060717.6 CI

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  • Release: 2016-04-08
  • Availabity: Public

Phenotype

Histogram representation of your phenotype Your phenotype is significantly associated with genetic variation present in the C. elegans population!

Manhattan Plot

A genome-wide representation of the association between variation in the C. elegans population and your phenotype. The x-axis corresponds to genomic position with chromosome number indicated as a roman numeral above each box. Dots represent single-nucleotide variants (SNV) present in the C. elegans population. The y-axis corresponds to the level of significance for the association test. Blue dots represent SNVs that are above the defined significance threshold, which is the thick gray line. Red boxes surrounding blue dots represent the QTL genomic region of interest, which we define as plus/minus 50 SNVs from the last signifincant SNV. The default threshold for significance is the Bonferroni-corrected value and is usually around 5.5.

QTL Genomic Region of Interest

Interval Peak Position -log10p V.E. Variants Coding Moderate High
V:1,021-1,503,828 V:82,026 6.04 27.2% - - - -
Moderate and High impact variants are terms used to describe the predicted severity of a variant as assigned by SnpEff. More information regarding the types of variants classified as Moderate or High impact is available in the help section.

Phenotype-by-Genotype


Phenotypic distributions represented as box plots are split by the genotype at the most significant SNV for a given QTL. The phenotype is on the y-axis, and the genotype is on the x-axis. The chromosome and position for the plotted SNV are indicated as roman numerals above each panel. REF refers to the reference N2 genotype, and ALT refers to the alternative variant phenotype. All of the SNVs in our data set are biallelic, so only two classes for any given SNV site exist.

Peak Summary

Switch between peaks below.



  • Peak Interval  V:1021-1503828
  • Peak Position  V:82026
  • Variance Explained  27.2%
Biotype # Genes # Genes w/ variants >=1 Moderate Impact >=1 High Impact # Variants
Total - - - - -
protein_coding - - - - -
pseudogene - - - - -
ncRNA - - - - -
miRNA - - - - -
piRNA - - - - -
tRNA - - - - -
lincRNA - - - - -
rRNA - - - - -
scRNA - - - - -
snoRNA - - - - -
snRNA - - - - -
asRNA - - - - -
Coding - - - - -
Noncoding - - - - -

Numbers listed under Moderate and High Impact correspond to the number of genes within the interval that have at least 1 variant classified as having a moderate or high impact.

Moderate and High impact variants are terms used to describe the predicted severity of a variant as assigned by SnpEff. More information regarding the types of variants classified as Moderate or High impact is available in the help section.

Variants

The table below lists variants, their predicted effects, and their correlation with the phenotype. Only protein coding genes have their variants correlated with phenotype.

Gene Name Wormbase ID Biotype Total Variants Max. Correlation Toggle Variants
srbc-38 WBGene00021707 protein_coding 23 0.445 Variants
cyp-33C11 WBGene00021710 protein_coding 31 0.439 Variants
srbc-37 WBGene00021708 protein_coding 24 0.439 Variants
ugt-29 WBGene00021709 protein_coding 18 0.439 Variants
F31F4.1 WBGene00017957 protein_coding 35 0.43 Variants
srx-5 WBGene00005896 protein_coding 30 0.427 Variants
srj-53 WBGene00005632 protein_coding 19 0.418 Variants
srj-25 WBGene00005613 protein_coding 2 0.413 Variants
srh-2 WBGene00005228 protein_coding 2 0.413 Variants
srx-7 WBGene00005898 protein_coding 8 0.413 Variants
C14C6.6 WBGene00015760 protein_coding 35 0.413 Variants
srt-17 WBGene00018617 protein_coding 2 0.413 Variants
  83 0.413 Variants
CHROM:POS REF/ALT Predicted Effect Annotation Putative Impact Correlation
V:632752 T / C -0.413
V:632773 G / A|C -0.413
V:633082 A / G -0.413
V:857577 G / A -0.413
V:630364 A / G -0.413
V:1022832 A / T -0.413
V:632668 A / G -0.413
V:925881 T / C -0.413
V:616493 G / A -0.4
V:584322 A / G -0.385
V:936849 G / A -0.358
V:1503045 G / C -0.336
V:539311 C / T|A -0.325
V:937344 C / A -0.322
V:585287 G / A -0.305
V:539256 G / A -0.305
V:585269 G / A -0.305
V:585274 A / G -0.305
V:539242 C / T -0.305
V:585293 C / G -0.302
V:584908 C / T -0.302
V:585178 C / T -0.302
V:585299 T / G -0.302
V:630372 G / C -0.302
V:584988 C / A -0.302
V:585198 T / A -0.302
V:583898 T / G -0.302
V:585083 T / C -0.302
V:585202 C / T -0.302
V:584776 T / A -0.302
V:585090 T / A -0.302
V:585208 T / C -0.302
V:584786 A / G -0.302
V:585095 A / G -0.302
V:550564 G / A -0.286
V:548721 C / A -0.286
V:550305 G / A -0.286
V:549619 C / T -0.286
V:549016 T / G -0.286
V:550402 G / T -0.286
V:549938 A / G -0.286
V:549378 A / T -0.286
V:548767 T / A -0.286
V:550329 T / C -0.286
V:549632 T / C -0.286
V:549017 C / G -0.286
V:550433 G / C|T -0.286
V:539292 A / G -0.286
V:549962 C / A|T -0.286
V:549579 A / T -0.286
V:548771 T / A -0.286
V:550345 C / T -0.286
V:549736 C / T -0.286
V:549166 C / T -0.286
V:550498 G / A -0.286
V:539517 A / C -0.286
V:550079 G / A -0.286
V:549581 T / G -0.286
V:548825 C / T -0.286
V:550357 G / A -0.286
V:549851 G / A -0.286
V:549271 C / T -0.286
V:550106 C / G -0.286
V:549614 T / C -0.286
V:548852 C / T -0.286
V:550399 C / G -0.286
V:549875 A / T -0.286
V:549375 T / A -0.286
V:632963 A / T|G -0.28
V:631247 A / G -0.28
V:632935 A / G -0.28
V:632995 A / G -0.28
V:632198 A / G -0.28
V:632938 G / A -0.28
V:630664 A / C -0.28
V:633351 T / G -0.28
V:632640 A / G -0.28
V:632962 A / T|G -0.28
V:630769 C / A -0.28
V:632715 A / T -0.28
V:631066 G / A -0.28
V:632896 T / C -0.28
V:570800 A / G -0.279

ZK488.6 WBGene00022758 protein_coding 25 0.413 Variants
K06H6.5 WBGene00019453 protein_coding 6 0.413 Variants
srp-2 WBGene00005643 protein_coding 3 0.413 Variants
srx-23 WBGene00005914 protein_coding 15 0.413 Variants
srx-21 WBGene00005912 protein_coding 2 0.413 Variants
srj-38 WBGene00005622 protein_coding 3 0.413 Variants
srg-53 WBGene00005210 protein_coding 4 0.413 Variants
srbc-40 WBGene00019242 protein_coding 11 0.413 Variants
srbc-39 WBGene00021706 protein_coding 15 0.413 Variants
R11G11.3 WBGene00020013 protein_coding 25 0.413 Variants
H25P19.1 WBGene00019244 protein_coding 3 0.413 Variants
F31F4.17 WBGene00017963 protein_coding 3 0.413 Variants
arid-1 WBGene00044689 protein_coding 1 0.413 Variants
H24K24.3 WBGene00019240 protein_coding 2 0.413 Variants
cyp-29A3 WBGene00021412 protein_coding 1 0.413 Variants
pals-31 WBGene00018614 protein_coding 1 0.413 Variants
nhr-270 WBGene00020062 protein_coding 1 0.413 Variants
nhr-180 WBGene00017961 protein_coding 1 0.413 Variants
nhr-251 WBGene00022756 protein_coding 2 0.413 Variants
Y50D4C.3 WBGene00021748 protein_coding 2 0.413 Variants
str-262 WBGene00006288 protein_coding 3 0.413 Variants
atg-9 WBGene00020706 protein_coding 1 0.413 Variants
phf-10 WBGene00018013 protein_coding 1 0.413 Variants
kin-33 WBGene00017083 protein_coding 1 0.413 Variants
nhr-252 WBGene00022637 protein_coding 1 0.413 Variants
ergo-1 WBGene00019971 protein_coding 3 0.413 Variants
K09C6.2 WBGene00019556 protein_coding 1 0.413 Variants
C05E4.15 WBGene00206359 protein_coding 1 0.413 Variants
icl-1 WBGene00001564 protein_coding 1 0.413 Variants
mltn-7 WBGene00021449 protein_coding 1 0.413 Variants
nhr-211 WBGene00020152 protein_coding 1 0.413 Variants
ZK6.8 WBGene00022643 protein_coding 1 0.413 Variants
srj-5 WBGene00005593 protein_coding 1 0.413 Variants
R09A1.2 WBGene00019972 protein_coding 1 0.413 Variants
Y50D4B.4 WBGene00021743 protein_coding 4 0.413 Variants
sqv-6 WBGene00005024 protein_coding 1 0.413 Variants
srbc-13 WBGene00019559 protein_coding 1 0.413 Variants
str-238 WBGene00006266 protein_coding 3 0.413 Variants
T02B11.6 WBGene00020157 protein_coding 1 0.413 Variants
K10C9.1 WBGene00019623 protein_coding 1 0.413 Variants
H24K24.2 WBGene00019239 protein_coding 2 0.413 Variants
W03F9.9 WBGene00021003 protein_coding 1 0.413 Variants
R13D11.1 WBGene00020056 protein_coding 2 0.413 Variants
srj-24 WBGene00005612 protein_coding 1 0.413 Variants
flp-34 WBGene00019975 protein_coding 1 0.413 Variants
Y50D4B.6 WBGene00021745 protein_coding 1 0.413 Variants
K09C6.6 WBGene00019560 protein_coding 1 0.413 Variants
F48G7.8 WBGene00018619 protein_coding 4 0.413 Variants
T21H3.5 WBGene00020664 protein_coding 2 0.413 Variants
F33E11.3 WBGene00018011 protein_coding 1 0.413 Variants
srp-1 WBGene00005642 protein_coding 1 0.413 Variants
cfap-36 WBGene00022435 protein_coding 1 0.413 Variants
srh-246 WBGene00005452 protein_coding 2 0.413 Variants
srbc-57 WBGene00019745 protein_coding 1 0.413 Variants
nra-4 WBGene00015344 protein_coding 2 0.413 Variants
Y50D4A.4 WBGene00021738 protein_coding 1 0.413 Variants
pqn-98 WBGene00004177 protein_coding 1 0.408 Variants
Y50D4B.2 WBGene00021741 protein_coding 2 0.405 Variants
dod-19 WBGene00022644 protein_coding 2 0.405 Variants
sri-73 WBGene00005585 protein_coding 10 0.404 Variants
lipl-3 WBGene00020016 protein_coding 8 0.404 Variants
C14C6.8 WBGene00015762 protein_coding 42 0.404 Variants
nstp-7 WBGene00019451 protein_coding 18 0.404 Variants
C14C6.3 WBGene00015757 protein_coding 23 0.404 Variants
nhr-58 WBGene00003648 protein_coding 12 0.404 Variants
C14C6.2 WBGene00015756 protein_coding 7 0.404 Variants
nhr-132 WBGene00003722 protein_coding 14 0.404 Variants
srw-107 WBGene00005854 protein_coding 14 0.404 Variants
srw-108 WBGene00005855 protein_coding 9 0.404 Variants
F41H8.2 WBGene00018313 protein_coding 1 0.404 Variants
F48G7.13 WBGene00018624 protein_coding 1 0.4 Variants
sru-25 WBGene00005688 protein_coding 1 0.399 Variants
nhr-210 WBGene00020015 protein_coding 1 0.399 Variants
nhr-190 WBGene00018622 protein_coding 1 0.396 Variants
F48G7.7 WBGene00018618 protein_coding 2 0.391 Variants
srw-109 WBGene00005856 protein_coding 5 0.387 Variants
wago-10 WBGene00020707 protein_coding 1 0.384 Variants
K09C6.8 WBGene00019562 protein_coding 3 0.367 Variants
C14C6.13 WBGene00015764 protein_coding 15 0.361 Variants
srx-4 WBGene00005895 protein_coding 20 0.353 Variants
K06H6.4 WBGene00019452 protein_coding 26 0.351 Variants
T02B11.10 WBGene00235327 protein_coding 2 0.341 Variants
fbxa-72 WBGene00017962 protein_coding 7 0.338 Variants
fpn-1.2 WBGene00019977 protein_coding 2 0.336 Variants
chil-14 WBGene00019980 protein_coding 1 0.336 Variants
Y75B7AL.2 WBGene00022285 protein_coding 2 0.336 Variants
ges-1 WBGene00001578 protein_coding 1 0.336 Variants
rga-4 WBGene00022286 protein_coding 1 0.336 Variants
nhr-155 WBGene00015758 protein_coding 5 0.33 Variants
srx-22 WBGene00005913 protein_coding 2 0.33 Variants
str-256 WBGene00006282 protein_coding 3 0.323 Variants
srbc-59 WBGene00019981 protein_coding 1 0.322 Variants
K09C6.7 WBGene00019561 protein_coding 4 0.322 Variants
tank-1 WBGene00004053 protein_coding 3 0.306 Variants
K06H6.2 WBGene00019450 protein_coding 14 0.302 Variants
K06H6.1 WBGene00019449 protein_coding 16 0.302 Variants
B0554.4 WBGene00015257 protein_coding 1 0.295 Variants
unc-34 WBGene00006770 protein_coding 1 0.29 Variants
ugt-42 WBGene00017959 protein_coding 1 0.288 Variants
C14C6.5 WBGene00015759 protein_coding 6 0.286 Variants
srx-8 WBGene00005899 protein_coding 5 0.286 Variants
srh-78 WBGene00005299 protein_coding 1 0.282 Variants
F41H8.1 WBGene00018312 protein_coding 1 0.282 Variants
srh-35 WBGene00005258 protein_coding 1 0.281 Variants
nhr-131 WBGene00003721 protein_coding 1 0.281 Variants
nhr-83 WBGene00003673 pseudogene 1 0.279 Variants

Global Distribution

Reference () Alternative ()

Variant

Reference

Tajima's D

Tajima's D is plotted across the most significant QTL genomic region of interest. Tajima's D suggests if a genomic region has an excess or paucity of rare variation. Values close to zero indicate that variation is drifting and not selected. Values less than zero suggest that rare variants are present, which could have arose during a selective sweep, population expansion after a bottleneck, or linkage to a swept allele. Values greater than zero suggest that balancing selection could have occurred or recent population contractions.




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