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Genomic ERROR codes - PUBLIC

K9

  • Full text of the error : K9 - Invalid cdcb Approved Partner fee code
  • Meaning : Fee code P should be assigned to an animal when the animal is participating in the CDDR (Cooperative Dairy DNA Repository) Partners program (see genomic fee codes), which is a genotype/evaluation exchange of bulls among partner countries. Because fee code P should be assigned only to bulls, this error and fee code change is made if the animal is female.
  • Correction : Correct the sex (see Gender is incorrect) or fee code (see Fee code is incorrect) as necessary.

L0 (Obsolete)

  • Full text of the error : L0 - Low Call Rate on either autosomal or X chromosome(s)
  • Meaning: Too many SNP calls are missing on either the autosomal (> 10%) or X (>20%) to be used in CDCB evaluation. Because call rate is an indication of the quality of the sample from which the DNA was obtained, CDCB avoids using samples with a low call rate.
  • Correction: Re-genotyping is necessary so that the SNP call rate can be improved to pass the CDCB criterion.

L5

  • Full text of the error : L5 - Two diff genotypes for same key on input
  • Meaning: Discrepancies were found between 2 genotypes for the same animal in the input file. An animal should have the same alleles regardless of the number of genotypes it has. When discrepancies between 2 genotypes are observed, one of the two (maybe both) genotypes is incorrect. If this error is detected in the Check process, the DateQC file will contain a conflicting_genotypes_within_fileset.txt, to remove a non-matching genotype. A submission will not proceed to loading if the check mode run contains this statement. If this error does manage to occur outside of the check process, one of the genotypes is assigned a negative key; therefore, reassignment of one or both may be necessary.
  • Correction: In the case where a conflicting_genotypes_within_fileset.txt is present: The best solution is to determine the correct assignments for the genotypes. If that is not possible, remove one of them so the submission can be loaded. The conflict/discovered dam/sire might give some hints regarding correct assignment of the genotype. In the case where this occurs outside of the check process and a negative key is assigned: the best solution is to reassign the negative key genotype to the correct animal, but this is not always possible. The conflict/discovered dam/sire might give some hints regarding correct assignment of the genotype. A negative key is never usable; therefore, leaving a key negative is allowed.

L7

  • Full text of the error : L7 - Conflicts with previous genotype existing gt is usable
  • Meaning: Discrepancies were found between 2 genotypes for this animal; one genotype is already in the CDCB database, and the other came in the input file. An animal should have the same alleles regardless of the number of genotypes it has. When discrepancies between 2 genotypes are observed, one of the two (maybe both) genotypes is incorrect. The CDCB system assumed that the original genotype is more reliable or valid. Therefore, the new genotype is assigned a negative key.
  • Correction: The best solution is to reassign the negative key genotype to the correct animal, but this is not always possible. The conflict/discovered might give some hints regarding correct assignment of the genotype. A negative key is never usable; therefore, leaving a key negative is allowed. REQUIRES PROCEDURE FOR NOMINATOR

M3 (Obsolete)

  • Full text of the error : M3 - Low Call Rate on autosomal chr
  • Meaning: Too many (>10%) SNP calls are missing on autosomal chromosomes to be used in CDCB evaluation. Because call rate is an indication of the quality of the sample from which the DNA was obtained, CDCB avoids using samples with a low call rate.
  • Correction: Re-genotyping is necessary so that the SNP call rate for autosomal chromosomes can be improved to pass the CDCB criterion of >90%.

M4 (Obsolete)

  • Full text of the error : M4 - Low Call Rate on X
  • Meaning: This is the same as low call rate on autosomes (see M3) but for X-chromosome SNP only. The call rate on X chromosomes is checked separately from autosomes to ensure adequate information for sex determination
  • Correction: Re-genotyping is necessary so that the SNP call rate for the X chromosome can be improved to pass the CDCB criterion of >80%.

M6

  • Full text of the error : M6 - Duplicates existing genotype of the same animal
  • Meaning: A genotype with less than 2.3% difference has been already assigned to the same key. Make sure this genotype was not loaded by mistake.
  • Correction: No action/correction needed. The genotype is usable.

M7

  • Full text of the error : M7 - Fewer than 5% differs from existing genotype
  • Meaning: The difference with another genotype for the same animal is greater than 0, but less than 5%.
  • Correction: No action/correction needed. The genotype is usable.

M8

  • Full text of the error : M8 - New genotype does not match existing genotype; the new genotype is used
  • Meaning: Discrepancies were found between 2 genotypes for this animal; one genotype is already in the CDCB database, and the other came in the input file.
    An animal should have the same alleles regardless of the number of genotypes it has. When discrepancies between 2 genotypes are observed, one of the two (maybe both) genotypes is incorrect. The CDCB system assumed that the genotype in the input file is more reliable or valid. Therefore, the existing (original) genotype is assigned a negative key.
  • Correction:The best solution is to reassign the negative key genotype to the correct animal, but this is not always possible. The conflict/discovered dam/sire might give some hints regarding correct assignment of the genotype. A negative key is never usable; therefore, leaving a key negative is allowed. REQUIRES PROCEDURE FOR NOMINATOR

N0

  • Full text of the error : N0 - Animal is unknown or is not identical to existing gt
  • Meaning : The genotype has a zero/negative key as a result of conflicting genotypes.
    This conflict is the consequence of multiple reasons, such as L5, L7, and M8.
  • Correction: The best solution is to reassign the negative key genotype to the correct animal, but this is not always possible. The conflict/discovered dam/sire might give some hints regarding correct assignment of the genotype A negative key genotype is never usable; therefore, leaving a key negative is allowed.

N1

  • Full text of the error : N1 - Sex Conflict for bull
  • Meaning: For males, sex conflict can be flagged when X-specific SNP calls are heterozygous and Y-specific SNP calls are few. Incorrect sex designation (most cases) or poor sample quality should be suspected.
  • Correction:Confirmation of sex and sample quality should be investigated to resolve this issue. See Corrections to pedigree (gender is incorrect) for instructions on how to change a sex designation using Format 1 submission.

N2

  • Full text of the error : N2 - Sex conflict for female
  • Meaning:For females, sex conflict can be flagged when heterozygous X-specific SNP calls are few and Y-specific SNP calls exist. Incorrect sex designation (most cases) or poor sample quality should be suspected.
  • Correction: Confirmation of sex and sample quality should be investigated to resolve this issue. See gender correction for instructions on how to change a sex designation using Format 1 submission.

N3

  • Full text of the error : N3 - Sire Conflict
  • Meaning:Genotypes of the animal and its pedigree sire have many Mendelian inheritance conflicts. In other words, genotype information indicates that the pedigree sire is not correct. Note: Such checks at CDCB are not restricted to ICAR's 200 parentage SNPs; CDCB checks all usable SNPs in common.
  • Correction:When such an event occurs, the CDCB system may provide a discovered sire ( see O3 - Discovered parent). This process is based on identifying bulls with few Mendelian inheritance conflicts with the animal. If, after consulting with the customer, the discovered sire is accepted, then pedigree information must be updated as indicated in Corrections to pedigree.

N4

  • Full text of the error : N4 - Dam Conflict
  • Meaning:Genotypes of the animal and its pedigree dam have many Mendelian inheritance conflicts. In other words, genotype information indicates that the pedigree dam is not correct. Note: Such checks at CDCB are not restricted to ICAR's 200 parentage SNPs; CDCB checks all usable SNPs in common.
  • Correction:When such an event occurs, the CDCB system may provide a discovered dam ( see O3 - Discovered parent). This process is based on identifying cows with few Mendelian inheritance conflicts with the animal. If, after consulting with the customer, the discovered dam is accepted, then pedigree information must be updated as indicated in Corrections to pedigree.

N5

  • Full text of the error : N5 - Progeny conflict
  • Meaning : Genotypes of the animal and its progeny have many Mendelian inheritance conflicts. In other words, genotype information indicates that the declared parent-progeny relationship does not exist. Note: Such checks at CDCB are not restricted to ICAR's 200 parentage SNPs; CDCB checks all usable SNPs in common.
  • Correction : When such an event occurs, the dam or sire's genotype usually is usable, but the progeny will have a sire/dam conflict, which makes its genotype unusable. See sire/dam conflict (N3/N4) for a description/correction of the conflict.

N6

  • Full text of the error : N6 - Clone conflict
  • Meaning : Two animals (or more) are indicated as clones (identical twin, split embryo, or nuclear transfer) via a clone record, but their genotypes are not identical ( >0.230 difference).
  • Correction : Clone records can be applied automatically, as described in Dealing_with_clone_records , or can be applied manually. There are two possible scenarios that would cause a clone conflict to appear:
    1. The two animals have a clone record established, but are not actually clones/identical twins etc. The clone record should be removed from the pair. For instructions to resolve this, please see the documentation in Dealing_with_clone_records.
    2. The genotypes of one of the clones is incorrectly assigned. The genotype in conflict should be moved from this animal. If the genotype has other parentage or duplicate errors, these will help find the correct animal to assign these genotypes.

N7

  • Full text of the error : N7 - Clone's progeny conflict
  • Meaning : This is the same as progeny conflict (see N5) except that the animal is identified as a clone of the progeny’s parent.
  • Correction : When such an event occurs, clone’s genotype is usually usable, but the progeny will have a sire/dam conflict, which makes its genotype unusable. See sire/dam conflict for a (N3/N4) description/correction of the conflict.

N8

  • Full text of the error : N8 - Parent's clone conflict
  • Meaning : A clone of the declared parent is in conflict with the genotype of the animal. In other words, this error resembles the sire/dam conflict (see N3/N4), except that the conflict is with a clone of the parent.
  • Correction : When such an event occurs, the CDCB system may provide a sire/dam conflict (see N3 - Sire Conflict/N4 - Dam Conflict) and a discovered sire/dam (see O3 - Discovered non-pedigree parent-progeny relationship). Clones are included in the conflict list because the CDCB system identifies all animals that have a low number of Mendelian inheritance conflicts with the input animal. There is usually no action required on this specific conflict, as it will clear out once the correct sire and dam are provided. If the discovered parent is confirmed by the customer, the pedigree information must be updated as indicated in Corrections to pedigree.

N9

  • Full text of the error : N9 - Discovered clone
  • Meaning : Identical genotypes and pedigrees were assigned to two animals, but they have not been associated as clones through submission of a clone record.
  • Correction : When this error is reported, correct the multiple birth code and clone record should be submitted to CDCB so that the animals are recognized as clones.

O0

  • Full text of the error : O0 - Discovered missing sire
  • Meaning : No sire is indicated in the pedigree, but the CDCB system discovered the missing sire. This process is based on identifying bulls with few Mendelian inheritance conflicts] with the animal. If, after consulting with the customer, the discovered sire is accepted, then pedigree information must be updated as indicated in corrections to pedigree.
  • Correction : Either accepting the discovered sire in the genotype query or submitting format 1 with the correct sire will add the discovered sire to the pedigree.

O1

  • Full text of the error : O1 - Discovered missing dam
  • Meaning : No dam is indicated in the pedigree, but the CDCB system discovered the missing dam. This process is based on identifying cows with few Mendelian inheritance conflicts with the animal. If, after consulting with the customer, the discovered dam is accepted, then pedigree information must be updated as indicated in corrections to pedigree.
  • Correction :Either accepting the discovered dam in the genotype query or submitting format 1 with the correct dam will add the dam to the pedigree.

O2

  • Full text of the error : O2 - Duplicate genotype identified
  • Meaning : Identical genotypes are assigned to two different animals with different parents and there is not a clone record established for the animal pair.
  • Correction : There are a few scenarios that can cause this error to occur:
    1. If the two animals are not related, and would not reasonably have identical genotypes: investigate the genotypes and reassign or withdraw the genotype incorrectly assigned if possible.
    2. If the animal is a clone, split embryo, or identical twin: Clone records can be automatically applied if the meet the conditions described in Dealing_with_clone_records. However, if they are not applied automatically, you can create them as outlined in Dealing_with_clone_records. Before applying clone records, make sure that the pedigree sire and dam are the same for the pair, animals have the same sex, and that the MBC and birth date given to the animals makes sense. For example:
      • For identical twins: the birth date should be the same and the MBC will be 2 for both animals.
      • For an animal that is a clone of another live animal: the clone should have a MBC of 5 and is younger than the DNA ID animal.
      • For animals that were born from split embryos: both animals should have a MBC of 4.
    3. If the animal is not a clone, but actually one animal that was genotyped under two IDs: Both of the genotypes should be under one animal ID, and the two IDs should be cross-referenced or should be removed if the ID is invalid.
      Follow these steps carefully:
      1. Move genotypes so that both are under 1 Animal ID
      2. Make sure both IDs have matching pedigrees: Sire, Dam, DOB
      3. Create a cross-reference between the two IDs, submitting the preferred ID in positions 3-19 in the Format 1 OR delete the invalid ID .
    4. If the genotypes belong to an embryo/live animal pair: Normally, embryos are merged with their live animal pair automatically, as described here Embryo_and_live_animal_merging_process. However, a duplicate error could occur if a discrepancy in the pedigrees of the pair (different sire/dam, incorrect MBC applied) prevents them from merging. In the case that you have an embryo/live animal pair that did not merge correctly, please open a ticket on Redmine.

O3 (Obsolete)

  • Full text of the error : O3 - Discovered non-pedigree parent-progeny relationship
  • Meaning : Based on low Mendelian inheritance conflicts the genotypes appear to be parent and progeny. Indication of progeny or sire/dam is determined based on birth date and sex code from each animals existing pedigree information.
  • Correction : If after consulting with the customer, a discovered sire/dam is agreed to, then pedigree information must be updated. The pedigree update can be performed by either accepting the discovered sire/dam in the genotype query[Fix_FMT1] or submitting a Format 1 with the discovered sire/dam. This error has been replaced by T1, T2, and T3 errors.

O4

  • Full text of the error : O4 - Change useable genotype to not useable
  • Meaning : The sire/dam has not been indicated as the progeny's parent but was discovered to be the progeny's parent through his/her genotype. The sire/dam's genotype is still usable. The progeny should have the sire/dam designated as unreported/discovered sire/dam. The progeny's genotype will not be usable until its parentage is corrected.
  • Correction : If an animal’s nominator also nominated the progeny, they must add the sire/dam as parent to make the progeny’s genotype usable.

O5

  • Full text of the error : O5 - Breed not evaluated
  • Meaning : The animal’s breed is not among the breeds evaluated by CDCB (AY, BS, GU, HO, JE, XX).
  • Correction : If the breed of the ID is incorrect and the animal is one of the above breeds, then submit a breed correction (format1) to make the correct breed the breed of the preferred ID. If the pedigree is B source, the nominator should work with the breed association. The XX breed should not be used for animals that are not some combination of the first 5 breeds above. Breeds SR, NR, and RE are treated as AY.

O6

  • Full text of the error : O6 - MGS is unlikely
  • Meaning: The pedigree grand sire (MGS) is unlikely to be correct because the genotype has enough SNP conflicts to make the Grand-Sire relationships unlikely. This could be because the dam on the animal's pedigree is wrong or the pedigree sire of the animal's dam is wrong.
  • Correction: Ideally the dam of the animal can be corrected or the dam's pedigree can be corrected to resolve this error, but this may require genotyping the dam. If the dam does not have a genotype, blanking the dam temporarily will allow the genotype to become usable. In the case that the dam IS genotyped and the progeny has a confirmed dam on their genotype, often it is the dam's genotype that has a conflict. In cases where the dam is confirmed, the dam cannot be blanked to resolve this issue. If the dam does have a sire conflict, her pedigree will need to be corrected in order for clear the MGS is unlikely error of her progeny.

O7

  • Full text of the error : O7 - PGS is unlikely
  • Meaning : The pedigree paternal grandsire (PGS) is unlikely to be correct because the genotype has enough SNP conflicts to make the Grand-Sire relationships unlikely. This could be because the pedigree sire or his sire is wrong.
  • Correction : Correction of the dam/PGS identification is ideal but may require genotyping the sire. When correct information for sire/PGS is not available, using blanks for the sire/PGS will allow the animal to be evaluated.

O8

  • Full text of the error : O8 - Unreliable genotype due to high parent progeny conflicts
  • Meaning : The animal’s genotype is considered to be unreliable because of more than the allowed number of Mendelian inheritance conflicts with one of its pedigree parents. Although the genotype does not have enough conflicts to be designated as a parent-progeny conflict, it has more than found between high-quality genotypes. The unreliable designation indicates that the parent or progeny should be re-genotyped.
  • Correction : Because the cause (incorrect pedigree or poor sample quality) of the conflicts is unknown, the nominator should provide another genotype from a good quality sample for the unreliable genotype.

O9

  • Full text of the error : O9 - Discovered possible parent/progeny relationship with high parent progeny conflicts
  • Meaning : A possible parent/progeny relationship was discovered based on fewer SNP conflicts (Mendelian inheritance conflicts) than for a parent-progeny conflict but still not few enough to report a parent-progeny relationship confidently.
  • Correction : Because the source (animal or potential parent) of the conflicts is unknown, both the genotypes should be considered for possible re-genotyping.

P0

  • Full text of the error : P0 - Suggested grandsires provided
  • Meaning : Suggested grandsires are provided when the CDCB system discovers a possible grandsire based on fewer SNP conflicts (Mendelian inheritance conflicts) than for an unlikely progeny-grandsire relationship. Note: The candidate grandsire is a suggestion based on genomic data comparison. Other bulls not suggested as the best candidate could still qualify as the grandsire. If, after consulting with the customer, the suggested grandsire is accepted, then pedigree information must be updated as indicated in corrections to pedigree.
  • Correction : Accepting the suggested grandsire by submitting format 1 for the parent with the correct sire indication will add the discovered sire to the pedigree.

P2

  • Full text of the error : P2 - Non-pedigree relative, close birth
  • Meaning : Two genotypes have a discovered parent-progeny relationship, but their birth dates are too close for a parent and progeny relationship.
  • Correction : if the parent-progeny relationship is confirmed with the customer, the parentage and birth date information should be updated in the pedigrees as indicated in corrections to pedigree.

Q0

  • Full text of the error : Q0 - Unreliable genotype due to high parent progeny conflicts when both sire and dam are considered
  • Meaning : More Mendelian inheritance conflicts are found than expected in normal parent-progeny relationships. The difference between O8 and Q0 is that O8 is reported when the number of SNP conflicts between a progeny and one of the parents is not significant but becomes significant when both parents are considered. If both parents are homozygous for the same allele and the progeny is heterozygous, then a conflict is detected. Because genotype is designated as unreliable, the parents are not designated as confirmed. This means that edits can change them.
  • Correction : The sample quality of the progeny should be suspected, and another genotype from a good quality sample should be submitted to resolve the conflict.

Q1

  • Full text of the error : Q1 - Unreliable genotype due to female with a Y SNP-count of 3 or 4
  • Meaning : A female's genotype indicates some calls for Y-chromosome specific SNPs. Because females do not have a Y chromosome, no calls for Y-chromosome specific SNPs should be found. Determining whether a female received 3 or 4 calls because she has a Y chromosome or genotyping errors occurred is difficult. When females have Y SNP calls, the animal is either a male or the genotype is unreliable; therefore, the genotype is not used in evaluation. However, if the animal is proven to be a normal female (progeny existence, enough heterozygous X-SNPs, etc) and just happened to have Y calls in error, then the genotype can be accepted as an exception if the nominator contacts CDCB.
  • Correction : If the Y calls were from genotyping errors, then submission of another genotype from good quality sample should resolve this issue. If the female is proven to be normal, then CDCB’s manually adding the animal to an exception list will enable it to be in the evaluation. However, if the animal has a Y chromosome, she will be excluded from evaluation.

Q2

  • Full text of the error : Q2 - New genotype on live animal does not match embryo genotype
  • Meaning : Differences were found between an embryo’s genotype and a genotype after birth. Regardless of whether the DNA is processed before or after the animal is born, the genotype should be the same. Because embryo genotypes are harder to call accurately, the difference might have come from genotyping errors or from an incorrectly assigned genotype.
  • Correction : If the conflict resulted from genotyping errors, then the nominator will have to contact CDCB to correct the data using the following steps:
    1. Move the embryo genotype to the live animal key.
    2. Withdraw the embryo genotype with the comment “Embryo conflict.”
    3. Delete pedigree of the embryo.

If the genotype was incorrectly assigned, the nominator should assign the embryo to the correct live animal. Contact CDCB to merge the embryo and live animal data using the same steps except that the comment will be “Embryo $ANIMALID.”

Q3

  • Full text of the error : Q3 - Probable XXY abnormality
  • Meaning : The animal has enough heterozygous X-specific SNPs to be declared as female but also has enough called Y SNPs to be male. If re-genotyping does not resolve the issue, the animal might have a condition called Klinefelter's syndrome. Karyotyping is needed to determine definitively that an extra X chromosome exists. As animals with this condition are infertile, the animal is excluded from evaluation.
  • Correction : Re-genotyping can be done to determine if the result was caused by genotyping errors. However, if re-genotyping shows the same results, the animal remains disqualified from being evaluated. If the animal is proven to be normal, then CDCB’s manually adding the animal to an exception list will enable it to be in the evaluation. However, if the animal has a Y chromosome, she will be excluded from evaluation.

Q4

  • Full text of the error : Q4 - Notification: Bull genotype has more heterozygous X-specific SNP than explainable as genotyping errors
  • Meaning : Bull has more heterozygous X-specific calls than expected but not enough to be considered a female. Bulls are not expected to have any heterozygous SNPs in the X-specific portion of the X chromosome as they only have 1 X chromosome. Note: This code is a notification only.
  • Correction: No action/correction needed. The genotype is usable.

Q5

  • Full text of the error : Q5 - Chromosome abnormality, deletion or 2 chr from same parent
  • Meaning : There are significant number of parent-progeny SNP conflicts due to mutation/chromosome abnormality. The most common example would be deletion in part of a chromosome. It is also possible that both chromosomes are inherited from one of the parents.
  • Correction : No action/correction needed. The genotype is usable.
  • Abnormality codes :
    1 = One member of chromosome xx pair missing for 1234567890
    2 = Missing chromosome xx from parent 12345678 with heterozygous SNPs; possible uniparental disomy
    3 = Missing chromosome xx from parent 12345678 with homozygous SNPs; possibly inherited deletion
  • Example :
    aaaaaaaaaaaa 1aaa28 88792693 Q5 major mutation
    It means that abnormality code 1 occurred in chromosome 28 for anim_key 88792693.
    Error code translation:
    One member of chromosome 28 pair missing for 88792693

Q6

  • Full text of the error : Q6 - Excessive homozygous SNPs
  • Meaning : Possibly an unfertilized ovum which is not viable and should be withdrawn.
  • Correction : Withdraw the genotype, if unfertilized ovum.

R0

  • Full text of the error : R0 - Unreliable sire
  • Meaning : Unreliable sire relationship between a HD and either a HD or LD (3K excluded). The input GT is HD with fewer confirmations than the existing genotype.
  • Correction : No action/correction needed. The genotype is usable.

R1

  • Full text of the error : R1 - Unreliable dam
  • Meaning : Unreliable dam relationship between a HD and either a HD or LD (3K excluded). The input GT is HD with fewer confirmations than the existing genotype
  • Correction : No action/correction needed. The genotype is usable.

R2

  • Full text of the error : R2 - Unreliable progeny
  • Meaning : Unreliable progeny relationship between a HD and either a HD or LD (3K excluded). The input GT is HD with fewer confirmations than the existing genotype.
  • Correction : No action/correction needed. The genotype is usable.

R3

  • Full text of the error : R3 - Unreliable clone’s progeny
  • Meaning : Unreliable clone's progeny relationship between a HD and either a HD or LD (3K excluded). The input GT is HD with fewer confirmations than the existing genotype.
  • Correction : No action/correction needed. The genotype is usable.

R4

  • Full text of the error : R4 - Unreliable parent’s clone
  • Meaning : Unreliable parent's clone relationship between a HD and either a HD or LD (3K excluded). The input GT is HD with fewer confirmations than the existing genotype.
  • Correction : No action/correction needed. The genotype is usable.

S1

  • Full text of the error : S1 - Discovered breed error
  • Meaning : The breed of the animal is not the breed of the highest breed based representation (BBR) and the BBR is > 85%. The BBR is the one calculated at loading, or from the weekly evaluation.
  • Correction : Submit breed correction to make the discovered breed, the breed of the preferred ID. If the pedigree is B source, the nominator should work with the breed association to make the change.

S2

  • Full text of the error : S2 - Breeds of animal and parent(s) differ
  • Meaning : The breed of the animal is not the same as the breed of a parent and the animal’s breed based representation (BBR) is >= 94%. The BBR is the one calculated at loading, or from the weekly evaluation.
  • Correction : Submit breed correction or change the preferred ID designation to make the breeds of the preferred IDs the same for animal and parent(s). If the pedigree is B source, the nominator should work with the breed association to make the change.

T1

  • Full text of the error : T1 - Discovered progeny
  • Meaning : A progeny has been discovered based on few Mendelian inheritance conflicts with the animal and birth date. If, after consulting with the customer, the discovered progeny is accepted, then pedigree information of the progeny must be updated as indicated in Corrections to pedigree.
  • Correction : Either accepting the discovered progeny in the genotype query or submitting format 1 of the discovered progeny, including the ID of the parent.

T2

  • Full text of the error : T2 - Discovered sire
  • Meaning : A sire has been discovered based on birth date and few Mendelian inheritance conflicts with the animal. If, after consulting with the customer, the discovered sire is accepted, then pedigree information must be updated as indicated in Corrections to pedigree.
  • Correction : Either accepting the discovered sire in the genotype query or submitting format 1 with the discovered sire will add the discovered sire to the pedigree.

T3

  • Full text of the error : T3 - Discovered dam
  • Meaning : A dam has been discovered based on birth date and few Mendelian inheritance conflicts with the animal. If, after consulting with the customer, the discovered dam is accepted, then pedigree information must be updated as indicated in Corrections to pedigree.
  • Correction : Either accepting the discovered dam in the genotype query or submitting format 1 with the discovered dam will add the discovered dam to the pedigree.

U1

  • Full text of the error : U1 – Unreliable genotype with itself (animal has two genotypes > 2.3% differences, but <= 5% differences)
  • Meaning : An animal has more than one genotype and there are more differences than normal, but not different enough the declare that it is from a different animal, The genotype in designated as unreliable so does not contribute to evaluations.
  • Correction : No action is necessary. The other genotype can represent the animal.

U3

  • Full text of the error : U3 – Unreliable genotype with sire (the two genotypes > .006, but < .050 differences)
  • Meaning : The genotype has more conflicts with its sire than allowed for a confirmation, but not so many as to declare a conflict, so the genotype is designated as unreliable so does not contribute to evaluations.
  • Correction : A new genotype may be required if there is not a different bull that could be the sire or an undetected chromosomal abnormality.

U4

  • Full text of the error : U4 – Unreliable genotype with dam (the two genotypes > .006, but < .050 differences)
  • Meaning : The genotype has more conflicts with its dam than allowed for a confirmation, but not so many as to declare a conflict, so the genotype is designated as unreliable so does not contribute to evaluations.
  • Correction : A new genotype may be required if there is not a different cow that could be the dam or an undetected chromosomal abnormality.

U5

  • Full text of the error : U5 – Unreliable genotype with progeny (the two genotypes > .006, but < .050 differences)
  • Meaning : The genotype has more conflicts with a progeny than allowed for a confirmation, but not so many as to declare a conflict, so the genotype is designated as unreliable so does not contribute to evaluations.
  • Correction : A new genotype may be required if there is not some other relationship that could cause the observed similarity.

U6

  • Full text of the error : U6 – Unreliable genotype with progeny's clone (the two genotypes > .006, but < .050 differences)
  • Meaning : The genotype has more conflicts with its progeny’s clone than allowed for a confirmation, but not so many as to declare a conflict, so the genotype is designated as unreliable so does not contribute to evaluations.
  • Correction : Determine if the progeny’s clone should be designated as a clone. A new genotype may be required.

U7

  • Full text of the error : U7 – Unreliable genotype with parent's clone (the two genotypes > .006, but < .050 differences)
  • Meaning : The genotype has more conflicts with its parent’s clone than allowed for a confirmation, but not so many as to declare a conflict, so the genotype is designated as unreliable so does not contribute to evaluations.
  • Correction : Determine if its parent’s clone should be designated as a clone. A new genotype may be required.

U8

  • Full text of the error : U8 – Unreliable progeny due to BOTH parents (More than 35 conflicts from TRIO compare)
  • Meaning : The genotype has more cases of cases where its SNP is heterozygous and both parents have the same homozygous SNP than allowed, so the genotype is designated as unreliable so does not contribute to evaluations.
  • Correction : Determine if it should be designated as a clone. A new genotype may be required if there is not a different bull that could be the sire or an undetected chromosomal abnormality.

U9

  • Full text of the error : U9 – Unreliable genotype due to sex error with another usable genotype (male failed X-text, but sufficient Y or female has excess Y-count and there is another usable genotype)
  • Meaning : The genotype has sex conflict and has another genotype without the conflict.
  • Correction : No action is necessary. The other genotype can represent the animal.

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