BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472447.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 = 21,028,752 number of mapped reads = 20,814,077 (98.98%) number of supplementary alignments = 78,942 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,444,133 number of mapped paired reads (second in pair) = 10,369,944 number of mapped paired reads (both in pair) = 20,682,180 number of mapped paired reads (singletons) = 131,897 number of mapped bases = 2,045,764,914 bp number of sequenced bases = 2,045,524,756 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,255,622 duplication rate = 48.13% >>>>>>> Insert size mean insert size = 20,130.3271 std insert size = 1,377,156.7551 median insert size = 233 >>>>>>> Mapping quality mean mapping quality = 54.6838 >>>>>>> ACTG content number of A's = 564,736,516 bp (27.61%) number of C's = 459,015,030 bp (22.44%) number of T's = 566,060,083 bp (27.67%) number of G's = 455,451,395 bp (22.27%) number of N's = 261,732 bp (0.01%) GC percentage = 44.71% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 11,776,341 number of insertions = 121,681 mapped reads with insertion percentage = 0.58% number of deletions = 105,014 mapped reads with deletion percentage = 0.5% homopolymer indels = 46.9% >>>>>>> Coverage mean coverageData = 0.6608X std coverageData = 19.9864X There is a 5.65% of reference with a coverageData >= 1X There is a 2.4% of reference with a coverageData >= 2X There is a 1.03% of reference with a coverageData >= 3X There is a 0.75% of reference with a coverageData >= 4X There is a 0.57% of reference with a coverageData >= 5X There is a 0.51% of reference with a coverageData >= 6X There is a 0.47% of reference with a coverageData >= 7X There is a 0.45% of reference with a coverageData >= 8X There is a 0.43% of reference with a coverageData >= 9X There is a 0.41% of reference with a coverageData >= 10X There is a 0.4% of reference with a coverageData >= 11X There is a 0.39% of reference with a coverageData >= 12X There is a 0.38% of reference with a coverageData >= 13X There is a 0.37% of reference with a coverageData >= 14X There is a 0.36% of reference with a coverageData >= 15X There is a 0.35% of reference with a coverageData >= 16X There is a 0.34% of reference with a coverageData >= 17X There is a 0.33% of reference with a coverageData >= 18X There is a 0.33% of reference with a coverageData >= 19X There is a 0.32% of reference with a coverageData >= 20X There is a 0.31% of reference with a coverageData >= 21X There is a 0.31% of reference with a coverageData >= 22X There is a 0.3% of reference with a coverageData >= 23X There is a 0.3% of reference with a coverageData >= 24X There is a 0.29% of reference with a coverageData >= 25X There is a 0.29% of reference with a coverageData >= 26X There is a 0.28% of reference with a coverageData >= 27X There is a 0.28% of reference with a coverageData >= 28X There is a 0.27% of reference with a coverageData >= 29X There is a 0.27% of reference with a coverageData >= 30X There is a 0.27% of reference with a coverageData >= 31X There is a 0.26% of reference with a coverageData >= 32X There is a 0.26% of reference with a coverageData >= 33X There is a 0.26% of reference with a coverageData >= 34X There is a 0.25% of reference with a coverageData >= 35X There is a 0.25% of reference with a coverageData >= 36X There is a 0.24% of reference with a coverageData >= 37X There is a 0.24% of reference with a coverageData >= 38X There is a 0.24% of reference with a coverageData >= 39X There is a 0.24% of reference with a coverageData >= 40X There is a 0.23% of reference with a coverageData >= 41X There is a 0.23% of reference with a coverageData >= 42X There is a 0.23% of reference with a coverageData >= 43X There is a 0.22% of reference with a coverageData >= 44X There is a 0.22% of reference with a coverageData >= 45X There is a 0.22% of reference with a coverageData >= 46X There is a 0.22% of reference with a coverageData >= 47X There is a 0.21% of reference with a coverageData >= 48X There is a 0.21% of reference with a coverageData >= 49X There is a 0.21% of reference with a coverageData >= 50X There is a 0.21% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 177219097 0.7110076447913845 19.281578675735602 chr2 243199373 178128459 0.7324379861785252 23.205961778596166 chr3 198022430 144570165 0.730069644130718 15.749491498050594 chr4 191154276 47886534 0.25051249180531016 8.296557941364787 chr5 180915260 78102914 0.4317099287257471 13.763157112018218 chr6 171115067 171778865 1.0038792492773299 24.19454843657163 chr7 159138663 125298985 0.7873572809895983 21.358554065175504 chr8 146364022 162664221 1.111367525825438 27.21952902537475 chr9 141213431 78032717 0.5525870765083245 12.703180319086668 chr10 135534747 37328474 0.27541626650175544 7.879900667413333 chr11 135006516 83348447 0.6173661054996783 21.466062811022216 chr12 133851895 109424961 0.8175077461548079 18.84974414217552 chr13 115169878 71622235 0.6218833973237342 22.130777537364093 chr14 107349540 44766741 0.41701847068930153 13.165275197845157 chr15 102531392 44779220 0.43673668255669446 15.645905322721784 chr16 90354753 85020285 0.9409608479589336 22.92134731740665 chr17 81195210 65449435 0.8060750751183475 16.59950269207969 chr18 78077248 10919088 0.1398498061816933 5.537763025192128 chr19 59128983 41619545 0.7038772339446461 14.594473622309406 chr20 63025520 127395241 2.0213278843236835 52.69240404199257 chr21 48129895 18973513 0.39421471831592403 19.398685074747373 chr22 51304566 17120795 0.3337089919053209 9.641941587411866 chrMT 16571 3878 0.23402329370587172 0.6432436991692557 chrX 155270560 123888211 0.7978860319689708 26.746563562210792 chrY 59373566 422888 0.0071224962300563185 0.684329809677771