[ensembl-dev] multiple stops in Taestivum annotation [MIPS v2.1, Ensembl v22]

Wed Apr 30 23:08:01 BST 2014

Dear Ensembl team,

I am currently working with a GFF3 annotation of Triticum aestivum (MIPS
v2.1, Ensembl v22).

ftp://ftp.ensemblgenomes.org/pub/plants/release-22/gff3/triticum_aestivum/Triticum_aestivum.IWGSP1.22.gff3.gz

In our study, we are examining single nucleotide polymorphism variants in
wheat and their effect on protein coding regions using SNPeff 3.5d (build
2014-03-05)

I see a warning message from SNPeff
"WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS" in 17,834 genes. Below are 10
examples of genes that have this warning and 10 that do not.

Do you know what might be causing such warning? Or refer me to someone who
can help?

Thank you in advance.

Best wishes,

Ksenia

-- 
Ksenia Krasileva, PhD

Post Doctoral Scholar
USDA NIFA Fellowship
The Dubcovsky Lab

Department of Plant Sciences
University of California, Davis
124 Robbins Hall
Davis, CA 95616
krasileva at ucdavis.edu

SNPeff data:

10 examples without warnings:
IWGSC_CSS_5BS_scaff_1487662     672     Kronos381       G       A
40.0    Pass
 seed_avail=Kronos381;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G280||Traes_5BS_38DA1CBC61.E1|||transcript:Traes_5BS_38DA1CBC61.2|1|1)
IWGSC_CSS_5BS_scaff_1537048     1688    Kronos244       C       T
40.0    Pass
 seed_avail=Kronos244;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A58V||CDS:Traes_5BS_B2CD001D1.2|||transcript:Traes_5BS_B2CD001D1.2|2|1)
IWGSC_CSS_5BS_scaff_1537048     1718    Kronos439       C       T
40.0    Pass
 seed_avail=Kronos439;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A68V||CDS:Traes_5BS_B2CD001D1.2|||transcript:Traes_5BS_B2CD001D1.2|2|1)
IWGSC_CSS_5BS_scaff_1646558     3136    Kronos684       G       A
40.0    Pass
 seed_avail=Kronos684;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T115||Traes_5BS_E2116F66A.E1|||transcript:Traes_5BS_E2116F66A.1|1|1)
IWGSC_CSS_5BS_scaff_168385      2625    Kronos2646      G       A
40.0    Pass
 seed_avail=Kronos2646;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E18K||Traes_5BS_91BD3E004.E1|||transcript:Traes_5BS_91BD3E004.1|1|1)
IWGSC_CSS_5BS_scaff_168385      2666    Kronos390       C       T
40.0    Pass
 seed_avail=Kronos390;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A31||Traes_5BS_91BD3E004.E1|||transcript:Traes_5BS_91BD3E004.1|1|1)
IWGSC_CSS_5BS_scaff_168385      2714    Kronos166       G       A
40.0    Pass
 seed_avail=Kronos166;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E47||Traes_5BS_91BD3E004.E1|||transcript:Traes_5BS_91BD3E004.1|1|1)
IWGSC_CSS_5BS_scaff_1712494     1012    Kronos447       C       T
40.0    Pass
 seed_avail=Kronos447;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Agg|G681R||Traes_5BS_6004CA039.E3|||transcript:Traes_5BS_6004CA039.1|1|1)
IWGSC_CSS_5BS_scaff_1712494     2037    Kronos2214      G       A
40.0    Pass
 seed_avail=Kronos2214;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S339F||Traes_5BS_6004CA039.E3|||transcript:Traes_5BS_6004CA039.1|1|1)
IWGSC_CSS_5BS_scaff_1712494     2086    Kronos199       G       A
40.0    Pass
 seed_avail=Kronos199;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P323S||Traes_5BS_6004CA039.E3|||transcript:Traes_5BS_6004CA039.1|1|1)

10 Examples with warnings:
IWGSC_CSS_1BS_scaff_1134305     892     Kronos2092      G       A
40.0    Pass
 seed_avail=Kronos2092;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V123I||Traes_1BS_9AD3B3BE2.E22|||transcript:Traes_1BS_9AD3B3BE2.1|4|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),SPLICE_SITE_REGION(LOW|||||Traes_1BS_9AD3B3BE2.E22|||transcript:Traes_1BS_9AD3B3BE2.1|4|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)
IWGSC_CSS_1BS_scaff_1134305     5997    Kronos2711      C       T
40.0    Pass
 seed_avail=Kronos2711;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A806V||Traes_1BS_9AD3B3BE2.E22|||transcript:Traes_1BS_9AD3B3BE2.1|18|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)
IWGSC_CSS_1BS_scaff_1260855     1972    Kronos375       G       A
40.0    Pass
 seed_avail=Kronos375;EFF=SYNONYMOUS_CODING(LOW|SILENT|cgG/cgA|R266||Traes_1BS_91DEF138E.E1|||transcript:Traes_1BS_91DEF138E.1|6|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)
IWGSC_CSS_1BS_scaff_1280056     767     Kronos166       C       T
40.0    Pass
 seed_avail=Kronos166;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N93||Traes_1BS_984B78A41.E3|||transcript:Traes_1BS_984B78A41.1|3|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)
IWGSC_CSS_1BS_scaff_1420918     702     Kronos209       G       A
40.0    Pass
 seed_avail=Kronos209;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gAg|G138E||Traes_1BS_4073CE3DB.E34|||transcript:Traes_1BS_4073CE3DB.1|1|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)
IWGSC_CSS_1BS_scaff_1420918     871     Kronos166       G       A
40.0    Pass
 seed_avail=Kronos166;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R194||Traes_1BS_4073CE3DB.E34|||transcript:Traes_1BS_4073CE3DB.1|1|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)
IWGSC_CSS_1BS_scaff_1420918     912     Kronos209       G       A
40.0    Pass
 seed_avail=Kronos209;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gAa|G208E||Traes_1BS_4073CE3DB.E34|||transcript:Traes_1BS_4073CE3DB.1|1|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)
IWGSC_CSS_1BS_scaff_1420918     5050    Kronos2553      G       A
40.0    Pass
 seed_avail=Kronos2553;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V692I||Traes_1BS_4073CE3DB.E34|||transcript:Traes_1BS_4073CE3DB.1|11|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),UPSTREAM(MODIFIER||1659|||Traes_1BS_587F929ED.E1|||transcript:Traes_1BS_587F929ED.1||1)
IWGSC_CSS_1BS_scaff_1912213     607     Kronos910       G       A
40.0    Pass
 seed_avail=Kronos910;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S59N||Traes_1BS_0039045F7.E21|||transcript:Traes_1BS_0039045F7.2|1|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)
IWGSC_CSS_1BS_scaff_1975885     313     Kronos684       G       A
40.0    Pass
 seed_avail=Kronos684;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Aga|G25R||Traes_1BS_CC1B13C13.E32|||transcript:Traes_1BS_CC1B13C13.1|1|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)

-- 
Ksenia Krasileva, PhD

Post Doctoral Scholar
USDA NIFA Fellowship
The Dubcovsky Lab

Department of Plant Sciences
University of California, Davis
124 Robbins Hall
Davis, CA 95616
krasileva at ucdavis.edu
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SNPeff data:

10 examples without warnings:
IWGSC_CSS_5BS_scaff_1487662     672     Kronos381       G       A       40.0    Pass    seed_avail=Kronos381;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G280||Traes_5BS_38DA1CBC61.E1|||transcript:Traes_5BS_38DA1CBC61.2|1|1)
IWGSC_CSS_5BS_scaff_1537048     1688    Kronos244       C       T       40.0    Pass    seed_avail=Kronos244;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A58V||CDS:Traes_5BS_B2CD001D1.2|||transcript:Traes_5BS_B2CD001D1.2|2|1)
IWGSC_CSS_5BS_scaff_1537048     1718    Kronos439       C       T       40.0    Pass    seed_avail=Kronos439;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A68V||CDS:Traes_5BS_B2CD001D1.2|||transcript:Traes_5BS_B2CD001D1.2|2|1)
IWGSC_CSS_5BS_scaff_1646558     3136    Kronos684       G       A       40.0    Pass    seed_avail=Kronos684;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T115||Traes_5BS_E2116F66A.E1|||transcript:Traes_5BS_E2116F66A.1|1|1)
IWGSC_CSS_5BS_scaff_168385      2625    Kronos2646      G       A       40.0    Pass    seed_avail=Kronos2646;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E18K||Traes_5BS_91BD3E004.E1|||transcript:Traes_5BS_91BD3E004.1|1|1)
IWGSC_CSS_5BS_scaff_168385      2666    Kronos390       C       T       40.0    Pass    seed_avail=Kronos390;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A31||Traes_5BS_91BD3E004.E1|||transcript:Traes_5BS_91BD3E004.1|1|1)
IWGSC_CSS_5BS_scaff_168385      2714    Kronos166       G       A       40.0    Pass    seed_avail=Kronos166;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E47||Traes_5BS_91BD3E004.E1|||transcript:Traes_5BS_91BD3E004.1|1|1)
IWGSC_CSS_5BS_scaff_1712494     1012    Kronos447       C       T       40.0    Pass    seed_avail=Kronos447;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Agg|G681R||Traes_5BS_6004CA039.E3|||transcript:Traes_5BS_6004CA039.1|1|1)
IWGSC_CSS_5BS_scaff_1712494     2037    Kronos2214      G       A       40.0    Pass    seed_avail=Kronos2214;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S339F||Traes_5BS_6004CA039.E3|||transcript:Traes_5BS_6004CA039.1|1|1)
IWGSC_CSS_5BS_scaff_1712494     2086    Kronos199       G       A       40.0    Pass    seed_avail=Kronos199;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P323S||Traes_5BS_6004CA039.E3|||transcript:Traes_5BS_6004CA039.1|1|1)

10 Examples with warnings:
IWGSC_CSS_1BS_scaff_1134305     892     Kronos2092      G       A       40.0    Pass    seed_avail=Kronos2092;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V123I||Traes_1BS_9AD3B3BE2.E22|||transcript:Traes_1BS_9AD3B3BE2.1|4|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),SPLICE_SITE_REGION(LOW|||||Traes_1BS_9AD3B3BE2.E22|||transcript:Traes_1BS_9AD3B3BE2.1|4|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)
IWGSC_CSS_1BS_scaff_1134305     5997    Kronos2711      C       T       40.0    Pass    seed_avail=Kronos2711;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A806V||Traes_1BS_9AD3B3BE2.E22|||transcript:Traes_1BS_9AD3B3BE2.1|18|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)
IWGSC_CSS_1BS_scaff_1260855     1972    Kronos375       G       A       40.0    Pass    seed_avail=Kronos375;EFF=SYNONYMOUS_CODING(LOW|SILENT|cgG/cgA|R266||Traes_1BS_91DEF138E.E1|||transcript:Traes_1BS_91DEF138E.1|6|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)
IWGSC_CSS_1BS_scaff_1280056     767     Kronos166       C       T       40.0    Pass    seed_avail=Kronos166;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N93||Traes_1BS_984B78A41.E3|||transcript:Traes_1BS_984B78A41.1|3|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)
IWGSC_CSS_1BS_scaff_1420918     702     Kronos209       G       A       40.0    Pass    seed_avail=Kronos209;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gAg|G138E||Traes_1BS_4073CE3DB.E34|||transcript:Traes_1BS_4073CE3DB.1|1|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)
IWGSC_CSS_1BS_scaff_1420918     871     Kronos166       G       A       40.0    Pass    seed_avail=Kronos166;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R194||Traes_1BS_4073CE3DB.E34|||transcript:Traes_1BS_4073CE3DB.1|1|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)
IWGSC_CSS_1BS_scaff_1420918     912     Kronos209       G       A       40.0    Pass    seed_avail=Kronos209;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gAa|G208E||Traes_1BS_4073CE3DB.E34|||transcript:Traes_1BS_4073CE3DB.1|1|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)
IWGSC_CSS_1BS_scaff_1420918     5050    Kronos2553      G       A       40.0    Pass    seed_avail=Kronos2553;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V692I||Traes_1BS_4073CE3DB.E34|||transcript:Traes_1BS_4073CE3DB.1|11|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),UPSTREAM(MODIFIER||1659|||Traes_1BS_587F929ED.E1|||transcript:Traes_1BS_587F929ED.1||1)
IWGSC_CSS_1BS_scaff_1912213     607     Kronos910       G       A       40.0    Pass    seed_avail=Kronos910;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S59N||Traes_1BS_0039045F7.E21|||transcript:Traes_1BS_0039045F7.2|1|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)
IWGSC_CSS_1BS_scaff_1975885     313     Kronos684       G       A       40.0    Pass    seed_avail=Kronos684;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Aga|G25R||Traes_1BS_CC1B13C13.E32|||transcript:Traes_1BS_CC1B13C13.1|1|1|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)