longest run of taxonomically confused hashes per taxonomy

[ctb]

I haven't figured out what to call this, but the table below is an incomplete answer to the question:

what’s the largest collection of hashes present in a single genome that leaves you in doubt as to what taxonomic unit it comes from, per given taxon?

For example, from the table below:

• there is a set of 364 hashes at scaled=10,000 (so, 3.64 MB!?) that belongs to 'GCA_001894475.1 Escherichia coli strain=687, ASM189447v1'.
• these 364 hashes belong to both this genome and other genome(s)
• based on just these hashes in combination, within the GDTB taxonomy you cannot distinguish anything more than that these hashes are from within d__Bacteria.

I actually can't figure out what its partner is that is in a different class than E. coli, so let me go to a different row to illustrate the partner aspect -

• there is a set of 54 hashes at scaled=10,000 (540kb!) that belongs to 'GCA_018658425.1 Candidatus Woesearchaeota archaeon, ASM1865842v1 ', an archaea.
• all 54 hashes belong both to d__Archaea and d__Bacteria.
• for example, 14 of these hashes belong to 'GCA_018663345.1 bacterium, ASM1866334v1'

in this case I'd guess it's contamination, but some of the others in the table below might not be.

Anyway, enjoy!

	overlap	lin	name
0	364	d__Bacteria	GCA_001894475.1 Escherichia coli strain=687, ASM189447v1
2	261	d__Bacteria;p__Proteobacteria	GCF_005503355.1 Sphingomonas sp. 1F27F7B strain=1F27F7B, ASM550335v1
1	251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria	GCF_003669905.1 Pseudomonas aeruginosa strain=Pa1810, ASM366990v1
4	159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales	GCF_018929655.1 Vibrio cholerae O1 strain=11_Lusaka_2018, ASM1892965v1
7	119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales	GCA_003472185.1 Parabacteroides merdae strain=AM14-15, ASM347218v1
14	103	d__Bacteria;p__Firmicutes_A;c__Clostridia	GCA_900553485.1 uncultured Clostridium sp., UMGS1619
26	88	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales	GCA_018698165.1 Candidatus Marinimicrobia bacterium, ASM1869816v1
16	77	d__Bacteria;p__Actinobacteriota;c__Actinomycetia	GCF_005889725.1 Nonomuraea zeae strain=DSM 100528, ASM588972v1
11	70	d__Bacteria;p__Firmicutes;c__Bacilli	GCF_905311015.1 Bacillus subtilis, NRS6094
15	70	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales	GCA_900766145.1 uncultured Oscillospiraceae bacterium, SRS295027_34
9	65	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria	GCA_014359905.1 Hoeflea sp., ASM1435990v1
46	62	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales	GCA_005954745.1 Halostella pelagica strain=DL-M4, ASM595474v1
3	54		GCA_018658425.1 Candidatus Woesearchaeota archaeon, ASM1865842v1
6	49	d__Bacteria;p__Bacteroidota;c__Bacteroidia	GCA_002256395.1 Bacteroidetes bacterium B1(2017), ASM225639v1
19	38	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales	GCF_001314305.1 Stenotrophomonas acidaminiphila strain=ZAC14D2_NAIMI4_2, ASM131430v1
8	37	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales	GCA_903833455.1 uncultured proteobacterium, freshwater MAG --- MJ120716B_bin-425
5	34	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales	GCA_002389265.1 Gammaproteobacteria bacterium UBA4475, ASM238926v1
24	34	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales	GCF_008764375.1 Bacillus safensis strain=DE0105, FS22
56	31	d__Bacteria;p__Desulfobacterota	GCA_009993185.1 Deltaproteobacteria bacterium, ASM999318v1
40	31	d__Bacteria;p__Bacteroidota	GCA_903878245.1 uncultured Bacteroidales bacterium, freshwater MAG --- Ja1_bin-1678
10	31	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales	GCF_018129525.1 Bradyrhizobium denitrificans strain=SZCCT0094, ASM1812952v1
25	29	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales	GCA_012927515.1 Cellulomonas sp., ASM1292751v1
81	26	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12	GCA_017509565.1 Kiritimatiellae bacterium, ASM1750956v1
17	24	d__Bacteria;p__Actinobacteriota	GCF_015560095.1 Bifidobacterium adolescentis strain=1001270J_160509_E8, ASM1556009v1
58	21	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales	GCA_018654935.1 Rhodospirillales bacterium, ASM1865493v1
29	21	d__Bacteria;p__Verrucomicrobiota	GCA_903961625.1 uncultured Victivallales bacterium, freshwater MAG --- Loc090907-8-6m_bin-024
39	20	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae	GCA_003224475.1 Acidobacteria bacterium, ASM322447v1
82	19	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia	GCA_002720365.1 Chloroflexi bacterium, ASM272036v1
96	19	d__Bacteria;p__Proteobacteria;c__Magnetococcia;o__Magnetococcales	GCA_015231925.1 Magnetococcales bacterium, ASM1523192v1
20	18	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales	GCA_902805565.1 uncultured Corynebacteriales bacterium, AVDCRST-MAG41
36	18	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales	GCA_900548495.1 uncultured Collinsella sp., UMGS1095
64	17	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales	GCF_000015865.1 Hungateiclostridium thermocellum ATCC 27405 strain=ATCC 27405, ASM1586v1
28	17	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae	GCA_018667255.1 Opitutae bacterium, ASM1866725v1
86	16	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales	GCA_016235585.1 Verrucomicrobia bacterium, ASM1623558v1
94	15	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia	GCA_016187735.1 candidate division NC10 bacterium, ASM1618773v1
87	14	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales	GCF_013337105.1 Paenibacillus sp. JMULE4 strain=JMULE4, ASM1333710v1
21	14	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales	GCA_900555595.1 uncultured Solobacterium sp., UMGS1844
83	14	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales	GCA_018667255.1 Opitutae bacterium, ASM1866725v1
97	13	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales	GCA_004294125.1 Oscillatoriales cyanobacterium, ASM429412v1
23	12	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales	GCA_017394825.1 Clostridia bacterium, ASM1739482v1
32	12	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales	GCF_015356865.1 Catenulispora pinisilvae strain=NH11, ASM1535686v1
101	12	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__UBA6902	GCA_011040095.1 Nitrospirae bacterium, ASM1104009v1
13	11	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales	GCF_018195745.1 Lactococcus lactis subsp. lactis strain=LEY6, ASM1819574v1
35	11	d__Bacteria;p__Acidobacteriota	GCA_002328195.1 Acidobacteria bacterium UBA2167, ASM232819v1

[ctb]

maybe: "longest hash chain" at that taxon?

[ctb]

ok, got a better way to do a breakdown of longest hash chain for specific taxa.

Per the table above, for d__Bacteria the longest hash chain is 364 hashes.

This hash chain is entirely part of
GCA_001894475, d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli,

which shares it across 165 partners - breakdown of top 10 partners and overlap below.

	partner_ident	partner_lin	n_hashes
0	GCF_001481655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium;s__Flavobacterium odoratimimum	46
1	GCF_012102505	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus;s__Vagococcus fluvialis	20
2	GCF_003039915	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus;s__Staphylococcus cohnii	15
3	GCF_009020275	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__Bacteroides uniformis	9
4	GCA_900758605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__Bacteroides sp900552405	9
5	GCF_013009155	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus suis_W	8
6	GCF_003311455	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus;s__Staphylococcus aureus	7
7	GCF_007293315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus_A;s__Alkalihalobacillus_A sp007293315	7
8	GCF_001865835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium;s__Flavobacterium odoratimimum	6
9	GCF_009648365	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus;s__Staphylococcus epidermidis	6