's = 358,472,902 bp (27.96%) number of C's = 284,381,814 bp (22.18%) number of T's = 356,183,017 bp (27.78%) number of G's = 282,832,183 bp (22.06%) number of N's = 248,073 bp (0.02%) GC percentage = 44.24% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 7,928,585 number of insertions = 77,725 mapped reads with insertion percentage = 0.59% number of deletions = 75,867 mapped reads with deletion percentage = 0.58% homopolymer indels = 45.17% >>>>>>> Coverage mean coverageData = 0.4142X std coverageData = 13.1834X There is a 3.94% of reference with a coverageData >= 1X There is a 1.72% of reference with a coverageData >= 2X There is a 0.8% of reference with a coverageData >= 3X There is a 0.59% of reference with a coverageData >= 4X There is a 0.46% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.26% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.23% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 133328531 0.5349175479085366 15.611924040003084 chr2 243199373 92860523 0.3818287927905143 12.016674397380045 chr3 198022430 159464189 0.805283467130466 19.63417828969015 chr4 191154276 49822182 0.2606385953929694 10.150093910602962 chr5 180915260 82885809 0.45814714026887504 16.569648953857797 chr6 171115067 67614306 0.3951394063972169 11.767286298951925 chr7 159138663 62020139 0.38972389129598256 13.423522636968446 chr8 146364022 60945831 0.41639899045682144 15.544108759425637 chr9 141213431 78568882 0.5563839179008405 14.367185549007315 chr10 135534747 44270890 0.32663867369745414 11.728544448686476 chr11 135006516 49537288 0.3669251638195004 12.169437163183721 chr12 133851895 62880054 0.4697733565893856 13.100283732841167 chr13 115169878 28520393 0.24763760711806954 9.248590876651072 chr14 107349540 31953159 0.29765529502967597 9.162690500144558 chr15 102531392 27577880 0.2689701120999118 8.210088739348066 chr16 90354753 36518892 0.4041723405519132 12.020974323409332 chr17 81195210 55751131 0.6866307877028707 15.777872136926698 chr18 78077248 25966713 0.33257720610234626 12.3917087031012 chr19 59128983 27784260 0.46989240454211767 11.6564805870841 chr20 63025520 21123200 0.33515312527369867 9.50730599577385 chr21 48129895 7368695 0.1531001677855312 6.148779194006949 chr22 51304566 11000584 0.2144172508934195 6.933267675984208 chrMT 16571 963 0.05811357190272162 0.26809468277406934 chrX 155270560 61987929 0.39922525557967975 13.589371629401267 chrY 59373566 2561584 0.04314350935229324 1.7367519373461304