Duplicated accessions in mitofish.12S.May2023.tsv

[aomlomics]

Duplicated accessions in mitofish.12S.May2023.tsv

[shenjean]

Hi @BELKHIR,

Thank you for your patience. I checked the 255 duplicated records and noticed that most of them (n=251) were erroneously caused by 16S rRNA false positives extracted from mitogenome annotations. I updated the code used to retrieve the 12S rRNA genes (particularly, by removing the s-RNA search term and adding a pipe to remove any other 16S rRNA gene sequences grep -v 16S). These were removed in the updated May2023 12S rRNA gene dataset and future data updates will be reviewed carefully for duplicates. Please note that four duplicated records (AP005998, KJ643927, NC_024573, OP326524) contain two copies of the 12S rRNA gene. These were retained in the updated May2023 12S rRNA gene dataset.

Here are the md5 checksum values for the updated files:

• mitofish.12S.May2023.tsv (48,076 records; md5:c2c61dabeab1ce9a2f3268b6376b244b)
• mitofish.12S.May2023_NR.fasta (md5:46940bbc6060b6fedfdef0d0c130d544)
• 12S-seqs-derep-uniq.qza (md5:36920cc2341fff8675729aebec94d3f8)
• 12S-tax-derep-uniq.qza (md5:acee23173f8e95d71f8bbb6be41adaac)
• 12S-16S-18S-seqs.qza (md5:74b6186d668d59fb6f0a87e1fb0ec560)
• 12S-16S-18S-tax.qza (md5:c8fa9121b567398be16a689705f9650f)

Please note that besides this fix, there will not be a database update this month (June 2023). The next update is scheduled for July 2023 as part of a student training program.