DGRPool

GWAS results were computed on dm3 genome.

If you want to make an independent analysis with DGRP2 or PLINK2, you can find here prepared input files for this phenotype: DGRP2 results PLINK2 results

Full results

Phenotype distribution and association to known covariates

Shapiro-Wilk test of normality (p-value=8.101e^-3)
Null Hypothesis is rejected (p<=0.05).
Interpretation: NOT NORMAL distribution of this phenotype

We tested for association of this phenotype with 6 known covariates Huang et al., 2014 using both ANOVA and Kruskal-Wallis association tests.

ANOVA test
No significant result.

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1904 significant hits at p-value < 0.001. The 1000 top results are displayed in the table below.

We performed a gene enrichment calculation (Fisher's exact test) of all GWAS-associated genes at p < 0.001. Genesets were taken from two database: the Gene Ontology (GO) and the FlyBase phenotypes. GO enrichment FlyBase phenotype enrichment

Variant impact HIGH MODERATE LOW MODIFIER

Show entries

Search:

Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
X	9686951	X_9686951_SNP [dm3] X_9792918_SNP [dm6]	A	T	4.040e^-6	0.894	INTRON CG32698
X	9686909	X_9686909_INS [dm3] X_9792876_INS [dm6]	T	TT	4.409e^-6	0.894	INTRON CG32698
2L	14530847	2L_14530847_SNP [dm3] 2L_14530847_SNP [dm6]	T	A	5.271e^-6	0.894	UPSTREAM tRNA:G3:35Bd DOWNSTREAM tRNA:G3:35Be INTERGENIC	TF binding site BDTNP1_TFBS_Med mE1_TFBS_cad
X	8665972	X_8665972_SNP [dm3] X_8771939_SNP [dm6]	T	C	5.690e^-6	0.894	INTRON Lim1	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3L	11746616	3L_11746616_SNP [dm3] 3L_11753516_SNP [dm6]	G	A	6.743e^-6	0.894	INTRON CG6024
3R	20039032	3R_20039032_SNP [dm3] 3R_24213310_SNP [dm6]	T	G	7.578e^-6	0.894	INTRON twin	TF binding site BDTNP1_TFBS_twi
X	9686901	X_9686901_DEL [dm3] X_9792868_DEL [dm6]	TTTCTT	T	7.805e^-6	0.894	INTRON CG32698
3L	2830226	3L_2830226_SNP [dm3] 3L_2830226_SNP [dm6]	A	G	7.939e^-6	0.894	INTRON CG43444
X	9686875	X_9686875_SNP [dm3] X_9792842_SNP [dm6]	G	A	7.980e^-6	0.894	INTRON CG32698
3R	26982367	3R_26982367_SNP [dm3] 3R_31156645_SNP [dm6]	T	C	8.706e^-6	0.894	INTRON Gycbeta100B
2R	17028111	2R_17028111_SNP [dm3] 2R_21140606_SNP [dm6]	T	C	8.732e^-6	0.894	UPSTREAM Magi INTRON Magi	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_HSA mE1_TFBS_sens
X	9686820	X_9686820_SNP [dm3] X_9792787_SNP [dm6]	G	T	8.845e^-6	0.894	INTRON CG32698
X	11103244	X_11103244_SNP [dm3] X_11209211_SNP [dm6]	C	T	9.130e^-6	0.894	INTERGENIC
3L	3987329	3L_3987329_SNP [dm3] 3L_3987329_SNP [dm6]	T	C	9.131e^-6	0.894	SYNONYMOUS_CODING scrt	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	6224806	2L_6224806_SNP [dm3] 2L_6224806_SNP [dm6]	C	A	9.186e^-6	0.894	UPSTREAM Ugt37b1 INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2L	4163550	2L_4163550_SNP [dm3] 2L_4163550_SNP [dm6]	T	C	1.112e^-5	0.894	INTERGENIC
3L	4734982	3L_4734982_SNP [dm3] 3L_4734982_SNP [dm6]	T	C	1.142e^-5	0.894	INTRON RhoGEF64C
2L	14900310	2L_14900310_SNP [dm3] 2L_14900310_SNP [dm6]	T	G	1.210e^-5	0.894	INTERGENIC
3L	17502954	3L_17502954_SNP [dm3] 3L_17509854_SNP [dm6]	A	C	1.285e^-5	0.894	INTRON Oatp74D	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	5268217	2R_5268217_SNP [dm3] 2R_9380712_SNP [dm6]	A	C	1.289e^-5	0.894	INTRON CG13954
2L	9731153	2L_9731153_SNP [dm3] 2L_9731153_SNP [dm6]	T	G	1.299e^-5	0.894	DOWNSTREAM CG13116 INTRON Nckx30C	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_HSA
3L	14978400	3L_14978400_SNP [dm3] 3L_14985300_SNP [dm6]	A	T	1.313e^-5	0.894	DOWNSTREAM CG5114 INTRON mnd	TF binding site mE1_TFBS_HSA mE1_TFBS_Kr
2R	18486446	2R_18486446_SNP [dm3] 2R_22598941_SNP [dm6]	A	T	1.337e^-5	0.894	UPSTREAM CG4269 INTRON CG4269
2L	20488836	2L_20488836_SNP [dm3] 2L_20488836_SNP [dm6]	G	T	1.343e^-5	0.894	UPSTREAM CR45359 DOWNSTREAM CR45360 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi
X	4467003	X_4467003_INS [dm3] X_4572970_INS [dm6]	A	AAACACA	1.375e^-5	0.894	INTRON CR32773
X	4467007	X_4467007_SNP [dm3] X_4572974_SNP [dm6]	A	G	1.375e^-5	0.894	INTRON CR32773
2L	14530734	2L_14530734_SNP [dm3] 2L_14530734_SNP [dm6]	T	G	1.408e^-5	0.894	UPSTREAM tRNA:G3:35Bd DOWNSTREAM tRNA:G3:35Be INTERGENIC	TF binding site BDTNP1_TFBS_Med mE1_TFBS_HSA
2L	14900306	2L_14900306_DEL [dm3] 2L_14900306_DEL [dm6]	AA	A	1.456e^-5	0.894	INTERGENIC
2R	12470586	2R_12470586_SNP [dm3] 2R_16583081_SNP [dm6]	C	T	1.504e^-5	0.894	INTRON Cdk4 EXON CR44375	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	6838314	3L_6838314_SNP [dm3] 3L_6845214_SNP [dm6]	A	G	1.551e^-5	0.894	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	1724626	2L_1724626_SNP [dm3] 2L_1724626_SNP [dm6]	C	T	1.575e^-5	0.894	UPSTREAM Rim2 DOWNSTREAM Eno INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Ubx
2L	1724618	2L_1724618_SNP [dm3] 2L_1724618_SNP [dm6]	C	T	1.582e^-5	0.894	UPSTREAM Rim2 DOWNSTREAM Eno INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Ubx
X	11103317	X_11103317_SNP [dm3] X_11209284_SNP [dm6]	T	C	1.779e^-5	0.894	INTERGENIC
2L	7005276	2L_7005276_DEL [dm3] 2L_7005276_DEL [dm6]	CCTGCAAGGAATGATGGCAC...	GTAAATA	1.797e^-5	0.894	INTRON uif
2L	7005429	2L_7005429_SNP [dm3] 2L_7005429_SNP [dm6]	A	T	1.840e^-5	0.894	INTRON uif
3R	11028843	3R_11028843_SNP [dm3] 3R_15203121_SNP [dm6]	C	T	1.851e^-5	0.894	UTR_3_PRIME Spn88Ea DOWNSTREAM CG42542	TF binding site mE1_TFBS_cad
2L	13416092	2L_13416092_SNP [dm3] 2L_13416092_SNP [dm6]	A	C	1.858e^-5	0.894	INTRON CG43850 & 1 other
X	2532640	X_2532640_DEL [dm3] X_2638607_DEL [dm6]	GG	G	1.885e^-5	0.894	INTRON sgg	TF binding site BDTNP1_TFBS_dl
2L	4803086	2L_4803086_SNP [dm3] 2L_4803086_SNP [dm6]	A	G	1.919e^-5	0.894	INTERGENIC
2L	3158308	2L_3158308_SNP [dm3] 2L_3158308_SNP [dm6]	T	A	1.933e^-5	0.894	INTRON Mad	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_Kr
2R	16482705	2R_16482705_SNP [dm3] 2R_20595200_SNP [dm6]	G	A	1.999e^-5	0.894	INTRON bl	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	14680256	2R_14680256_SNP [dm3] 2R_18792751_SNP [dm6]	T	C	2.056e^-5	0.894	SYNONYMOUS_CODING CG15080	TF binding site mE1_TFBS_cad
2R	10814069	2R_10814069_SNP [dm3] 2R_14926564_SNP [dm6]	T	C	2.067e^-5	0.894	UTR_5_PRIME CG10249	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2R	10621287	2R_10621287_SNP [dm3] 2R_14733782_SNP [dm6]	T	G	2.163e^-5	0.907	INTERGENIC
2R	15409784	2R_15409784_SNP [dm3] 2R_19522279_SNP [dm6]	C	T	2.327e^-5	0.907	UTR_3_PRIME sm
2L	5006057	2L_5006057_SNP [dm3] 2L_5006057_SNP [dm6]	T	A	2.359e^-5	0.907	INTRON Rtnl1
2L	16266046	2L_16266046_SNP [dm3] 2L_16266046_SNP [dm6]	T	C	2.455e^-5	0.907	SYNONYMOUS_CODING crp	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	14506237	3L_14506237_SNP [dm3] 3L_14513137_SNP [dm6]	G	A	2.506e^-5	0.907	NON_SYNONYMOUS_CODING bbg	TF binding site mE1_TFBS_bab1
2L	13416265	2L_13416265_SNP [dm3] 2L_13416265_SNP [dm6]	C	A	2.605e^-5	0.907	INTRON CG43850 & 1 other
2L	20546332	2L_20546332_SNP [dm3] 2L_20546332_SNP [dm6]	T	G	2.611e^-5	0.907	INTERGENIC
3L	3987332	3L_3987332_SNP [dm3] 3L_3987332_SNP [dm6]	T	A	2.622e^-5	0.907	SYNONYMOUS_CODING scrt	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	9314246	2L_9314246_SNP [dm3] 2L_9314246_SNP [dm6]	G	A	2.781e^-5	0.907	INTERGENIC
3R	25138858	3R_25138858_SNP [dm3] 3R_29313136_SNP [dm6]	T	A	2.796e^-5	0.907	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_zfh1
3L	6441914	3L_6441914_SNP [dm3] 3L_6448814_SNP [dm6]	A	C	2.814e^-5	0.907	INTRON CG42747
2L	13209737	2L_13209737_SNP [dm3] 2L_13209737_SNP [dm6]	C	T	2.815e^-5	0.907	SYNONYMOUS_CODING Pect
2L	9314245	2L_9314245_SNP [dm3] 2L_9314245_SNP [dm6]	A	G	2.856e^-5	0.907	INTERGENIC
2R	15410066	2R_15410066_SNP [dm3] 2R_19522561_SNP [dm6]	T	G	2.893e^-5	0.907	UTR_3_PRIME sm
2R	15385928	2R_15385928_SNP [dm3] 2R_19498423_SNP [dm6]	T	G	2.955e^-5	0.907	INTRON CG15120	TF binding site mE1_TFBS_cad
X	4444716	X_4444716_SNP [dm3] X_4550683_SNP [dm6]	G	C	3.157e^-5	0.907	SYNONYMOUS_CODING CG11436 DOWNSTREAM CG15912 INTRON CR32773	TF binding site mE1_TFBS_sens
X	9686809	X_9686809_SNP [dm3] X_9792776_SNP [dm6]	T	C	3.322e^-5	0.907	INTRON CG32698
3L	11886013	3L_11886013_SNP [dm3] 3L_11892913_SNP [dm6]	G	T	3.333e^-5	0.907	INTRON CG44837
2L	11088403	2L_11088403_SNP [dm3] 2L_11088403_SNP [dm6]	A	G	3.454e^-5	0.907	SYNONYMOUS_CODING CG16854
2R	3418130	2R_3418130_SNP [dm3] 2R_7530625_SNP [dm6]	G	A	3.488e^-5	0.907	UTR_5_PRIME Drat INTRON Drat	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens
3L	18483976	3L_18483976_SNP [dm3] 3L_18490876_SNP [dm6]	C	A	3.566e^-5	0.907	INTRON AstC-R2
X	9686815	X_9686815_SNP [dm3] X_9792782_SNP [dm6]	T	G	3.611e^-5	0.907	INTRON CG32698
2R	15409776	2R_15409776_SNP [dm3] 2R_19522271_SNP [dm6]	C	T	3.698e^-5	0.907	UTR_3_PRIME sm
3L	2830210	3L_2830210_SNP [dm3] 3L_2830210_SNP [dm6]	G	A	3.806e^-5	0.907	INTRON CG43444
3R	21229670	3R_21229670_SNP [dm3] 3R_25403948_SNP [dm6]	T	C	3.868e^-5	0.907	INTRON Fur1
3L	14059798	3L_14059798_SNP [dm3] 3L_14066698_SNP [dm6]	G	A	3.984e^-5	0.907	SYNONYMOUS_CODING CG32138	TF binding site mE1_TFBS_cad
2L	1724693	2L_1724693_DEL [dm3] 2L_1724693_DEL [dm6]	GCCT	AG	4.094e^-5	0.907	UPSTREAM Rim2 DOWNSTREAM Eno INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Ubx
2R	17372222	2R_17372222_SNP [dm3] 2R_21484717_SNP [dm6]	T	C	4.100e^-5	0.907	SPLICE_SITE_REGION Sara INTRON Sara	TF binding site mE1_TFBS_cad
2R	16872782	2R_16872782_SNP [dm3] 2R_20985277_SNP [dm6]	A	G	4.118e^-5	0.907	INTRON CG15651	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	9686974	X_9686974_SNP [dm3] X_9792941_SNP [dm6]	C	T	4.173e^-5	0.907	INTRON CG32698
3L	2830232	3L_2830232_SNP [dm3] 3L_2830232_SNP [dm6]	T	A	4.191e^-5	0.907	INTRON CG43444
2L	4804254	2L_4804254_SNP [dm3] 2L_4804254_SNP [dm6]	C	A	4.236e^-5	0.907	INTERGENIC
2L	12244720	2L_12244720_SNP [dm3] 2L_12244720_SNP [dm6]	G	T	4.267e^-5	0.907	INTRON aret
2R	11622961	2R_11622961_SNP [dm3] 2R_15735456_SNP [dm6]	T	C	4.298e^-5	0.907	SYNONYMOUS_CODING CG30089 UPSTREAM CG30089	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Mad BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens
2L	12839203	2L_12839203_SNP [dm3] 2L_12839203_SNP [dm6]	C	A	4.417e^-5	0.907	INTERGENIC
2L	12839428	2L_12839428_SNP [dm3] 2L_12839428_SNP [dm6]	C	T	4.423e^-5	0.907	INTERGENIC
3L	10032835	3L_10032835_SNP [dm3] 3L_10039735_SNP [dm6]	A	G	4.513e^-5	0.907	INTRON dpr6	TF binding site BDTNP1_TFBS_dl
X	5552011	X_5552011_SNP [dm3] X_5657978_SNP [dm6]	C	T	4.555e^-5	0.907	INTRON CG42265
2R	7271177	2R_7271177_SNP [dm3] 2R_11383672_SNP [dm6]	G	A	4.561e^-5	0.907	INTRON Sod3	TF binding site BDTNP1_TFBS_hb BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3L	4828593	3L_4828593_SNP [dm3] 3L_4828593_SNP [dm6]	T	C	4.707e^-5	0.907	SYNONYMOUS_CODING Aats-leu DOWNSTREAM CG13708
3L	10032609	3L_10032609_SNP [dm3] 3L_10039509_SNP [dm6]	T	A	4.781e^-5	0.907	INTRON dpr6
3L	10033386	3L_10033386_INS [dm3] 3L_10040286_INS [dm6]	T	TTCAGC	4.781e^-5	0.907	INTRON dpr6	TF binding site BDTNP1_TFBS_dl
3L	10033388	3L_10033388_INS [dm3] 3L_10040288_INS [dm6]	T	TTCA	4.781e^-5	0.907	INTRON dpr6	TF binding site BDTNP1_TFBS_dl
2L	4804253	2L_4804253_SNP [dm3] 2L_4804253_SNP [dm6]	T	C	4.817e^-5	0.907	INTERGENIC
3L	18064306	3L_18064306_SNP [dm3] 3L_18071206_SNP [dm6]	T	C	4.858e^-5	0.907	SYNONYMOUS_CODING CG44005
2R	10013673	2R_10013673_SNP [dm3] 2R_14126168_SNP [dm6]	C	T	4.888e^-5	0.907	INTRON Prosap
3L	2802783	3L_2802783_SNP [dm3] 3L_2802783_SNP [dm6]	C	T	4.917e^-5	0.907	INTRON CG43444
2L	14531019	2L_14531019_SNP [dm3] 2L_14531019_SNP [dm6]	A	G	4.947e^-5	0.907	UPSTREAM tRNA:G3:35Bd & 1 other INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
X	4325119	X_4325119_SNP [dm3] X_4431086_SNP [dm6]	G	C	5.051e^-5	0.907	INTRON CR32773 & 1 other	regulatory region REDfly_CRMs
3L	7728688	3L_7728688_SNP [dm3] 3L_7735588_SNP [dm6]	T	G	5.257e^-5	0.907	INTRON CG32373 & 1 other
2R	16244182	2R_16244182_SNP [dm3] 2R_20356677_SNP [dm6]	C	T	5.347e^-5	0.907	INTERGENIC
X	11103358	X_11103358_SNP [dm3] X_11209325_SNP [dm6]	G	A	5.364e^-5	0.907	INTERGENIC
2R	10889822	2R_10889822_INS [dm3] 2R_15002317_INS [dm6]	T	TAGCT	5.473e^-5	0.907	INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
2R	7231617	2R_7231617_SNP [dm3] 2R_11344112_SNP [dm6]	A	G	5.539e^-5	0.907	DOWNSTREAM alphaTry INTERGENIC
2R	7231635	2R_7231635_SNP [dm3] 2R_11344130_SNP [dm6]	T	A	5.539e^-5	0.907	DOWNSTREAM alphaTry INTERGENIC
2R	7231637	2R_7231637_SNP [dm3] 2R_11344132_SNP [dm6]	C	T	5.539e^-5	0.907	DOWNSTREAM alphaTry INTERGENIC
2R	7231639	2R_7231639_SNP [dm3] 2R_11344134_SNP [dm6]	A	T	5.539e^-5	0.907	DOWNSTREAM alphaTry INTERGENIC

Showing 1 to 100 of 1,000 entries

Previous1 2 3 4 5…10Next

By genomic position
Variant impact
Gene name

pc_Lactobacillaceae phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results