1.CHROM : Chromosome
2.POS : Position
3.REF ： Reference allele
4.ALT : Alternative allele
5.wild.AF : wild bulk alternative allele frequency (the same as snp-index)
6.mutant.AF : mutant bulk alternative allele frequency (the same as snp-index)
7.AFD(deltaSNP) : Alternative allele frequency difference (mutant.AF - wild.AF)
8.REF_FRQ : total ref allele coverage of two bulk / total coverage (both refer and allele) of two bulk
9.wild.DP : wild bulk read coverage depth
10.mutant.DP : mutant bulk read coverage depth
11.nSNPs: number of SNPs in a slide window
12.tricubeDeltaSNP: tricube-smoothed statistics of tow bulk snp-index
13.Gprime : G prime value (please read more the G prime method)
14.negLog10Pval : -log10(Pvalue)
15.qvalue : the false discovery rate
16.minDP : minimum read coverage depth of two bulk
17.CI_95 : the two-sided 95% confidence intervals
18.CI_99 : the two-sided 99% confidence intervals
19.Feature ： Variant impact type
20.Gene : Gene ID on this locus
21.Transcript : Transcript ID on this locus



Citation:

QTLseqr:
Mansfeld B.N. and Grumet R, QTLseqr: An R package for bulk segregant analysis with next-generation sequencing The Plant Genome doi:10.3835/plantgenome2018.01.0006

SNPindex and deltaSNP method:

Takagi, H., Abe, A., Yoshida, K., Kosugi, S., Natsume, S., Mitsuoka, C., Uemura, A., Utsushi, H., Tamiru, M., Takuno, S., Innan, H., Cano, L. M., Kamoun, S. and Terauchi, R. (2013), QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant J, 74: 174–183. doi:10.1111/tpj.12105l

G prime method:

Magwene PM, Willis JH, Kelly JK (2011) The Statistics of Bulk Segregant Analysis Using Next Generation Sequencing. PLOS Computational Biology 7(11): e1002255. doi.org/10.1371/journal.pcbi.1002255
