ACTACAAACTACAA 123

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Traits

123

Report Name ACTACAAACTACAA
Trait Name 123
Data release 20170531
CeNDR version 1.2.8
cegwas version v1.01 @2c21292 [2018-02-22]
Report version v2
Strains for trait "123" 240
Traits 1
Status complete
Submitted 2018-05-10   02:05:28 UTC
Started 2018-05-10   02:05:33 UTC
Completed 2018-05-10   03:05:07 UTC
Duration 30m 33s
Log View Log
Report Mode public
Share http://www.elegansvariation.org/report/actacaaactacaa/123

Log

####-##-## ##:##:## Task ID: debfb213-0742-4d49-a755-db1c59cb43bf
2018-05-10 02:05:33 Session info ------------------------------------------------------------------
2018-05-10 02:05:33 Packages ----------------------------------------------------------------------
2018-05-10 03:05:07 [I 180510 03:14:07 run:135] <trait:debfb213-0742-4d49-a755-db1c59cb43bf>
2018-05-10 03:05:07 Fetching Task: ACTACAAACTACAA - 123
2018-05-10 03:05:07 $ECS_CONTAINER_METADATA_FILE
2018-05-10 03:05:07 ── Attaching packages ─────────────────────────────────────── tidyverse 1.2.1 ──
2018-05-10 03:05:07 ✔ ggplot2 2.2.1 ✔ purrr 0.2.4
2018-05-10 03:05:07 ✔ tibble 1.4.2 ✔ dplyr 0.7.4
2018-05-10 03:05:07 ✔ tidyr 0.8.0 ✔ stringr 1.3.0
2018-05-10 03:05:07 ✔ readr 1.1.1 ✔ forcats 0.2.0
2018-05-10 03:05:07 ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
2018-05-10 03:05:07 ✖ dplyr::filter() masks stats::filter()
2018-05-10 03:05:07 ✖ dplyr::lag() masks stats::lag()
2018-05-10 03:05:07 Loading required package: methods
2018-05-10 03:05:07 Attaching package: ‘jsonlite’
2018-05-10 03:05:07 The following object is masked from ‘package:purrr’:
2018-05-10 03:05:07 flatten
2018-05-10 03:05:07 Session info ------------------------------------------------------------------
2018-05-10 03:05:07 setting value
2018-05-10 03:05:07 version R version 3.4.3 (2017-11-30)
2018-05-10 03:05:07 system x86_64, linux-gnu
2018-05-10 03:05:07 ui X11
2018-05-10 03:05:07 language (EN)
2018-05-10 03:05:07 collate en_US.UTF-8
2018-05-10 03:05:07 tz UTC
2018-05-10 03:05:07 date 2018-05-10
2018-05-10 03:05:07 Packages ----------------------------------------------------------------------
2018-05-10 03:05:07 package * version date source
2018-05-10 03:05:07 assertthat 0.2.0 2017-04-11 CRAN (R 3.4.3)
2018-05-10 03:05:07 aws.s3 * 0.3.3 2017-06-14 CRAN (R 3.4.3)
2018-05-10 03:05:07 aws.signature 0.3.5 2017-07-01 CRAN (R 3.4.3)
2018-05-10 03:05:07 base * 3.4.3 2017-11-30 local
2018-05-10 03:05:07 base64enc 0.1-3 2015-07-28 CRAN (R 3.4.3)
2018-05-10 03:05:07 bindr 0.1 2016-11-13 CRAN (R 3.4.3)
2018-05-10 03:05:07 bindrcpp 0.2 2017-06-17 CRAN (R 3.4.3)
2018-05-10 03:05:07 broom 0.4.3 2017-11-20 CRAN (R 3.4.3)
2018-05-10 03:05:07 cegwas * 1.01 2018-02-22 Github (Andersenlab/cegwas@2c21292)
2018-05-10 03:05:07 cellranger 1.1.0 2016-07-27 CRAN (R 3.4.3)
2018-05-10 03:05:07 cli 1.0.0 2017-11-05 CRAN (R 3.4.3)
2018-05-10 03:05:07 codetools 0.2-15 2016-10-05 CRAN (R 3.4.2)
2018-05-10 03:05:07 colorspace 1.3-2 2016-12-14 CRAN (R 3.4.3)
2018-05-10 03:05:07 compiler 3.4.3 2017-11-30 local
2018-05-10 03:05:07 crayon 1.3.4 2017-09-16 CRAN (R 3.4.3)
2018-05-10 03:05:07 datasets * 3.4.3 2017-11-30 local
2018-05-10 03:05:07 devtools * 1.13.4 2017-11-09 CRAN (R 3.4.3)
2018-05-10 03:05:07 digest 0.6.15 2018-01-28 CRAN (R 3.4.3)
2018-05-10 03:05:07 dplyr * 0.7.4 2017-09-28 CRAN (R 3.4.3)
2018-05-10 03:05:07 forcats * 0.2.0 2017-01-23 CRAN (R 3.4.3)
2018-05-10 03:05:07 foreach 1.4.4 2017-12-12 CRAN (R 3.4.3)
2018-05-10 03:05:07 foreign 0.8-69 2017-06-21 CRAN (R 3.4.2)
2018-05-10 03:05:07 ggplot2 * 2.2.1 2016-12-30 CRAN (R 3.4.3)
2018-05-10 03:05:07 glue 1.2.0 2017-10-29 CRAN (R 3.4.3)
2018-05-10 03:05:07 graphics * 3.4.3 2017-11-30 local
2018-05-10 03:05:07 grDevices * 3.4.3 2017-11-30 local
2018-05-10 03:05:07 grid 3.4.3 2017-11-30 local
2018-05-10 03:05:07 gtable 0.2.0 2016-02-26 CRAN (R 3.4.3)
2018-05-10 03:05:07 haven 1.1.1 2018-01-18 CRAN (R 3.4.3)
2018-05-10 03:05:07 hms 0.4.1 2018-01-24 CRAN (R 3.4.3)
2018-05-10 03:05:07 httr 1.3.1 2017-08-20 CRAN (R 3.4.3)
2018-05-10 03:05:07 iterators 1.0.9 2017-12-12 CRAN (R 3.4.3)
2018-05-10 03:05:07 jsonlite * 1.5 2017-06-01 CRAN (R 3.4.3)
2018-05-10 03:05:07 lattice 0.20-35 2017-03-25 CRAN (R 3.4.2)
2018-05-10 03:05:07 lazyeval 0.2.1 2017-10-29 CRAN (R 3.4.3)
2018-05-10 03:05:07 lubridate 1.7.2 2018-02-06 CRAN (R 3.4.3)
2018-05-10 03:05:07 magrittr 1.5 2014-11-22 CRAN (R 3.4.3)
2018-05-10 03:05:07 memoise * 1.1.0 2017-04-21 CRAN (R 3.4.3)
2018-05-10 03:05:07 methods * 3.4.3 2017-11-30 local
2018-05-10 03:05:07 mnormt 1.5-5 2016-10-15 CRAN (R 3.4.3)
2018-05-10 03:05:07 modelr 0.1.1 2017-07-24 CRAN (R 3.4.3)
2018-05-10 03:05:07 munsell 0.4.3 2016-02-13 CRAN (R 3.4.3)
2018-05-10 03:05:07 nlme 3.1-131 2017-02-06 CRAN (R 3.4.2)
2018-05-10 03:05:07 parallel 3.4.3 2017-11-30 local
2018-05-10 03:05:07 pillar 1.1.0 2018-01-14 CRAN (R 3.4.3)
2018-05-10 03:05:07 pkgconfig 2.0.1 2017-03-21 CRAN (R 3.4.3)
2018-05-10 03:05:07 plyr 1.8.4 2016-06-08 CRAN (R 3.4.3)
2018-05-10 03:05:07 psych 1.7.8 2017-09-09 CRAN (R 3.4.3)
2018-05-10 03:05:07 purrr * 0.2.4 2017-10-18 CRAN (R 3.4.3)
2018-05-10 03:05:07 R6 2.2.2 2017-06-17 CRAN (R 3.4.3)
2018-05-10 03:05:07 Rcpp 0.12.15 2018-01-20 CRAN (R 3.4.3)
2018-05-10 03:05:07 readr * 1.1.1 2017-05-16 CRAN (R 3.4.3)
2018-05-10 03:05:07 readxl 1.0.0 2017-04-18 CRAN (R 3.4.3)
2018-05-10 03:05:07 reshape2 1.4.3 2017-12-11 CRAN (R 3.4.3)
2018-05-10 03:05:07 rlang 0.1.6 2017-12-21 CRAN (R 3.4.3)
2018-05-10 03:05:07 rstudioapi 0.7 2017-09-07 CRAN (R 3.4.3)
2018-05-10 03:05:07 rvest 0.3.2 2016-06-17 CRAN (R 3.4.3)
2018-05-10 03:05:07 scales 0.5.0 2017-08-24 CRAN (R 3.4.3)
2018-05-10 03:05:07 stats * 3.4.3 2017-11-30 local
2018-05-10 03:05:07 stringi 1.1.6 2017-11-17 CRAN (R 3.4.3)
2018-05-10 03:05:07 stringr * 1.3.0 2018-02-19 cran (@1.3.0)
2018-05-10 03:05:07 tibble * 1.4.2 2018-01-22 CRAN (R 3.4.3)
2018-05-10 03:05:07 tidyr * 0.8.0 2018-01-29 CRAN (R 3.4.3)
2018-05-10 03:05:07 tidyverse * 1.2.1 2017-11-14 CRAN (R 3.4.3)
2018-05-10 03:05:07 tools 3.4.3 2017-11-30 local
2018-05-10 03:05:07 utils * 3.4.3 2017-11-30 local
2018-05-10 03:05:07 withr 2.1.1 2017-12-19 CRAN (R 3.4.3)
2018-05-10 03:05:07 xml2 1.2.0 2018-01-24 CRAN (R 3.4.3)
2018-05-10 03:05:07 Parsed with column specification:
2018-05-10 03:05:07 cols(
2018-05-10 03:05:07 ISOTYPE = col_character(),
2018-05-10 03:05:07 STRAIN = col_character(),
2018-05-10 03:05:07 `123` = col_double()
2018-05-10 03:05:07 )
2018-05-10 03:05:07 Joining, by = c("strain", "isotype")
2018-05-10 03:05:07 Adding missing grouping variables: `trait`
2018-05-10 03:05:07 There were 50 or more warnings (use warnings() to see the first 50)
2018-05-10 03:05:07 Warning message:
2018-05-10 03:05:07 Removed 14978 rows containing missing values (geom_rect).
2018-05-10 03:05:07 Warning message:
2018-05-10 03:05:07 Removed 14978 rows containing missing values (geom_rect).
2018-05-10 03:05:07 R exited with code 0
2018-05-10 03:05:07 Uploading data/mapping.tsv.gz to reports/v2/debfb213-0742-4d49-a755-db1c59cb43bf/mapping.tsv.gz
2018-05-10 03:05:07 Uploading data/Manhattan.png to reports/v2/debfb213-0742-4d49-a755-db1c59cb43bf/Manhattan.png
2018-05-10 03:05:07 Uploading data/mapping.Rdata to reports/v2/debfb213-0742-4d49-a755-db1c59cb43bf/mapping.Rdata

Phenotype

Unfortunately your phenotype was not significantly associated with genetic variation present in the C. elegans population. This could be due to noisy trait data - have you performed heritability analysis for your phenotype using our heritability strain panel? If you have and the heritability was found to be high for this trait, the trait might not have reached statistical significance because it is highly complex and more strains need to be phenotyped.

If you have phenotyped the entire 152 wild-isolate collection, you can patiently wait for more isolates to be added to the collection, or generate an F2 recombinant inbred line (RIL) panel generated between strains with high and low phenotypes.

Manhattan

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. The red line corresponds to the Bonferroni-corrected significance threshold, which is defined as .




1.2.8