BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926910.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 = 32,697,328 number of mapped reads = 27,543,768 (84.24%) number of supplementary alignments = 493,118 (1.51%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,833,221 number of mapped paired reads (second in pair) = 13,710,547 number of mapped paired reads (both in pair) = 27,115,036 number of mapped paired reads (singletons) = 428,732 number of mapped bases = 2,534,568,238 bp number of sequenced bases = 2,532,668,760 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,098,643 duplication rate = 6.03% >>>>>>> Insert size mean insert size = 191,358.1604 std insert size = 4,317,693.8987 median insert size = 189 >>>>>>> Mapping quality mean mapping quality = 52.877 >>>>>>> ACTG content number of A's = 712,920,948 bp (28.15%) number of C's = 507,259,788 bp (20.03%) number of T's = 720,873,739 bp (28.46%) number of G's = 591,391,335 bp (23.35%) number of N's = 222,950 bp (0.01%) GC percentage = 43.38% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 26,428,755 number of insertions = 409,067 mapped reads with insertion percentage = 1.46% number of deletions = 1,319,882 mapped reads with deletion percentage = 4.67% homopolymer indels = 52.27% >>>>>>> Coverage mean coverageData = 0.8187X std coverageData = 3.2268X There is a 33.52% of reference with a coverageData >= 1X There is a 18.11% of reference with a coverageData >= 2X There is a 10.32% of reference with a coverageData >= 3X There is a 6.31% of reference with a coverageData >= 4X There is a 4.01% of reference with a coverageData >= 5X There is a 2.63% of reference with a coverageData >= 6X There is a 1.76% of reference with a coverageData >= 7X There is a 1.2% of reference with a coverageData >= 8X There is a 0.83% of reference with a coverageData >= 9X There is a 0.59% of reference with a coverageData >= 10X There is a 0.42% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.22% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.09% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% 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 0.02% 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 0.01% 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% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 210866438 0.8460016554983829 2.712595556520479 chr2 243199373 218271606 0.8975006938031868 3.8292150059239654 chr3 198022430 170847200 0.8627669097889568 1.8049719975628085 chr4 191154276 147746866 0.7729194925255033 1.8701366443570038 chr5 180915260 151039128 0.8348611830754354 1.7023455531141078 chr6 171115067 143450118 0.8383254643496706 1.7099685824051667 chr7 159138663 130716073 0.8213973307039786 1.8806197577560912 chr8 146364022 128210343 0.8759689795898066 1.9099634072025373 chr9 141213431 107844955 0.7637018252180277 2.851779451389099 chr10 135534747 129110995 0.9526043900757051 10.882589182131957 chr11 135006516 120405803 0.8918517903239574 2.0348394818628828 chr12 133851895 113547272 0.8483053004217833 1.792368742544715 chr13 115169878 74942599 0.6507135398719447 1.5126020940505205 chr14 107349540 75492857 0.7032434139913408 1.6086437172914918 chr15 102531392 76581505 0.7469078835874968 1.730996807052824 chr16 90354753 82535387 0.9134592731386251 4.52237265565601 chr17 81195210 69332751 0.8539019851047863 1.978550302236849 chr18 78077248 66315245 0.8493542830812889 2.81804940579905 chr19 59128983 44694760 0.7558858233702412 2.001955184053428 chr20 63025520 61283971 0.9723675584112594 1.9860513000370457 chr21 48129895 32263113 0.6703341654911152 2.2158040027033867 chr22 51304566 34512117 0.6726909452854547 1.7157161632201676 chrMT 16571 34001 2.051837547522781 2.0468420859842245 chrX 155270560 140725233 0.9063226989069918 1.8707715441247257 chrY 59373566 3797902 0.06396621014813225 1.3395170999155412