Type strain record present in latest NCBI_16S build not visible on https://ya16sdb.labmed.uw.edu/

[marykstewart]

I'm coming at this from the perspective of this sv and a few other S. maltophilia-ish svs in the NGS16S case https://share.labmed.uw.edu/molmicro/markergene/23N0214_NGS16S/report/23R169-19/details-sv-0085:23R169-19.html#tab_plottab.

I was looking to see where the S. maltophilia type strains are, NCBI indicates there are many including NR_119220_1_1500, which is in the latest build.

grep "NR_119220.1" /molmicro/common/ncbi/16s/output/LATEST/dedup/1200bp/named/filtered/trusted/seq_info.csv
NR_119220_1_1500,NR_119220.1,NR_119220,NR_119220,"Stenotrophomonas maltophilia strain LMG 958 16S ribosomal RNA, partial sequence",40324,12-Mar-2019,12-Jul-2019,1,Stenotrophomonas maltophilia,RefSeq,Stenotrophomonas maltophilia,1500,1,LMG 958,rRNA,,,1,1500,29,1514,,,,40324,40323,Stenotrophomonas maltophilia,Stenotrophomonas,True,True,True,True,type,,,,,,,,,,,,cab8c8fe29c0259f18a178d94abf7230ead38212,JF343225_1_1237,0.000809,False,21.0,0.0034076332023561,-0.0002546308763511,True,0.0809,438.0

I only see one (DQ067559_1_1412) listed in https://ya16sdb.labmed.uw.edu/. Is there a row limit? The minimum dist_pct I see is 0.91, so I suspect that's the case but wanted to confirm.

[crosenth]

Hi Mary, has this been resolved?

[marykstewart]

Hi Chris, I think this is indeed some sort of display issue. When I scroll through the list of Stenotrophomonas maltophilia records as far as I can go, I still only see DQ067559_1_1412 identified as a type strain. However, if I search for NR_119220_1_1500 using the search box, which I didn't think to try 2 years ago, it comes up and is identified as a type strain record. So, no...not resolved. But not a huge deal either.

[crosenth]

There is a MAX_TABLE_RECORDS=500 being set https://github.com/nhoffman/ya16sdb/blob/master/dash/app.py#L25 and I do not have any notes about why that is set. It would probably be fine if I turned this off and pulled in all records. Let's try it

[crosenth]

Okay it takes forever to load if I allow all rows. It is sorted by dist, outliers at the top. Maybe I will put some kind of table filter so it is clear only 500 records are shown and allow some sorting modifications.

[crosenth]

Maybe we can do some paging as well: https://dash.plotly.com/datatable/interactivity