Internal sequence–reference differences

Internal nucleotide differences between a catalogued mature piRNA sequence and an accepted genomic locus. These records are not automatically interpreted as genomic variants.

Interpretation. A difference can reflect genomic variation, RNA editing, sequencing error, mapping ambiguity or an incorrect locus assignment. Terminal A/U differences are excluded from this table. The default table contains differences observed in raw sequencing reads at the assigned locus and passing the stated read-quality, depth and statistical criteria. dbSNP, ClinVar, COSMIC and REDIportal matches are separate annotations and are not substitutes for the raw-read comparison.

Internal differences detected in sequencing reads

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Criteria applied to sequencing reads

Available small-RNA sequencing samples were examined at the assigned genomic locus. Samples were labelled as PIWI-IP, oxidation-treated or comparison libraries when indicated by their study metadata. A record passed the read checks when the difference base had Q ≥ 30, informative Q30 depth was at least 10, at least 3 reads carried the piRNA base, and the sample-specific binomial test passed BH correction at q ≤ 0.05.

“Passed all read checks” reports records meeting these requirements in at least one sequencing sample.
“Passed all read checks in ≥2 samples” reports records meeting the same requirements in at least two sequencing samples.
“Other small-RNA sequencing sample(s)” means that the passing sample was not assigned to the PIWI-IP, oxidation-treated or comparison categories. It does not mean that reads or sample metadata were absent.
External matches identify the named dbSNP, ClinVar, COSMIC or REDIportal record; they do not replace the raw-read checks.

Browse records

piRNA, locus or difference identifier

Species

Raw-read result

Passing sample type

External database

Chromosome

— records

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Nucleotide substitutions

Substitution classes among records that passed all raw-read checks. The stored matrix combines human, mouse, rat and Drosophila and is therefore not presented as a Human-only result.

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The result cards and default table contain only records that passed all raw-read checks. Counts refer to locus-specific difference records unless explicitly labelled as distinct piRNAs or distinct genomic events. The same mature piRNA sequence can contribute more than one record when it is assigned to more than one accepted locus.