BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038472.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 = 13,254,238 number of mapped reads = 12,895,791 (97.3%) number of supplementary alignments = 257,101 (1.94%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,535,928 number of mapped paired reads (second in pair) = 6,359,863 number of mapped paired reads (both in pair) = 12,701,528 number of mapped paired reads (singletons) = 194,263 number of mapped bases = 1,841,731,505 bp number of sequenced bases = 1,840,247,775 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,168,965 duplication rate = 9.46% >>>>>>> Insert size mean insert size = 73,207.6 std insert size = 2,528,433.7493 median insert size = 253 >>>>>>> Mapping quality mean mapping quality = 53.7335 >>>>>>> ACTG content number of A's = 546,607,887 bp (29.7%) number of C's = 368,280,326 bp (20.01%) number of T's = 546,545,249 bp (29.7%) number of G's = 378,775,866 bp (20.58%) number of N's = 38,447 bp (0%) GC percentage = 40.6% >>>>>>> Mismatches and indels general error rate = 0.0164 number of mismatches = 28,964,981 number of insertions = 387,013 mapped reads with insertion percentage = 2.8% number of deletions = 712,704 mapped reads with deletion percentage = 5.29% homopolymer indels = 46.79% >>>>>>> Coverage mean coverageData = 0.5949X std coverageData = 10.8643X There is a 25.79% of reference with a coverageData >= 1X There is a 13.29% of reference with a coverageData >= 2X There is a 6.5% of reference with a coverageData >= 3X There is a 3.6% of reference with a coverageData >= 4X There is a 1.94% of reference with a coverageData >= 5X There is a 1.11% of reference with a coverageData >= 6X There is a 0.64% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.24% of reference with a coverageData >= 9X There is a 0.16% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% 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 0.02% 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 0.01% 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 122098077 0.48986067320570487 14.944226715305938 chr2 243199373 183516797 0.7545940383653867 13.337330651639155 chr3 198022430 112593615 0.5685902097050319 1.349036180053885 chr4 191154276 103048272 0.5390843153307228 13.167476988324463 chr5 180915260 107925301 0.59655167286607 1.4790755235537598 chr6 171115067 125729822 0.7347676870558687 12.063510314447322 chr7 159138663 135253877 0.849912110924295 10.318943071067842 chr8 146364022 74816728 0.5111688444855663 3.0185236242024254 chr9 141213431 76807459 0.5439104372444573 17.647384807993582 chr10 135534747 82781107 0.6107740548628463 22.565443643978167 chr11 135006516 93631492 0.6935331328748606 7.628198441528721 chr12 133851895 58584113 0.4376786223310473 1.1496687809746113 chr13 115169878 108997756 0.9464085392189093 1.755225154574997 chr14 107349540 34842859 0.32457390129477964 1.1729389196144397 chr15 102531392 32486201 0.3168415093789032 0.90185875904014 chr16 90354753 74060933 0.8196683687464676 14.470627862225903 chr17 81195210 42311982 0.5211142627748607 5.536913418353122 chr18 78077248 31386919 0.40199827483673606 14.588554739445595 chr19 59128983 22770019 0.3850906585016015 8.183544833373823 chr20 63025520 56892880 0.9026959238099107 4.175546602552201 chr21 48129895 17528927 0.36420039977232443 5.725190889634903 chr22 51304566 10259866 0.1999795885613768 0.8288667357666667 chrMT 16571 4033820 243.42646792589463 137.68952260965148 chrX 155270560 93226290 0.6004118874820829 2.250906695041949 chrY 59373566 36146393 0.6087960591755597 18.769719465227755