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<HTML>
<HEAD>
<TITLE>
Quality Control Reports
</TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF">
<HR NOSHADE>
<H1>MGI Quality Control Reports</H1>
<HR>
QC reports are generated nightly from the MGD Production Database (unless otherwise noted).
They are intended for internal use only (i.e. not available for public consumption, although they may
be used at times to test reports for <I>future</I> public consumption.)
<HR>
<B>Table of Contents</B>
<UL>
<LI><A HREF="#references">References</A>
<LI><A HREF="#alleles">Alleles</A>
<LI><A HREF="#variants">Allele Variants</A>
<LI><A HREF="#phenoannot">Phenotype and Disease Vocabulary Annotation</A>
<LI><A HREF="#gxd">GXD</A>
<LI><A HREF="#gxdht">GXD HT Experiments</A>
<LI><A HREF="#recomb">Recombinase and Transgenic Reporter Data</A>
<LI><A HREF="#go">GO</A>
<LI><A HREF="#nomenclature">Nomenclature</A>
<LI><A HREF="#strains">Strains</A>
<LI><A HREF="#strainsjax">Strains - JAX</A>
<LI><A HREF="#sequencegroup">Sequence Group</A>
<LI><A HREF="#sequence">Sequence</A>
<LI><A HREF="#homology">Homology</A>
<LI><A HREF="#metrics">Curation Metrics</A>
<LI><A HREF="#dataloads">Data Loads</A>
<LI><A HREF="<!--#include file="includes/ftp_url.html" -->/reports/index.html">Public Reports</A>
</UL>
<HR>
<A NAME="references"><B>References</B></A>
<OL>
<LI><A HREF="/data/reports/qcreports_db/output/BIB_NoAbstract.sql.rpt">References w/ PubMed ID and No Abstract</A> <B>(jeo)</B>
<LI><A HREF="/data/reports/qcreports_db/output/BIB_DupPM_DOI.sql.rpt">References w/ Duplicated PubMed and DOI IDs</A> <B>(jeo)</B>
<LI><A HREF="/data/reports/qcreports_db/output/MRK_BIB_Discard.sql.rpt">MGI Discard References with associated data</A> <B>(jeo, neb)</B>
<LI><A HREF="/data/loads/mgi/littriageload/logs/littriageload.error.shtml">Lit Triage Errors</A> <B>(jeo, neb)</B>
<LI><A HREF="/data/reports/qcreports_db/output/BIB_MissingPDFs.sql.rpt">J#'s missing PDF's</A> <B>(jeo)</B>
<LI><A HREF="/data/reports/qcreports_db/output/WF_SupplementalData.rpt">Supplemental Data Needed</A> <B>(jeo, neb)</B>
<LI><A HREF="/data/reports/qcreports_db/output/BIB_Covid.rpt">Coronaviruas related references</A> <B>(cjb, csmith)</B>
<LI><A HREF="/data/reports/qcreports_db/output/BIB_COVRefTagCounts.rpt">COV reference tag count report</A> <B>(cjb, csmith)</B>
<LI><A HREF="/data/loads/mgi/pdfdownload/logs/noPdfs.log">Missing PDFs from PMC - automated downloads attempted, but could not find a PDF file</A> <B>(jeo, neb)</B>
<LI><A HREF="/data/reports/qcreports_db/output/BIB_MissingDOI.sql.rpt">References Missing DOI number</A> <B>(neb)</B>
<LI><A HREF="/data/reports/qcreports_db/output/BIB_Duplicates.sql">References with Duplicate Titles</A> <B>(cms)</B>
</OL>
<A NAME="alleles"><B>Alleles (csmith, smb, dlb, honda, mnk)</B> </A>
<OL>
<LI><A HREF="/data/reports/qcreports_db/output/MRK_Alleles.sql.rpt">Allele Anomalies</A> <B>(mnk)</B>
<LI><A HREF="/data/reports/qcreports_db/output/ALL_Progress.current.rpt">Allele Progress Report</A> <B>(csmith)</B>
<LI><A HREF="/data/reports/qcreports_db/archive/alleles">Allele Progress Archive</A> <B>(csmith)</B>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_DupGenotype.rpt">Duplicate Genotypes</A> <B>(mnk)</B>
<LI><A HREF="/data/reports/qcreports_db/output/ALL_NoMolMutation.rpt">Alleles that have Molecular Notes but no Molecular Mutation</A> <B>(mnk)</B>
<LI><A HREF="/data/reports/qcreports_db/output/ALL_MolNotesNoMP.rpt">Alleles that have Molecular Notes but no MP Annotations</A> <B>(mnk)</B>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_WildType.sql.rpt">Genotypes where Allele 1 is "wild type"</A> <B>(mnk)</B>
<LI><A HREF="/data/reports/qcreports_db/output/ALL_CellLineProvider.sql.rpt">Mutant ES Cell Line Provider Check</A> <B>(csmith)</B>
<LI><A HREF="/data/reports/qcreports_db/output/PHENO_ImageCheck.sql.rpt">Image Check</A> <B>(monikat)</B>
<LI><A HREF="/data/reports/qcreports_db/output/PHENO_Images.rpt">Phenotype Annotations Requiring Images</A> <B>(monikat)</B>
<LI><A HREF="/data/reports/qcreports_db/output/ALL_GermlineTransmission.sql.rpt">Germline Transmission Checks</A> <B>(mnk)</B>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_AllelePairCheck.sql.rpt">Genotypes where Allele Pairs are associated with different Markers</A> <B>(mnk)</B>
<LI><A HREF="/data/reports/qcreports_db/output/ALL_NoMCL.sql.rpt">Alleles of type Targeted or Gene Trap that have no MCL association</A> <B>(csmith)</B>
<LI><A HREF="/data/reports/qcreports_db/output/ALL_Notes.rpt">Allele Notes with HTML errors</A> <B>(mnk)</B>
<LI><A HREF="/data/reports/qcreports_db/output/ALL_NewAllele.current.rpt">New Allele Report</A> <B>(honda)</B>
<LI><A HREF="/data/reports/qcreports_db/output/ALL_RefCounts.rpt">Number of Allele References By Year</A> <B>(csmith, jason.beckwith@jax.org)</B>
<LI><A HREF="/data/reports/qcreports_db/output/ALL_ExpressedComp.sql.rpt">Allele Missing Expressed Component Attribute</A> <B>(mnk)</B>
<LI><A HREF="/data/reports/qcreports_db/output/ALL_WithdrawnMarker.sql.rpt">Alleles with Withdrawn Markers</A> <B>(mnk)</B>
<LI><A HREF="/data/reports/qcreports_db/archive/alleles">New Allele Archive</A> <B>(honda)</B>
<LI><A HREF="/data/reports/qcreports_db/output/ALL_NoSubType.rpt">Alleles with molecular notes but no attribute</A> <B>(mnk)</B>
<LI><A HREF="/data/reports/qcreports_db/output/ALL_ExpressedSeq.rpt">Alleles with molecular notes and expressed sequence attribute</A> <B>(mnk)</B>
<LI><A HREF="/data/reports/qcreports_db/output/WF_AP_NewAlleleNomenTag.rpt">Review for AP:NewAlleleNomenclature tag</A> <B> (mnk)</B>
<LI><A HREF="/data/reports/qcreports_db/output/ALL_ConditionalNeedsReview.rpt">Genotypes where the conditional flag setting needs review</A> <B>(smb)</B>
<LI><A HREF="/data/reports/qcreports_db/output/WF_AP_Tags.rpt">AP tagged references for curation</A> <B> (mnk)</B>
<LI><A HREF="/data/reports/qcreports_db/output/WF_AP_IndexingNeeded.rpt">AP:Indexing_needed papers with genes</A> <B> (csmith)</B>
<LI><A HREF="/data/reports/qcreports_db/output/ALL_NomenCheck.rpt">Alleles with Potentially Improper Nomenclature in Symbols and Synonyms and Names</A> <B> (anna)</B>
<LI><A HREF="/data/reports/qcreports_db/output/MRK_NonMouseNotInEG.rpt">Non-Mouse Expressed Component/Driver Component whose Marker does not exist in EntrezGene</A> <B>(smb)</B>
<LI><A HREF="/data/reports/qcreports_db/output/ALL_NoDriver.rpt">Allele Missing Driver Relationship</A> <B>(smb)</B>
<LI><A HREF="/data/reports/qcreports_db/output/TAL_dupe_allele.rpt">Duplicated GenTar Targeted Alleles</A> <B>(anna)</B>
<LI><A HREF="/data/reports/qcreports_db/output/TAL_check_superscript.rpt">TAL Allele Superscript Mismatches (excluding Derivative Alleles)</A> <B>(anna)</B>
<LI><A HREF="/data/reports/qcreports_db/output/TAL_multiple_project_ids.rpt">Marker/Allele Superscripts with multiple Project IDs in the TAL input file</A> <B>(anna)</B>
<LI><A HREF="/data/reports/qcreports_db/output/ALL_PM2GeneNoMP.rpt">Papers not in public MGI for genes with no MP annotations</A> <B>(csmith)</B>
</OL>
<A NAME="variants"><B>Allele Variants (laurens)</B> </A>
<OL>
<LI><A HREF="/data/reports/qcreports_db/output/ALL_VariantSeqCoords.genomic">Variants with curated coordinates outside the variants gene</A>
<LI><A HREF="/data/reports/qcreports_db/output/ALL_VariantSeqCoords.transcript">Variants with curated coordinates inconsistent with the length of the transcript sequence</A>
<LI><A HREF="/data/reports/qcreports_db/output/ALL_VariantSeqCoords.protein">Variants with curated coordinates inconsistent with the length of the protein sequence</A>
<LI><A HREF="/data/reports/qcreports_db/output/ALL_VariantSeqAssoc.transcript">Variants where transcript ID not associated with the variants marker or associated with a different marker</A>
<LI><A HREF="/data/reports/qcreports_db/output/ALL_VariantSeqAssoc.protein">Variants where protein ID not associated with the variants marker or associated with a different marker</A>
<LI><A HREF="/data/reports/qcreports_db/output/ALL_VariantCheckComplement.rpt">Variants where the reference or variant transcript sequence is NOT the reverse complement of the reference or variant genomic sequence</A>
<LI><A HREF="/data/reports/qcreports_db/output/ALL_Variant.rpt">Sequence variants associated with phenotypic alleles. Tab-delimited</A>
<LI><A HREF="/data/reports/qcreports_db/output/ALL_Variant.json.rpt">Sequence variants associated with phenotypic alleles. JSON</A>
<LI><A HREF="/data/reports/qcreports_db/output/ALL_VariantCheckRefVarSeq.rpt">Variants where reference and variant sequences are the same.</A>
<LI><A HREF="/data/reports/qcreports_db/output/ALL_VariantCurationActivity.rpt">Variant Curation Activity Report</A> <B>(cbult)</B>
</OL>
<A NAME="phenoannot"><B>Phenotype and Disease Vocabulary Annotation (csmith, smb, dlb, honda, mnk)</B> </A>
<OL>
<LI><A HREF="/data/reports/qcreports_db/output/VOC_MPObsolete.sql.rpt">Genotype Annotations to Obsolete MP Terms</A>
<LI><A HREF="/data/reports/qcreports_db/output/VOC_DOObsolete.sql.rpt">Genotype Annotations to Obsolete DO Terms</A>
<LI><A HREF="/data/reports/qcreports_db/output/VOC_MPDups.sql.rpt">Duplicate MP Annotations</A>
<LI><A HREF="/data/loads/mgi/vocload/OMIM/OMIMtermcheck.current.rpt">OMIM term or ID changes</A>
<LI><A HREF="/data/reports/qcreports_db/output/ALL_MPAnnot.rpt">Total MP Annotations per Gene</A>
<LI><A HREF="/data/reports/qcreports_db/output/VOC_MPNewTerms.rpt">MP Ontology terms added in the last week</A>
<LI><A HREF="/data/reports/qcreports_db/output/MGI_GenoNoMarker.sql.rpt">Genotype Alleles that Contain No Markers</A>
<LI><A HREF="/data/reports/qcreports_db/output/ALL_DONoMP.rpt">Alleles with DO Annotation, but no MP Annotation</A>
<LI><A HREF="/data/reports/qcreports_db/output/VOC_OMIMDOMult.rpt">DO terms that have multiple OMIM xrefs</A>
<LI><A HREF="/data/reports/qcreports_db/output/VOC_OMIMDOObsolete.rpt">Obsolete OMIM terms in DO as xrefs</A>
<LI><A HREF="/data/reports/qcreports_db/output/VOC_DOAnnotNotInSlim.sql.rpt">DO terms not in the DO slim</A>
<LI><A HREF="/data/reports/qcreports_db/output/VOC_DODups.sql.rpt">Duplicate Disease Annotations</A>
</OL>
<A NAME="gxd"><B>GXD (cms, jfinger, ijm, terryh)</B></A>
<OL>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_NotInCache.sql.rpt">GXD Assays missing from GXD Expression Cache Table</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_SpecTheilerAge.rpt">GXD Specimens with incompatible Theiler stages and ages</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_SpecNoAge.sql.rpt">Specimens with incorrect age/age range values</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_SameStructure.rpt">GXD Specimens/Lanes that use the same Structure > 1</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_SpecTheiler.sql.rpt">Specimens annotated to structures of > 1 Theiler Stage or Sex</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_ExpPresNotPres.rpt">Assays in which the same anatomical structure is annotated as having expression both present and absent</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_ChildExpNotParent.rpt">Expression present in child but not parent</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_FullCodeGene.sql.rpt">Full Coded References that contain indexed Genes that have not been full coded</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_FullCodeMissingIndex.sql.rpt">Full Coded References that are missing a Gene in the Index</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_AssayInCacheNotInIndex.rpt">Full coded assays that were not indexed</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_AssayInIndexNotInCache.rpt">Full coded references that contain indexed assays that have not been full coded</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_ProbeAntibody.sql.rpt">Problems with GXD Assay Probes/Antibodies</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_GenotypeRef.sql.rpt">References where GXD and Pheno differ in Genotype</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_References.sql.rpt">Reference where group = GXD, status = 'Routed' or 'Chosen'</A>
<LI><A HREF="/data/reports/qcreports_db/output/BIB_StatusMismatch_GXD.sql.rpt">References with GXD status not matching curated data</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_WithdrawnMarker.rpt">Withdrawn markers with GXD data</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_ImagesUnused.rpt">Unused image panes from full coded references</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_ImageCheck.sql.rpt">GXD Image Check</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_ImageSpecimen.rpt">Image panes annotated to >1 specimens in same assay</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_Images.rpt">Papers Requiring Images</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_LackingImages.rpt">Papers Requiring Permissions</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_ImagePanes.rpt">Panes Lacking Coordinates</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_FullCodeableIndexed.rpt">Indexed-Full-Coded gene list</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_FullCodeable2.rpt">Papers containing genes that are not in the full coded portion of the database</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_FullCodeable.rpt">Markers that have no full coded data</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_EMAPA_Terms.rpt">EMAPA Terms</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_EMAPS_Terms.rpt">EMAPS Terms</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_CellType_Terms.rpt">Cell Type Terms</A>
<LI><A HREF="/data/reports/qcreports_db/output/PRB_CellLine.sql.rpt">Cell Lines</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_Stats.current.rpt">GXD Statistics</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_Triage.sql.current.rpt">GXD Triage (weekly)</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_NonGeneMarkers.rpt">Non-gene markers with GXD annotations</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_NoSequence.rpt">Genes without Sequence with GXD Annotations</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_GenotypeNA.sql.rpt">GXD Annotations to "Not Applicable" Genotype</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_GelBand.sql.rpt">GXD Blot w/ Control = No and Strength = Not Applicable</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_CellLine_Obsolete.sql.rpt">Annotations to obsolete CL terms</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_DupPrimers.sql.rpt">Duplicate Primer Sets used in GXD</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_DuplicateSpecimenLabel.sql.rpt">Duplicate Specimen Labels used in GXD</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_FullCodeableLargeScale.rpt">Full-coded data only from large scale screens</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_FullCodeableAdultSpecs.rpt">Full-coded data only from adult specimens</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_DevBiol.rpt">Dev Biol papers to full code</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_DevDyn.rpt">Dev Dyn papers to full code</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_Development.rpt">Development papers to full code</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_GeneExprPatterns.rpt">Gene Expr Patterns papers to full code</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_EarlyEmbPapers.rpt">Early embryonic expression papers</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_StatsMonthly.rpt">GXD Monthly Statistics by Assay</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_DistinctAge.sql.rpt">Distinct Age, AgeMin, AgeMax</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_GenotypeHemi.sql.rpt">Hemizygous Genotype Check</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_KnockInGene.sql.rpt">GXD Knock Ins where the assayed Gene is not the Gene which is mutated in the Genotype</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_SpecimenTypeConflict.rpt">Specimen Type (Hybridization) Conflict</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_SeqID.rpt">Probes used in GXD Assay w/ Seq IDs/Seq ID Attached to another Marker</A>
<LI><A HREF="/data/reports/qcreports_db/output/PRB_Reference.sql.rpt">Probe/Antigen issues</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_NotRouted.rpt">Papers used by GXD that were Not Routed</A>
<LI><A HREF="/data/reports/qcreports_db/archive/gxd">Archived GXD Reports</A>
</OL>
<A NAME="gxdht"><B>GXD HT Experiments (cms)</B></A>
<OL>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_HTExpCuration.rpt">GXD HT Experiments where Curation State set to Done, but other attributes are Not Curated</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_HTSampleGenotypeNA.rpt">GXD HT Samples whose Relevance = Yes but whose genotype is Not Applicable</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_HTSampleTheilerAge.rpt">GXD HT Samples with incompatible Theiler stages and ages</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_HTSampleNoAge.sql.rpt">GXD HT Samples with incorrect age/age range values</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_HTSampleNoStructure.rpt">GXD HT Samples whose Relevance = Yes but the structure field is null</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_HTOverview.rpt">All GXD HT Experiments</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_HTExpPubMedID.sql.rpt">HT Experiments with PMIDs used by GXD</A>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_HTDistinctAge.sql.rpt">Distinct Age, AgeMin, AgeMax</A>
</OL>
<A NAME="recomb"><B>Recombinase and Transgenic Reporter Data (cms, csmith)</B></A>
<OL>
<LI><A HREF="/data/reports/qcreports_db/output/RECOMB_NotInCache.sql.rpt">Recombinant/Transgenic Assays missing from Cache Table</A>
<LI><A HREF="/data/reports/qcreports_db/output/RECOMB_SpecNoAge.sql.rpt">Recombinant/Transgenic Specimens with incorrect age/age range values</A>
<LI><A HREF="/data/reports/qcreports_db/output/RECOMB_SpecTheiler.sql.rpt">Recombinant/Transgenic Specimens annotated to structures of > 1 Theiler Stage or Sex</A>
<LI><A HREF="/data/reports/qcreports_db/output/RECOMB_SpecTheilerAge.rpt">Recombinant/Transgenic Specimens with incompatible Theiler stages and ages</A>
<LI><A HREF="/data/reports/qcreports_db/output/RECOMB_GenotypeHemi.sql.rpt">Recombinant/Transgenic Hemizygous Genotype Check</A>
<LI><A HREF="/data/reports/qcreports_db/output/RECOMB_SameStructure.rpt">Recombinant/Transgenic Specimens that use the same Structure > 1</A>
<LI><A HREF="/data/reports/qcreports_db/output/RECOMB_ExpPresNotPres.rpt">Signal present and absent in the same structure in the same Recombinant/Transgenic Assay</A>
<LI><A HREF="/data/reports/qcreports_db/output/RECOMB_ChildExpNotParent.rpt">Signal present in child but not parent in the same Recombination/Transgenic Assay</A>
<LI><A HREF="/data/reports/qcreports_db/output/RECOMB_Images.rpt">Recombinase Papers Requiring Images</A>
<LI><A HREF="/data/reports/qcreports_db/output/RECOMB_LackingImages.rpt">Recombinase Papers Requiring Permissions</A>
<LI><A HREF="/data/reports/qcreports_db/output/RECOMB_Reporter.sql.rpt">Tg reporter and RR assays where the assayed Gene is not the Gene which is mutated in the Genotype</A>
<LI><A HREF="/data/reports/qcreports_db/output/RECOMB_ReporterCheck.rpt">Recombinase reporter specimen genotype check</A>
<LI><A HREF="/data/reports/qcreports_db/output/RECOMB_NoDriver.rpt">Recombinase Allele Check</A>
</OL>
<A NAME="go"> <B>GO (dmitrys, krc, ln, csmith)</B></A>
<OL>
<LI><A HREF="/data/reports/qcreports_db/output/MRK_GOUnknown.rpt">QC: All genes with 'unknown' annotations with new indexed literature</A> <B>(dmitrys)</B>
<LI><A HREF="/data/reports/qcreports_db/output/GO_done.mgi">QC: "Done" Genes with Literature</A> <B>(ln)</B>
<LI><A HREF="/data/reports/qcreports_db/output/MRK_GOSymbolChange.sql.rpt">QC: MGI gene symbols that have changed and with GO annotations</A> <B>(ln)</B>
<LI><A HREF="/data/reports/qcreports_db/output/MRK_NoGO_D.html">QC: Genes with no GO Annotations with references with GO status = Indexed but not yet annotated</A> <B>(dmitrys)</B>
<LI><A HREF="/data/reports/qcreports_db/output/MRK_GOIEA.html">QC: Genes with only IEA GO Annotations with references with GO status = Indexed or Chosen but not yet annotated</A> <B>(ln)</B>
<LI><A HREF="/data/reports/qcreports_db/output/GO_MRK_NoGO_Has_Alleles.rpt">QC: Mouse Genes that have Alleles but no GO Annotations</A> <B>(ln)</B>
<LI><A HREF="/data/loads/mgi/goload/input/pubmed.error">QC: GO/invalid pubmedids</A> <B>(ln)</B>
<LI><A HREF="/data/loads/mgi/goload/output/goload.annot.error">QC: GO/obsolete terms/duplicate annotations</A> <B>(ln)</B>
<LI><A HREF="/data/reports/qcreports_db/output/GO_Unannotationed.rpt">QC: Underannotated genes</A> <B>(dmitrys, csmith)</B>
<LI><A HREF="/data/reports/qcreports_db/output/MRK_RatNoGO.sql.rpt">Report: Mouse Genes that have Rat/Human Homologs but no GO Annotations</A> <B>(csmith)</B>
<LI><A HREF="/data/reports/qcreports_db/output/GO_MRK_NoGO.rpt">Report: Mouse Genes with no GO Annotations</A> <B>(csmith)</B>
<LI><A HREF="/data/reports/qcreports_db/output/MRK_GOGold_B.rpt">Report: All Genes with Annotations to IDA, IGI, IMP, IPI</A> <B>(csmith)</B>
<LI><A HREF="/data/reports/qcreports_db/output/MRK_GOGold_D.rpt">Report: All Genes with multiple Annotations to IDA, IGI, IMP, IPI</A> <B>(csmith)</B>
<LI><A HREF="/data/reports/qcreports_db/archive/go">Report: Archive of GO Statistics and Reports</A> <B>(csmith)</B>
<LI><A HREF="/data/reports/qcreports_db/output/GO_Combined_Report.rpt">Report: Combined QC Report</A> <B>(krc)</B>
<LI><A HREF="/data/reports/qcreports_db/output/GO_stats.rpt">Report: GO Statistics</A> <B>(krc)</B>
<LI><A HREF="/data/reports/qcreports_db/output/GO_MGIGAF.rpt">Report: GO MGI GAF</A> <B>(krc)</B>
<LI><A HREF="/data/reports/qcreports_db/output/GO_InvalidInferredFrom.rpt">Report: IC Annotations with Invalid GO IDs in With/Inferred From</A> <B>(dmitrys)</B>
<LI><A HREF="/data/reports/qcreports_db/output/VOC_InvalidInferred.rpt">Report: Invalid "Inferred From" Values in GO Annotations</A> <B>(ln)</B>
<LI><A HREF="/data/reports/qcreports_db/output/VOC_InvalidProperties.rpt">Report: Invalid "Properties" Values in GO Annotations</A> <B>(ln)</B>
<LI><A HREF="/usrlocalmgi/live/dataload/goload/index.html">Report: GO Load</A> <B>(krc, ln)</B>
<LI><A HREF="/data/reports/qcreports_db/output/GO_NotGene.sql.rpt">Report: Non-Gene Markers with GO Annotations</A> <B>(krc)</B>
<LI><A HREF="/data/reports/qcreports_db/output/WF_GO_FullCodeNoAnnot.rpt">Report: Papers marked as Full-coded with no GO annotations</A> <B>(ln)</B>
<LI><A HREF="/data/reports/qcreports_db/output/GO_EvidenceCodeStats.sql.rpt">Report: Total # of Annotations by GO Evidence Code</A> <B>(csmith)</B>
<LI><A HREF="/data/reports/qcreports_db/output/MRK_GOAnnot.rpt">Report: Total GO Annotations per Gene</A> <B>(csmith)</B>
<LI><A HREF="/data/reports/qcreports_db/output/GO_GPI_verify.rpt">Report: Verify GPI file</A> <B>(ln)</B>
<LI><A HREF="/data/reports/qcreports_db/output/GO_PM2GeneRefsNotInMGI.rpt">Report: Papers not in MGI for genes without experimental GO annotations</A> <B>(krc)</B>
<LI><A HREF="/data/loads/mgi/goload/logs/inferredfrom.log">Report: Sunday/Inferred From Text/linkout errors</A> <B>(ln)</B>
</OL>
<A NAME="nomenclature"><B>Nomenclature (mmh)</B></A>
<OL>
<LI><A HREF="/data/reports/qcreports_db/output/MRK_Reserved.sql.rpt">Reserved Symbols Within Last 3 Days</A>
<LI><A HREF="/data/reports/qcreports_db/output/HMD_SymbolDiffs1.rpt">MGI Symbols differing from Human Ortholog Symbols, excludes RIKEN (one-to-one)</A>
<LI><A HREF="/data/reports/qcreports_db/output/HMD_SymbolDiffs2.rpt">MGI Symbols differing from Human Ortholog Symbols, excludes RIKEN (many-to-many, one-to-many)</A>
<LI><A HREF="/data/reports/qcreports_db/output/HMD_SymbolDiffs3.rpt">MGI Symbols differing from Human Ortholog Symbols, RIKEN only</A>
<LI><A HREF="/data/reports/qcreports_db/output/MRK_Withdrawn.sql.rpt">Withdrawn Markers</A>
</OL>
<A NAME="strains"><B>Strains (csmith)</B></A>
<OL>
<LI><A HREF="/data/reports/qcreports_db/output/PRB_StrainStd.sql.rpt">Strains (Standard only)</A>
<LI><A HREF="/data/reports/qcreports_db/output/PRB_StrainNonStd.sql.rpt">Strains (Non Standard excluding F1 and F2)</A>
<LI><A HREF="/data/reports/qcreports_db/output/PRB_StrainF1F2.sql.rpt">Strains Containing F1 or F2</A>
<LI><A HREF="/data/reports/qcreports_db/output/PRB_Strain_NonStdNoAttributes.rpt">Strains (Non Standard - Sorted by Creation Date)</A>
<LI><A HREF="/data/reports/qcreports_db/output/PRB_Strain.rpt">Tab-delimited File of All Strains (MGI Acc ID, Strain, Markers, Synonyms, External Acc IDs)</A>
<LI><A HREF="/data/reports/qcreports_db/output/PRB_Strain2.rpt">Tab-delimited File of All Strains (Strain/Standard)</A>
<LI><A HREF="/data/reports/qcreports_db/output/PRB_StrainNonStdNoData.sql.rpt">Non-Standard Strains with no JR# and no data attached</A>
<LI><A HREF="/data/reports/qcreports_db/output/MLP_Nomenclature.sql.rpt">Strains Affected by recent Nomenclature changes</A>
<LI><A HREF="/data/reports/qcreports_db/output/PRB_Strain4.rpt">Strains with MGI IDs that have more than one additional external ID</A>
</OL>
<A NAME="strainsjax"><B>Strains - JAX (honda)</B></A>
<OL>
<LI><A HREF="/data/reports/qcreports_db/output/PRB_StrainJAX2.jrs.current.rpt">Public JAX strains/Alleles used in Genotype/No Strain/Genotype Association</A>
<LI><A HREF="/data/reports/qcreports_db/output/PRB_StrainJAX3.jrs.rpt">JAX Strains w/ Genotype Associations where the Markers/Alleles of the Strain record do not exactly match the Markers/Alleles of the Genotype record</A>
<LI><A HREF="/data/reports/qcreports_db/output/PRB_StrainJAX4.sql.current.rpt">New JR#s created in the past week</A> <B>(dlb)</B>
<LI><A HREF="/data/reports/qcreports_db/output/PRB_StrainJAX5.sql.current.rpt">JR#s with alleles added within the past week</A>
<LI><A HREF="/data/reports/qcreports_db/archive/strain">Strain Archive</A>
<LI><A HREF="/data/reports/qcreports_db/output/PRB_StrainJAX7.sql.current.rpt">New MMRRC JR#s created in the past week</A>
</OL>
<A NAME="sequencegroup"><B>Sequence Group (rmb, cjb, , yz)</B></A>
<OL>
<LI><A HREF="/data/reports/qcreports_db/output/SEQ_NMs.rpt">NM Sequences that are not associated with a MGI Marker</A> <B>(yz)</B>
<LI><A HREF="/data/reports/qcreports_db/output/MGI_GenesAndPseudogenesWithSequence.rpt">Genes & Pseudogenes with at least one Sequence association</A> <B>(yz)</B>
<LI><A HREF="/data/reports/qcreports_db/output/MGI_ENSEMBL_Associations.rpt">Ensembl Associations</A> <B>(yz)</B>
<LI><A HREF="/data/reports/qcreports_db/output/MGI_NCBI_Associations.rpt">NCBI Associations</A> <B>(yz)</B>
<LI><A HREF="/data/reports/qcreports_db/output/MRK_GmNoGeneModel.sql.rpt">Gm Markers without Gene Model Associations</A> <B>(yz)</B>
<LI><A HREF="/data/reports/qcreports_db/output/MGI_ObsoleteGeneModel.sql.rpt">Obsolete Gene Models associated with Markers</A> <B>(yz)</B>
<LI><A HREF="/data/reports/qcreports_db/output/MRK_GeneNoMcvAnnot.rpt">Genes with no MCV Annotation</A> <B>(yz)</B>
<LI><A HREF="/data/reports/qcreports_db/output/MRK_McvAnnotByFeature.rpt">MCV Annotations by Feature</A> <B>(yz)</B>
<LI><A HREF="/data/reports/qcreports_db/output/MRK_McvAnnot.rpt">Marker MCV Annotations</A> <B>(yz)</B>
<LI><A HREF="/usrlocalmgi/live/dataload/mcvload/index.html">MCV Annotation Load - these reports are refreshed only when a batch annotation load is run</A> <B>(yz)</B>
<LI><A HREF="/data/loads/mgi/mrkcacheload/logs/mrkmcv.curator.log">MCV Cache Load - this report is refreshed nightly M-F</A> <B>(yz)</B>
<BR>This report contains the following sections:
<OL>
<LI>Markers with conflict between the Marker Type and the MCV Marker Type
<LI>Markers Annotated to Grouping Terms
<LI>Markers with Multiple MCV Annotations
</OL>
<LI>The following logs report: <B>(yz)</B>
<BR>* Gene Models in MGI that have been obsoleted by the provider
<BR> * Gene Model biotypes not loaded because unable to translate biotype.
<OL>
<LI><A HREF="/data/loads/mgi/genemodelload/logs/ensembl_seqgenemodelload.log"> Ensembl Sequence Gene Model Information Load</A>
<LI><A HREF="/data/loads/mgi/genemodelload/logs/ncbi_seqgenemodelload.log"> NCBI Sequence Gene Model Information Load</A>
</OL>
<LI><A HREF="/data/reports/qcreports_db/output/GIA_MRK_ENSEMBL.rpt">Ensembl Associations for Gene Index</A> <B>(yz)</B>
<LI><A HREF="/data/reports/qcreports_db/output/GIA_MRK_Sequence.rpt">Sequence Associations for Gene Index</A> <B>(yz)</B>
<LI><A HREF="/data/reports/reports_db/output/MGI_BioTypeConflict.rpt">MGI Biotype Conflict Public Report</A> <B>(cjb)</B>
<LI>QTL Reports (yz)
<OL>
<LI><A HREF="/data/reports/qcreports_db/output/MRK_QTL_1.rpt">QTL markers that have no mapping and no allele associations</A>
<LI><A HREF="/data/reports/qcreports_db/output/MRK_QTL_2.rpt">QTL markers that have mapping but no allele associations</A>
<LI><A HREF="/data/reports/qcreports_db/output/MRK_QTL_3.rpt">QTL markers that have no mapping but have allele associations</A>
<LI><A HREF="/data/reports/qcreports_db/output/MRK_QTL_4.rpt">QTL markers that have assigned reference of J:23000 or J:85000</A>
<LI><A HREF="/data/reports/qcreports_db/output/MRK_QTL_5.rpt">QTL markers that are in Nomen and have not been broadcast</A>
<LI><A HREF="/data/reports/qcreports_db/output/QTL_Triage.rpt">Literature Triage QTL Report</A>
<LI><A HREF="/data/reports/qcreports_db/output/MGI_QTL_ReferenceNotes.sql.rpt">QTL Public Reference Notes</A>
<LI><A HREF="/data/reports/qcreports_db/output/MRK_QTLCandidateGene.rpt">QTL-to-Candidate Gene Relationships</A>
</OL>
<LI><A HREF="/data/reports/qcreports_db/output/MRK_C4AM_GeneModel.rpt">Markers with C4AM Coords and Gene Models</A> <B>(yz)</B>
<LI><A HREF="/data/reports/qcreports_db/output/MRK_C4AM.rpt">Genes/Pseudogenes with C4AM Coordinates from provider collection “MGI"</A> <B>(yz)</B>
</OL>
<A NAME="sequence"><B>Sequences (rmb, cjb, yz)</B></A>
<OL>
<LI><A HREF="/data/reports/qcreports_db/output/SEQ_Deleted.sql.rpt">Deleted Sequences with MGI Associations</A>
<LI><A HREF="/data/reports/qcreports_db/output/SEQ_Split.sql.rpt">Split Sequences</A>
<LI><A HREF="/data/reports/qcreports_db/output/SEQ_MarkerAnnotation.sql.rpt">Markers Annotated to a Secondary Sequence Accession ID</A>
<LI><A HREF="/data/reports/qcreports_db/output/SEQ_Dummy.sql.rpt">Dummy Sequences Annotated to Mouse Marker (report a) & Molecular Segments (report b) </A>
<LI><A HREF="/data/reports/qcreports_db/output/MRK_MultCoordinate.sql.rpt">Symbols w/ > 1 Ensembl, NCBI Gene Model Association</A> <B>(yz)</B>
<LI><A HREF="/data/reports/qcreports_db/output/MRK_MultMarkerGeneModels.sql.rpt">Ensembl, NCBI Gene Models w/ > 1 Marker Association</A> <B>(yz)</B>
<LI><A HREF="/data/reports/qcreports_db/output/MRK_NoENSEMBL.rpt">Ensembl Gene Models with no Marker Association</A> <B>(yz)</B>
<LI><A HREF="/data/reports/qcreports_db/output/MRK_NoNCBI.rpt">NCBI Gene Models with no Marker Association</A> <B>(yz)</B>
<LI><A HREF="/data/reports/qcreports_db/output/MRK_PAR_NCBIID.rpt">PARtner_NCBI_Discrepancy</A> <B>(yz)</B>
</OL>
<A NAME="homology"><B>Homology (csmith) </B></A>
<OL>
<LI><A HREF="/data/reports/qcreports_db/output/MRK_Homology_Class1.rpt">Classes for which there are > 10 Genes From a Single Species</A>
</OL>
<A NAME="metrics"><B>Curation Metrics</B></A>
<OL>
<LI><A HREF="/data/reports/qcreports_db/output/BIB_CurationMetrics.sql.rpt">J: Numbers Assigned</A> <B>(jfinger)</B>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_CurationMetrics_Index.sql.rpt">GXD Curation - Index</A> <B>(jfinger)</B>
<LI><A HREF="/data/reports/qcreports_db/output/GXD_CurationMetrics_FullCoded.sql.rpt">GXD Curation - Full-coded</A> <B>(jfinger)</B>
<LI><A HREF="/data/reports/qcreports_db/output/PHENO_CurationMetrics.sql.rpt">Pheno Curation</A> <B>(mnk)</B>
<LI><A HREF="/data/reports/qcreports_db/output/BIB_JournalByYear.rpt">Lit triage: journals x year of publication</A> <B>(csmith)</B>
<LI><A HREF="/data/reports/qcreports_db/output/BIB_JournalByYearKD.rpt">Lit triage: journals keep/discard numbers</A> <B>(csmith)</B>
<LI><A HREF="/data/reports/qcreports_db/output/BIB_JournalByGroupYear_AP.rpt">Lit triage: journals x AP</A> <B>(csmith)</B>
<LI><A HREF="/data/reports/qcreports_db/output/BIB_JournalByGroupYear_GXD.rpt">Lit triage: journals x GXD</A> <B>(cms)</B>
<LI><A HREF="/data/reports/qcreports_db/output/BIB_JournalByGroupYear_GO.rpt">Lit triage: journals x GO</A> <B>(csmith)</B>
<LI><A HREF="/data/reports/qcreports_db/output/BIB_JournalByGroupYear_Tumor.rpt">Lit triage: journals x Tumor</A> <B>(dmk)</B>
</OL>
<A NAME="dataloads"><B>Data Loads</B></A>
<OL>
<LI><A HREF="/usrlocalmgi/live/dataload/littriageload/index.html">Literature Triage Load</A> <B>(jfinger)</B>
<LI><A HREF="/usrlocalmgi/live/dataload/pubmed2geneload/index.html">PubMed to Gene Load</A> <B>(jfinger)</B>
<LI><A HREF="/usrlocalmgi/live/pdfdownload/index.html">PDF Download (PLOS, etc.)</A> <B>(jfinger)</B>
<LI><A HREF="/usrlocalmgi/live/dataload/egload/index.html">EntrezGene Load Mouse</A> <B>(yz)</B>
<LI><A HREF="/usrlocalmgi/live/dataload/uniprotload">UniProt Load Data and Logs</A> <B>(yz)</B>
<LI><A HREF="/usrlocalmgi/live/dataload/genemodelload/index.html">Gene Model/Association Loads</A> <B>(yz)</B>
<LI><A HREF="/usrlocalmgi/live/dataload/mcvload/index.html">MCV Annotation Load</A> <B>(yz)</B>
<LI><A HREF="/data/loads/mgi/mrkcacheload/logs/mrkmcv.curator.log">MCV Cache Load</A> <B>(yz)</B>
<LI><A HREF="/usrlocalmgi/live/dataload/vocload/MAindex.html">Adult Mouse Anatomy Vocabulary/DAG Load</A> <B>(terryh)</B>
<LI><A HREF="/usrlocalmgi/live/dataload/mp_emapaload/index.html">MP/EMAPA Relationships Load</A> <B>(terryh)</B>
<LI><A HREF="/usrlocalmgi/live/dataload/emageload/index.html">EMAGE Load</A> <B>(cms)</B>
<LI><A HREF="/usrlocalmgi/live/dataload/geoload/index.html">GEO Load</A> <B>(cms)</B>
<LI><A HREF="/usrlocalmgi/live/dataload/gxdhtload/index.html">GXD HT GEO and ArrayExpress Loads</A> <B>(cms)</B>
<LI><A HREF="/usrlocalmgi/live/dataload/vocload/GOindex.html">GO Vocabulary/DAG Load</A> <B>(ln)</B>
<LI><A HREF="/usrlocalmgi/live/dataload/vocload/CLindex.html">Cell Ontology (CL) Vocabulary Load</A> <B>(ln)</B>
<LI><A HREF="/usrlocalmgi/live/dataload/homologyload/index.html">Homology Load</A> <B>(mmh)</B>
<LI><A HREF="/usrlocalmgi/live/dataload/vocload/OMIMindex.html">OMIM Vocabulary Load</A> <B>(smb)</B>
<LI><A HREF="/usrlocalmgi/live/dataload/vocload/DOindex.html">Disease Ontology (DO) Vocabulary Load</A> <B>(smb)</B>
<LI><A HREF="/usrlocalmgi/live/dataload/omim_hpoload/index.html">OMIM/HPO Annotation Load</A> <B>(smb)</B>
<LI><A HREF="/usrlocalmgi/live/dataload/mp_hpoload/index.html">MP HPO Header Mapping Load </A> <B>(smb)</B>
<LI><A HREF="/usrlocalmgi/live/dataload/mp_hpmappingload/index.html">MP HPO Relationship Load </A> <B>(smb)</B>
<LI><A HREF="/usrlocalmgi/live/dataload/vocload/MPindex.html">Mammalian Phenotype Vocabulary/DAG Load</A> <B>(csmith)</B>
<LI><A HREF="/usrlocalmgi/live/dataload/alomrkload/index.html">ALO Marker Load</A> <B>(csmith)</B>
<LI><A HREF="/usrlocalmgi/live/dataload/htmpload/index.html">HTMP load: IMPC/Lacz</A> <B>(csmith)</B>
<LI><A HREF="/usrlocalmgi/live/dataload/pirsfload/index.html">PIRSF Load</A> <B>(csmith)</B>
<LI><A HREF="/usrlocalmgi/live/dataload/gotextload/index.html">GO Text Load</A> <B>(csmith)</B>
<LI><A HREF="/usrlocalmgi/live/dataload/tssgeneload/index.html">TSS-to-Gene Load</A> <B>(paul hale)</B>
<LI><A HREF="/usrlocalmgi/live/dataload/emalload/index.html">Endonuclease-mediated Allele Load (IMPC CRISPR)</A> <B>(laurens)</B>
<LI><A HREF="/usrlocalmgi/live/dataload/entrezgeneload/index.html">EntrezGene Load Human/Rat/etc</A>
</OL>
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