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=2.944e^-6)
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

2019 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

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Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
2R	5979369	2R_5979369_SNP [dm3] 2R_10091864_SNP [dm6]	T	C	5.185e^-7	0.259	SYNONYMOUS_CODING CG2269 INTRON CG2269
2R	5979385	2R_5979385_SNP [dm3] 2R_10091880_SNP [dm6]	A	G	5.185e^-7	0.259	NON_SYNONYMOUS_CODING CG2269 INTRON CG2269
3R	25045750	3R_25045750_DEL [dm3] 3R_29220028_DEL [dm6]	GTG	AA	5.585e^-7	0.259	UPSTREAM Ef1gamma DOWNSTREAM CR31044 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_run mE1_TFBS_Ubx
2R	5979670	2R_5979670_SNP [dm3] 2R_10092165_SNP [dm6]	C	T	6.111e^-7	0.259	INTRON CG2269
2R	12380058	2R_12380058_SNP [dm3] 2R_16492553_SNP [dm6]	C	T	7.393e^-7	0.259	SYNONYMOUS_CODING S-Lap8	TF binding site BDTNP1_TFBS_prd mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	5979659	2R_5979659_SNP [dm3] 2R_10092154_SNP [dm6]	G	A	9.733e^-7	0.259	INTRON CG2269
2L	4248350	2L_4248350_SNP [dm3] 2L_4248350_SNP [dm6]	G	T	1.079e^-6	0.259	INTRON CR44059
3R	20440363	3R_20440363_SNP [dm3] 3R_24614641_SNP [dm6]	G	T	1.112e^-6	0.259	INTRON mld
X	1606967	X_1606967_DEL [dm3] X_1712934_DEL [dm6]	TCT	GG	1.291e^-6	0.267	INTERGENIC
2L	12502753	2L_12502753_SNP [dm3] 2L_12502753_SNP [dm6]	G	A	1.501e^-6	0.279	INTRON bun
2R	12380049	2R_12380049_SNP [dm3] 2R_16492544_SNP [dm6]	C	A	2.692e^-6	0.336	SYNONYMOUS_CODING S-Lap8	TF binding site BDTNP1_TFBS_prd mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	3335838	3L_3335838_SNP [dm3] 3L_3335838_SNP [dm6]	C	T	2.763e^-6	0.336	UPSTREAM CG14969 & 1 other DOWNSTREAM Drsl6 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	13783484	3L_13783484_SNP [dm3] 3L_13790384_SNP [dm6]	A	G	2.776e^-6	0.336	INTRON bru-3
3R	25469172	3R_25469172_SNP [dm3] 3R_29643450_SNP [dm6]	A	C	3.720e^-6	0.336	INTRON Dop1R2	TF binding site mE1_TFBS_chinmo
2R	12378211	2R_12378211_SNP [dm3] 2R_16490706_SNP [dm6]	T	C	3.918e^-6	0.336	UPSTREAM S-Lap8 INTERGENIC
X	1607716	X_1607716_SNP [dm3] X_1713683_SNP [dm6]	G	C	4.076e^-6	0.336	INTERGENIC
2R	1381457	2R_1381457_SNP [dm3] 2R_5493952_SNP [dm6]	T	G	4.091e^-6	0.336	NON_SYNONYMOUS_CODING CG30440
2R	12380079	2R_12380079_SNP [dm3] 2R_16492574_SNP [dm6]	A	G	4.163e^-6	0.336	SYNONYMOUS_CODING S-Lap8	TF binding site BDTNP1_TFBS_prd mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	22291347	3R_22291347_SNP [dm3] 3R_26465625_SNP [dm6]	A	G	4.656e^-6	0.336	START_GAINED CG5455 UTR_5_PRIME CG5455 INTRON CG5455
3L	20175380	3L_20175380_SNP [dm3] 3L_20182280_SNP [dm6]	T	G	4.745e^-6	0.336	INTRON CG42674	TF binding site BDTNP1_TFBS_twi
3R	25460457	3R_25460457_SNP [dm3] 3R_29634735_SNP [dm6]	C	G	5.344e^-6	0.336	INTRON Dop1R2
2R	12379906	2R_12379906_SNP [dm3] 2R_16492401_SNP [dm6]	C	T	5.497e^-6	0.336	SYNONYMOUS_CODING S-Lap8	TF binding site BDTNP1_TFBS_prd mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	12380853	2R_12380853_SNP [dm3] 2R_16493348_SNP [dm6]	C	G	5.497e^-6	0.336	DOWNSTREAM S-Lap8 INTERGENIC	TF binding site BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	12381105	2R_12381105_INS [dm3] 2R_16493600_INS [dm6]	T	TTT	5.497e^-6	0.336	DOWNSTREAM S-Lap8 INTERGENIC	TF binding site BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	12381155	2R_12381155_SNP [dm3] 2R_16493650_SNP [dm6]	C	A	5.497e^-6	0.336	DOWNSTREAM S-Lap8 INTERGENIC	TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA
3R	9656852	3R_9656852_SNP [dm3] 3R_13831130_SNP [dm6]	G	A	5.719e^-6	0.336	INTERGENIC	TF binding site BDTNP1_TFBS_twi
3R	9656854	3R_9656854_SNP [dm3] 3R_13831132_SNP [dm6]	A	G	5.719e^-6	0.336	INTERGENIC	TF binding site BDTNP1_TFBS_twi
X	1607708	X_1607708_SNP [dm3] X_1713675_SNP [dm6]	C	A	5.738e^-6	0.336	INTERGENIC
2L	4248403	2L_4248403_INS [dm3] 2L_4248403_INS [dm6]	G	GGG	5.968e^-6	0.336	INTRON CR44059
2L	8166521	2L_8166521_SNP [dm3] 2L_8166521_SNP [dm6]	A	T	6.148e^-6	0.336	INTRON Piezo	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA
2R	5978419	2R_5978419_INS [dm3] 2R_10090914_INS [dm6]	C	CC	6.239e^-6	0.336	INTRON CG2269
2R	5977950	2R_5977950_SNP [dm3] 2R_10090445_SNP [dm6]	T	G	6.330e^-6	0.336	INTRON CG2269
2R	5978006	2R_5978006_SNP [dm3] 2R_10090501_SNP [dm6]	T	A	6.330e^-6	0.336	INTRON CG2269
2R	5978397	2R_5978397_SNP [dm3] 2R_10090892_SNP [dm6]	T	C	6.330e^-6	0.336	INTRON CG2269
3R	25460307	3R_25460307_SNP [dm3] 3R_29634585_SNP [dm6]	T	C	6.480e^-6	0.336	INTRON Dop1R2
2L	17936393	2L_17936393_SNP [dm3] 2L_17936393_SNP [dm6]	T	G	6.504e^-6	0.336	INTERGENIC
X	1606960	X_1606960_SNP [dm3] X_1712927_SNP [dm6]	T	C	7.100e^-6	0.357	INTERGENIC
2L	17936426	2L_17936426_SNP [dm3] 2L_17936426_SNP [dm6]	T	C	7.793e^-6	0.376	INTERGENIC
2R	17315862	2R_17315862_SNP [dm3] 2R_21428357_SNP [dm6]	C	G	7.882e^-6	0.376	INTRON Sdc
2L	18291841	2L_18291841_SNP [dm3] 2L_18291841_SNP [dm6]	C	T	8.090e^-6	0.376	UPSTREAM CR44696 & 2 others EXON CR44693
X	1611956	X_1611956_SNP [dm3] X_1717923_SNP [dm6]	T	C	9.240e^-6	0.419	INTERGENIC	TF binding site mE1_TFBS_chinmo
X	1606963	X_1606963_SNP [dm3] X_1712930_SNP [dm6]	C	A	9.542e^-6	0.423	INTERGENIC
2R	18748484	2R_18748484_SNP [dm3] 2R_22860961_SNP [dm6]	T	A	1.015e^-5	0.428	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
X	1605934	X_1605934_SNP [dm3] X_1711901_SNP [dm6]	C	G	1.048e^-5	0.428	INTERGENIC	TF binding site mE1_TFBS_chinmo
3R	13757149	3R_13757149_INS [dm3] 3R_17931427_INS [dm6]	A	AGTA	1.066e^-5	0.428	UPSTREAM cpo INTRON cpo
2L	17936412	2L_17936412_SNP [dm3] 2L_17936412_SNP [dm6]	A	G	1.080e^-5	0.428	INTERGENIC
2L	17936427	2L_17936427_SNP [dm3] 2L_17936427_SNP [dm6]	G	T	1.080e^-5	0.428	INTERGENIC
2R	5979705	2R_5979705_SNP [dm3] 2R_10092200_SNP [dm6]	A	T	1.127e^-5	0.43	INTRON CG2269
X	1605040	X_1605040_SNP [dm3] X_1711007_SNP [dm6]	C	A	1.132e^-5	0.43	UPSTREAM CG3795 INTERGENIC	TF binding site mE1_TFBS_chinmo
3L	23395146	3L_23395146_INS [dm3] 3L_23402046_INS [dm6]	A	CGGCAAAAGATGCAATTGAA...	1.195e^-5	0.445	INTERGENIC
2L	17936436	2L_17936436_SNP [dm3] 2L_17936436_SNP [dm6]	C	T	1.260e^-5	0.46	INTERGENIC
X	1605041	X_1605041_SNP [dm3] X_1711008_SNP [dm6]	A	G	1.315e^-5	0.468	UPSTREAM CG3795 INTERGENIC	TF binding site mE1_TFBS_chinmo
3L	18103113	3L_18103113_SNP [dm3] 3L_18110013_SNP [dm6]	G	A	1.339e^-5	0.468	SYNONYMOUS_CODING mus304 UPSTREAM CG5147	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3R	9656859	3R_9656859_DEL [dm3] 3R_13831137_DEL [dm6]	TGTAT	T	1.362e^-5	0.468	INTERGENIC	TF binding site BDTNP1_TFBS_twi
3R	25046166	3R_25046166_SNP [dm3] 3R_29220444_SNP [dm6]	C	T	1.387e^-5	0.468	SYNONYMOUS_CODING Ef1gamma DOWNSTREAM CR31044	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_run mE1_TFBS_sens mE1_TFBS_Ubx
2L	18298775	2L_18298775_SNP [dm3] 2L_18298775_SNP [dm6]	T	G	1.413e^-5	0.468	INTERGENIC	TF binding site mE1_TFBS_inv
2L	14930352	2L_14930352_SNP [dm3] 2L_14930352_SNP [dm6]	G	C	1.434e^-5	0.468	UTR_3_PRIME CG3491 INTRON CG42313
3R	21568715	3R_21568715_SNP [dm3] 3R_25742993_SNP [dm6]	A	C	1.465e^-5	0.47	INTRON LpR1
X	1607705	X_1607705_SNP [dm3] X_1713672_SNP [dm6]	A	G	1.490e^-5	0.47	INTERGENIC
3L	20088124	3L_20088124_SNP [dm3] 3L_20095024_SNP [dm6]	C	A	1.600e^-5	0.479	INTERGENIC
3R	10043131	3R_10043131_SNP [dm3] 3R_14217409_SNP [dm6]	A	G	1.610e^-5	0.479	DOWNSTREAM CG31326 INTRON CG9649
2L	17936539	2L_17936539_INS [dm3] 2L_17936539_INS [dm6]	A	GCTGTCGGCCTGCTG...	1.654e^-5	0.479	INTERGENIC
2R	13138839	2R_13138839_SNP [dm3] 2R_17251334_SNP [dm6]	G	A	1.660e^-5	0.479	INTRON mbl
2L	17936374	2L_17936374_SNP [dm3] 2L_17936374_SNP [dm6]	A	G	1.666e^-5	0.479	INTERGENIC
X	1605933	X_1605933_SNP [dm3] X_1711900_SNP [dm6]	A	G	1.682e^-5	0.479	INTERGENIC	TF binding site mE1_TFBS_chinmo
X	5418719	X_5418719_SNP [dm3] X_5524686_SNP [dm6]	G	T	1.698e^-5	0.479	UPSTREAM snoRNA:Psi28S-3342 INTERGENIC	TF binding site BDTNP1_TFBS_z mE1_TFBS_bab1 mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_kn
2R	14176198	2R_14176198_DEL [dm3] 2R_18288693_DEL [dm6]	CTC	C	1.769e^-5	0.487	UTR_5_PRIME sbb UPSTREAM CG14502 INTRON sbb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
2R	17315817	2R_17315817_SNP [dm3] 2R_21428312_SNP [dm6]	T	C	1.800e^-5	0.487	INTRON Sdc
3L	2994853	3L_2994853_SNP [dm3] 3L_2994853_SNP [dm6]	T	C	1.806e^-5	0.487	UPSTREAM CG2113 INTERGENIC
3R	22723082	3R_22723082_SNP [dm3] 3R_26897360_SNP [dm6]	C	T	1.861e^-5	0.495	INTRON T48	regulatory region REDfly_CRMs
X	5418503	X_5418503_SNP [dm3] X_5524470_SNP [dm6]	T	G	1.927e^-5	0.496	UPSTREAM snoRNA:Psi28S-3342 INTERGENIC	TF binding site BDTNP1_TFBS_z mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_kn
3L	1098678	3L_1098678_SNP [dm3] 3L_1098678_SNP [dm6]	T	G	1.984e^-5	0.496	INTRON bab1	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
2R	12380127	2R_12380127_SNP [dm3] 2R_16492622_SNP [dm6]	C	T	1.997e^-5	0.496	SYNONYMOUS_CODING S-Lap8	TF binding site BDTNP1_TFBS_prd mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	15914852	2R_15914852_SNP [dm3] 2R_20027347_SNP [dm6]	A	G	2.011e^-5	0.496	INTERGENIC
3L	13783444	3L_13783444_SNP [dm3] 3L_13790344_SNP [dm6]	A	G	2.024e^-5	0.496	INTRON bru-3
2L	17936474	2L_17936474_SNP [dm3] 2L_17936474_SNP [dm6]	G	T	2.025e^-5	0.496	INTERGENIC
X	10820394	X_10820394_SNP [dm3] X_10926361_SNP [dm6]	G	A	2.101e^-5	0.504	DOWNSTREAM v INTERGENIC	TF binding site BDTNP1_TFBS_dl
X	9934213	X_9934213_SNP [dm3] X_10040180_SNP [dm6]	A	G	2.112e^-5	0.504	NON_SYNONYMOUS_CODING Cht6 INTRON Cht6
X	1607086	X_1607086_SNP [dm3] X_1713053_SNP [dm6]	C	A	2.223e^-5	0.524	INTERGENIC
X	1606961	X_1606961_INS [dm3] X_1712928_INS [dm6]	G	GAG	2.264e^-5	0.524	INTERGENIC
3L	3335935	3L_3335935_SNP [dm3] 3L_3335935_SNP [dm6]	T	C	2.280e^-5	0.524	UPSTREAM CG14969 & 2 others DOWNSTREAM Drsl6 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
3R	4824664	3R_4824664_SNP [dm3] 3R_8998942_SNP [dm6]	A	G	2.393e^-5	0.542	DOWNSTREAM CG11977 INTRON CG31100
X	8508370	X_8508370_SNP [dm3] X_8614337_SNP [dm6]	T	C	2.416e^-5	0.542	INTERGENIC
X	11266212	X_11266212_SNP [dm3] X_11372179_SNP [dm6]	T	G	2.465e^-5	0.542	UPSTREAM dlg1 INTRON dlg1
2R	5979693	2R_5979693_INS [dm3] 2R_10092188_INS [dm6]	A	ATGCTTTGTTGAA...	2.477e^-5	0.542	INTRON CG2269
2L	18434844	2L_18434844_SNP [dm3] 2L_18434844_SNP [dm6]	A	G	2.644e^-5	0.565	DOWNSTREAM CR44488 INTERGENIC
2L	7853585	2L_7853585_SNP [dm3] 2L_7853585_SNP [dm6]	A	G	2.649e^-5	0.565	INTRON CG14535	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	12538262	2R_12538262_SNP [dm3] 2R_16650757_SNP [dm6]	A	T	2.673e^-5	0.565	UTR_3_PRIME gprs DOWNSTREAM Amyrel INTRON gprs
X	5415233	X_5415233_SNP [dm3] X_5521200_SNP [dm6]	T	A	2.753e^-5	0.573	INTERGENIC
X	7911034	X_7911034_SNP [dm3] X_8017001_SNP [dm6]	T	C	2.880e^-5	0.573	INTRON Tbh
2R	19346120	2R_19346120_SNP [dm3] 2R_23458597_SNP [dm6]	T	C	2.882e^-5	0.573	SYNONYMOUS_CODING skpF INTRON CG43795	TF binding site mE1_TFBS_chinmo
3L	12541416	3L_12541416_SNP [dm3] 3L_12548316_SNP [dm6]	G	A	2.929e^-5	0.573	INTRON sowah
3R	18215850	3R_18215850_SNP [dm3] 3R_22390128_SNP [dm6]	C	G	2.956e^-5	0.573	UTR_5_PRIME CG7059 UPSTREAM CG5379 & 1 other INTRON CG7059	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
X	5418881	X_5418881_INS [dm3] X_5524848_INS [dm6]	C	CTTCT	2.965e^-5	0.573	UPSTREAM snoRNA:Psi28S-3342 INTERGENIC	TF binding site BDTNP1_TFBS_z mE1_TFBS_bab1 mE1_TFBS_h mE1_TFBS_HSA
2R	13138790	2R_13138790_SNP [dm3] 2R_17251285_SNP [dm6]	A	G	3.003e^-5	0.573	INTRON mbl
2L	18260131	2L_18260131_SNP [dm3] 2L_18260131_SNP [dm6]	A	G	3.048e^-5	0.573	DOWNSTREAM CR44901 INTRON CG42750	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	15675421	3L_15675421_SNP [dm3] 3L_15682321_SNP [dm6]	T	A	3.070e^-5	0.573	DOWNSTREAM CG7304 INTRON CG7579
2L	15475771	2L_15475771_INS [dm3] 2L_15475771_INS [dm6]	T	TGT	3.084e^-5	0.573	DOWNSTREAM sna INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
X	8508472	X_8508472_SNP [dm3] X_8614439_SNP [dm6]	C	G	3.092e^-5	0.573	INTERGENIC
X	5418656	X_5418656_SNP [dm3] X_5524623_SNP [dm6]	G	T	3.104e^-5	0.573	UPSTREAM snoRNA:Psi28S-3342 INTERGENIC	TF binding site BDTNP1_TFBS_z mE1_TFBS_bab1 mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_kn

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By genomic position
Variant impact
Gene name

Microbiota_OTU003 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results