BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038436.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 17,049,544 number of mapped reads = 16,127,441 (94.59%) number of supplementary alignments = 229,414 (1.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,146,586 number of mapped paired reads (second in pair) = 7,980,855 number of mapped paired reads (both in pair) = 15,937,822 number of mapped paired reads (singletons) = 189,619 number of mapped bases = 2,329,238,674 bp number of sequenced bases = 2,327,700,545 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,606,274 duplication rate = 11% >>>>>>> Insert size mean insert size = 71,697.5257 std insert size = 2,564,808.8161 median insert size = 245 >>>>>>> Mapping quality mean mapping quality = 53.9591 >>>>>>> ACTG content number of A's = 681,252,923 bp (29.27%) number of C's = 478,421,512 bp (20.55%) number of T's = 679,293,542 bp (29.18%) number of G's = 488,682,809 bp (20.99%) number of N's = 49,759 bp (0%) GC percentage = 41.55% >>>>>>> Mismatches and indels general error rate = 0.0142 number of mismatches = 32,022,316 number of insertions = 391,356 mapped reads with insertion percentage = 2.3% number of deletions = 815,442 mapped reads with deletion percentage = 4.87% homopolymer indels = 47.62% >>>>>>> Coverage mean coverageData = 0.7524X std coverageData = 10.8008X There is a 27.07% of reference with a coverageData >= 1X There is a 16.28% of reference with a coverageData >= 2X There is a 9.44% of reference with a coverageData >= 3X There is a 6.06% of reference with a coverageData >= 4X There is a 3.8% of reference with a coverageData >= 5X There is a 2.49% of reference with a coverageData >= 6X There is a 1.63% of reference with a coverageData >= 7X There is a 1.09% of reference with a coverageData >= 8X There is a 0.74% of reference with a coverageData >= 9X There is a 0.51% of reference with a coverageData >= 10X There is a 0.36% of reference with a coverageData >= 11X There is a 0.25% of reference with a coverageData >= 12X There is a 0.18% of reference with a coverageData >= 13X There is a 0.13% of reference with a coverageData >= 14X There is a 0.1% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% 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 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% 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 182576141 0.7325002452050059 12.483419273613775 chr2 243199373 219812858 0.9038380950102203 14.751497587455765 chr3 198022430 161895439 0.8175611166876399 1.7986732116777437 chr4 191154276 156386729 0.8181178693590929 6.043317685591326 chr5 180915260 145231132 0.8027577773151916 1.9171670725469174 chr6 171115067 145944659 0.8529036136835337 15.600564180223252 chr7 159138663 123869993 0.7783777409264774 11.229271183699076 chr8 146364022 121299014 0.828748843756152 3.5472381164472644 chr9 141213431 103650780 0.7340008614336408 23.65617219835972 chr10 135534747 123335120 0.9099889344243215 17.954274449390407 chr11 135006516 110454353 0.8181409036583094 7.788717432704161 chr12 133851895 101894925 0.7612512695468375 1.7786997604157273 chr13 115169878 73402902 0.6373446188768213 1.543612007253979 chr14 107349540 68302905 0.6362663966701674 1.728343178592525 chr15 102531392 63260207 0.6169837916567055 1.5562003926278893 chr16 90354753 77594214 0.8587729081612342 14.104874160217898 chr17 81195210 53498112 0.6588826114249843 8.8711600106603 chr18 78077248 69882786 0.8950467362784098 19.567497648729702 chr19 59128983 27744525 0.46922039907231283 7.073238095457285 chr20 63025520 47901932 0.7600402503620756 2.4231428771717796 chr21 48129895 29947588 0.6222242537616174 3.323958196372471 chr22 51304566 20284333 0.39537091104132915 1.311266546470975 chrMT 16571 2270236 137.00054311749443 79.90932068405488 chrX 155270560 72950301 0.46982699746816137 2.413399517387519 chrY 59373566 25847490 0.4353366614361684 9.86516874062664