Duplicate entries in the contigs

Microbial community profiling PanPhlAn
1

Dear Authors,

While browsing through the Pangenome files, we noticed a strange pattern: For some contigs, we see genes that have the same start-end position but different Uniref90 IDs annotated (in a single contig).

Here, we attach some examples:

From Mycolicibacterium_obuense.

UniRef90_A0A0M2WDJ6     WN67_31095      GCA_000974925   LAUZ02000002.1  72597   93944
...
UniRef90_A0A0J6VR76     WN67_31095      GCA_000974925   LAUZ02000002.1  72597   93944

From Lysobacter_capsici

UniRef90_A0A0Q8IVI6     dltA    GCA_001442785   CP011130.1      2970103 2990550
...
UniRef90_A0A0Q8J2G6     dltA    GCA_001442785   CP011130.1      2970103 2990550
...
UniRef90_A0A108U5G5     dltA    GCA_001442785   CP011130.1      2970103 2990550
...
UniRef90_A0A0Q8J5V4     dltA    GCA_001442785   CP011130.1      2970103 2990550

From Azospirillum_lipoferum

UniRef90_D3NZV3 potB    GCA_000010725   AP010946.1      379665  380549
UniRef90_D3P1E1 potB    GCA_000010725   AP010946.1      379665  380549
UniRef90_A0A2K1G431     potB    GCA_000010725   AP010946.1      379665  380549
UniRef90_D3P3T7 potB    GCA_000010725   AP010946.1      379665  380549
UniRef90_D3NRD9 potB    GCA_000010725   AP010946.1      379665  380549
UniRef90_D3P6E0 potB    GCA_000010725   AP010946.1      379665  380549
UniRef90_D3P2M5 potB    GCA_000010725   AP010946.1      379665  380549
UniRef90_D3P3Y5 potB    GCA_000010725   AP010946.1      379665  380549

We are suspecting that this is due to the fact that the annotations are constantly updated, however are still not sure if this behaviour was wanted.

Best,
Eric Cho

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