BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094124.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 = 511,912 number of mapped reads = 490,131 (95.75%) number of supplementary alignments = 3,847 (0.75%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 245,964 number of mapped paired reads (second in pair) = 244,167 number of mapped paired reads (both in pair) = 487,408 number of mapped paired reads (singletons) = 2,723 number of mapped bases = 72,668,061 bp number of sequenced bases = 72,606,065 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 491,141 duplication rate = 49.88% >>>>>>> Insert size mean insert size = 7,388.9037 std insert size = 574,440.5862 median insert size = 233 >>>>>>> Mapping quality mean mapping quality = 11.6478 >>>>>>> ACTG content number of A's = 19,994,937 bp (27.54%) number of C's = 15,322,914 bp (21.1%) number of T's = 21,037,342 bp (28.97%) number of G's = 16,250,103 bp (22.38%) number of N's = 769 bp (0%) GC percentage = 43.49% >>>>>>> Mismatches and indels general error rate = 0.0166 number of mismatches = 1,166,174 number of insertions = 26,659 mapped reads with insertion percentage = 5.38% number of deletions = 52,528 mapped reads with deletion percentage = 10.49% homopolymer indels = 65.29% >>>>>>> Coverage mean coverageData = 0.0235X std coverageData = 42.3556X 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 10915 4.3791265017550346E-5 0.02529688346987043 chr2 243199373 706434 0.0029047525546046535 2.4544880951611 chr3 198022430 19648 9.922108318739448E-5 0.062280162658756064 chr4 191154276 8031 4.2013185203348526E-5 0.019231791252397334 chr5 180915260 9342 5.1637435117413536E-5 0.03751742138790697 chr6 171115067 3478 2.032550412407576E-5 0.008503734442956807 chr7 159138663 4992 3.136886980130027E-5 0.009602495116897704 chr8 146364022 6212 4.2442124199074004E-5 0.013887890510667574 chr9 141213431 1183 8.37739010816896E-6 0.00398276835282546 chr10 135534747 11392 8.405224676444041E-5 0.034231934458324106 chr11 135006516 49582 3.672563478343519E-4 0.6497536733856883 chr12 133851895 4767 3.561398962637025E-5 0.01889656003636872 chr13 115169878 2881 2.501522142795011E-5 0.01189697967440225 chr14 107349540 108285 0.001008714150055976 1.1665543264719769 chr15 102531392 2512 2.4499813676576245E-5 0.009462185504241688 chr16 90354753 1124 1.2439854713564433E-5 0.004976834316424838 chr17 81195210 1722 2.1208147623486658E-5 0.00593803430947272 chr18 78077248 1597 2.0454102070810694E-5 0.005736104703323515 chr19 59128983 4441 7.510699110113224E-5 0.02593567825029391 chr20 63025520 1626 2.5799073137357693E-5 0.00570314337936216 chr21 48129895 803 1.6684017282813518E-5 0.005696802978395882 chr22 51304566 1141 2.223973593305516E-5 0.006603170628278244 chrMT 16571 71373080 4307.107597610283 17790.431981996637 chrX 155270560 331832 0.0021371211645014997 1.524369773577139 chrY 59373566 1041 1.7533055029910112E-5 0.009267128323903013