BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094017.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 32,038 number of mapped reads = 1,024 (3.2%) number of supplementary alignments = 35 (0.11%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 404 number of mapped paired reads (second in pair) = 620 number of mapped paired reads (both in pair) = 698 number of mapped paired reads (singletons) = 326 number of mapped bases = 77,841 bp number of sequenced bases = 76,190 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 655 duplication rate = 23.27% >>>>>>> Insert size mean insert size = 298,489.3642 std insert size = 5,453,409.6231 median insert size = 36 >>>>>>> Mapping quality mean mapping quality = 7.5061 >>>>>>> ACTG content number of A's = 14,903 bp (19.56%) number of C's = 12,463 bp (16.36%) number of T's = 13,338 bp (17.51%) number of G's = 35,486 bp (46.58%) number of N's = 0 bp (0%) GC percentage = 62.93% >>>>>>> Mismatches and indels general error rate = 0.0404 number of mismatches = 2,804 number of insertions = 59 mapped reads with insertion percentage = 4.3% number of deletions = 131 mapped reads with deletion percentage = 12.5% homopolymer indels = 31.58% >>>>>>> Coverage mean coverageData = 0X std coverageData = 0.032X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% 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 210 8.425254836175514E-7 0.001048472434051602 chr2 243199373 24147 9.928890729500359E-5 0.09388694241012265 chr3 198022430 879 4.438891089256909E-6 0.0026013247651974327 chr4 191154276 1261 6.5967658500090265E-6 0.0056179045298680895 chr5 180915260 513 2.835581697199009E-6 0.00215349088967275 chr6 171115067 1894 1.1068575276308076E-5 0.0055611543599729685 chr7 159138663 657 4.128475051974013E-6 0.002649343112331449 chr8 146364022 2257 1.5420456264859954E-5 0.025963038200795648 chr9 141213431 5895 4.1745320953217265E-5 0.030724047771742296 chr10 135534747 457 3.371829070518721E-6 0.0023507970518885954 chr11 135006516 1747 1.2940116164467202E-5 0.006348354135283519 chr12 133851895 819 6.1187030635614085E-6 0.0032108978885726177 chr13 115169878 2228 1.9345336112972177E-5 0.007385468898422833 chr14 107349540 216 2.0121185428461083E-6 0.0015741291800355696 chr15 102531392 783 7.636685552849999E-6 0.003909356961929784 chr16 90354753 89 9.850062895971836E-7 9.92474341915091E-4 chr17 81195210 842 1.0370069860032383E-5 0.004710979901448188 chr18 78077248 164 2.1004838695134336E-6 0.0014493030937250317 chr19 59128983 77 1.302237855164869E-6 0.0011411556245058943 chr20 63025520 333 5.283574018905358E-6 0.0029298116903627306 chr21 48129895 396 8.227734550428584E-6 0.0037030829347673463 chr22 51304566 31 6.042347186018492E-7 7.773251272808915E-4 chrMT 16571 1507 0.09094200712087382 0.42918077265445737 chrX 155270560 30321 1.9527848679105686E-4 0.06951249169507953 chrY 59373566 118 1.987416420297208E-6 0.0019681904934614144