BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926968.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 24,095,590 number of mapped reads = 23,711,901 (98.41%) number of supplementary alignments = 174,137 (0.72%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,914,035 number of mapped paired reads (second in pair) = 11,797,866 number of mapped paired reads (both in pair) = 23,508,316 number of mapped paired reads (singletons) = 203,585 number of mapped bases = 2,273,275,045 bp number of sequenced bases = 2,271,589,460 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,357,031 duplication rate = 4.36% >>>>>>> Insert size mean insert size = 75,627.1107 std insert size = 2,709,171.9054 median insert size = 183 >>>>>>> Mapping quality mean mapping quality = 53.6459 >>>>>>> ACTG content number of A's = 645,455,666 bp (28.41%) number of C's = 466,326,245 bp (20.53%) number of T's = 651,895,161 bp (28.7%) number of G's = 507,746,829 bp (22.35%) number of N's = 165,559 bp (0.01%) GC percentage = 42.88% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 21,764,012 number of insertions = 362,643 mapped reads with insertion percentage = 1.5% number of deletions = 1,187,345 mapped reads with deletion percentage = 4.88% homopolymer indels = 52.82% >>>>>>> Coverage mean coverageData = 0.7343X std coverageData = 3.0324X There is a 29.81% of reference with a coverageData >= 1X There is a 16.45% of reference with a coverageData >= 2X There is a 9.34% of reference with a coverageData >= 3X There is a 5.69% of reference with a coverageData >= 4X There is a 3.57% of reference with a coverageData >= 5X There is a 2.31% of reference with a coverageData >= 6X There is a 1.53% of reference with a coverageData >= 7X There is a 1.03% of reference with a coverageData >= 8X There is a 0.71% of reference with a coverageData >= 9X There is a 0.49% of reference with a coverageData >= 10X There is a 0.35% 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 0.03% 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 0.01% 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 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% 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 186570601 0.7485261230302009 3.653422352878379 chr2 243199373 201341125 0.8278850496871963 5.0513201409761646 chr3 198022430 149834582 0.7566545971585138 1.624761445208251 chr4 191154276 138728816 0.725742677082463 2.3376643137219686 chr5 180915260 134163313 0.7415809644802765 1.6033121148641547 chr6 171115067 133743712 0.7816010264017254 2.0957338025761287 chr7 159138663 121125187 0.7611298518952619 2.46914250367237 chr8 146364022 105709388 0.7222361517231332 1.8643733972909167 chr9 141213431 97221081 0.6884690805366807 4.270441668636142 chr10 135534747 112023880 0.8265325496199141 4.3336384154417065 chr11 135006516 107599995 0.7969985315375444 2.8550774278520334 chr12 133851895 103565955 0.7737354409513589 1.7628247181071328 chr13 115169878 67012906 0.5818613960848339 1.4409840008728694 chr14 107349540 69668496 0.6489873733972218 1.574328593697094 chr15 102531392 71587559 0.6982013762185146 1.6542326396915534 chr16 90354753 78462729 0.8683851861119027 6.067140798734217 chr17 81195210 58962256 0.7261789950417026 2.9961082074096925 chr18 78077248 58597626 0.7505083427120792 4.16727295455027 chr19 59128983 36492541 0.6171684197578707 2.331708693611967 chr20 63025520 56100509 0.890123699098397 1.9329958697370293 chr21 48129895 28238894 0.5867225349234608 2.6080980648017626 chr22 51304566 28905666 0.5634131277906141 1.5681908915004765 chrMT 16571 387229 23.367871582885765 16.493578315536066 chrX 155270560 123517327 0.7954974014391395 1.9374035951370305 chrY 59373566 3713672 0.06254756535930485 1.7818278085148713