Afumigatus_pangenome / full_v072 / locus summary

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248 loci, one focal species. Exploratory: the unresolved type is the majority, and swap_candidate is verified on one locus only. Starship overlap uses Af293 coordinates. Strip colours: gene in place; DNA at site, no gene; DNA checked, absent; not DNA-checked; elsewhere or contig break.

Types: unresolved 137, monomorphic 41, content_variants 40, swap_candidate 24, rare_content 5, absent_in_focal 1

All loci: carrier fraction against locus type.

Af293 loci with Starship spans (Af293 only).

Selected loci: one row per strain, Mash-clade order.

Strips for all loci (PDF)

Swap candidates (TSV)

key	label	type	size	n_strains	content_n	content_frac	n_states	tier	starship	pair
L001	MAT	swap_candidate	7	293	272	0.928	19	full		PPPPPPP(125) vs PPPPAAP(134)
L002	MAT	swap_candidate	8	293	266	0.908	9	full		PPPPPPPP(131) vs PPPPAAPP(123)
L003		unresolved	8	293	0	0.000	8	full
L004		swap_candidate	7	293	95	0.324	10	full		PPPPPPP(93) vs AAAAAPP(150)
L005		swap_candidate	11	293	206	0.703	8	full		PPPPPPPPPPP(117) vs PPPPPPPPPPA(88)
L006		swap_candidate	9	293	201	0.686	12	full		PPPPPPPPP(152) vs PAAAAAAAP(82)
L007		swap_candidate	7	293	279	0.952	11	full		PPPPPPP(82) vs PPPPAPP(161)
L008		swap_candidate	15	293	271	0.925	23	full		PPPPPPPPPPPPPPP(79) vs PPPPPPAAAAAPPPP(181)
L009		swap_candidate	11	293	193	0.659	13	short_flanks		PPPPPPPPPPP(79) vs PAAAPPPPPPP(112)
L010		swap_candidate	11	293	275	0.939	23	short_flanks		PPPPPPPPPPP(112) vs PPPPPAAPPPP(75)
L011		swap_candidate	11	293	266	0.908	12	full		PPPPPPPPPAP(198) vs AAAAPPPPPAP(65)
L012		swap_candidate	11	293	269	0.918	16	full		PPPPPPPPPPP(203) vs AAAPPPPPPPP(65)
L013		swap_candidate	8	293	194	0.662	19	full		PPPPPPPP(107) vs PPPPAAAA(58)
L014		swap_candidate	11	293	261	0.891	22	contig_end		PPPPPPPPPPP(191) vs PPPPPPPPAAA(63)
L015		swap_candidate	9	293	275	0.939	21	full		PPPPPPPPP(124) vs AAAPPPPPP(63)
L016		swap_candidate	8	293	269	0.918	23	full		PPPPPPPP(176) vs PPPAAAAP(41)
L017		unresolved	26	293	74	0.253	86	full	Osiris-h4
L018		content_variants	10	293	252	0.860	8	full
L019		content_variants	9	293	249	0.850	13	full
L020		swap_candidate	16	293	58	0.198	29	full		PPPPAAAAAAAAAAAA(193) vs PPAAAAAAAAAAAAAA(36)
L021		swap_candidate	16	293	58	0.198	29	full		AAAAAAAAAAAAAPPP(193) vs AAAAAAAAAAAAAAAP(36)
L022		swap_candidate	16	293	57	0.195	31	full		AAAAAAAAAAAAAPPP(193) vs AAAAAAAAAAAAAAAP(36)
L023		swap_candidate	16	293	58	0.198	31	full		PPPAAAAAAAAAAAAA(193) vs PAAAAAAAAAAAAAAA(36)
L024		content_variants	7	293	274	0.935	10	full
L025		unresolved	10	293	116	0.396	15	full
L026		content_variants	9	293	241	0.823	13	full
L027		content_variants	11	293	220	0.751	17	full
L028		swap_candidate	7	293	60	0.205	16	full		?P??P??(83) vs AAAAAPP(94)
L029		unresolved	7	293	124	0.423	12	full
L030		content_variants	8	293	151	0.515	13	full
L031		content_variants	11	293	283	0.966	18	full
L032		unresolved	8	293	182	0.621	17	full
L033		unresolved	10	293	159	0.543	28	full
L034		content_variants	10	293	287	0.980	18	contig_end
L035		content_variants	9	293	259	0.884	12	full
L036		monomorphic	10	293	293	1.000	11	full
L037		monomorphic	10	293	293	1.000	10	full
L038		monomorphic	10	293	292	0.997	12	full
L039		monomorphic	10	293	293	1.000	12	full
L040		content_variants	10	293	287	0.980	21	contig_end
L041		unresolved	9	293	119	0.406	33	full
L042		content_variants	17	293	266	0.908	10	full
L043		unresolved	21	293	116	0.396	74	full
L044		content_variants	26	293	177	0.604	75	full
L045		unresolved	10	293	0	0.000	7	short_flanks
L046		content_variants	8	293	215	0.734	9	full
L047		unresolved	11	293	122	0.416	29	full
L048		unresolved	18	293	9	0.031	39	full	Osiris-h3
L049		unresolved	17	293	16	0.055	47	full
L050		rare_content	32	293	17	0.058	23	full	Lamia-h4
L051		rare_content	32	293	13	0.044	22	full	Lamia-h4
L052		content_variants	20	293	54	0.184	29	full	Lamia-h4
L053		content_variants	20	293	56	0.191	33	full	Lamia-h4
L054		unresolved	38	293	71	0.242	131	full	Gnosis-h1
L055		unresolved	9	293	87	0.297	20	full
L056		unresolved	12	293	11	0.038	19	full
L057		unresolved	12	293	7	0.024	16	full
L058		content_variants	57	293	149	0.509	85	full	Tardis-h1
L059		content_variants	12	293	203	0.693	15	full	Tardis-h1
L060		unresolved	8	293	130	0.444	23	full
L061		swap_candidate	14	293	0	0.000	15	full		AAAAAAPAAAAAAA(221) vs AAAAAAAAAAAAAA(37)
L062		absent_in_focal	11	293	0	0.000	3	full
L063		swap_candidate	9	293	0	0.000	6	full		AAAAAAAPP(133) vs AAAAAAAAA(101)
L064		rare_content	21	293	10	0.034	13	full
L065		unresolved	14	293	0	0.000	13	full
L066		unresolved	29	293	22	0.075	78	full
L067		monomorphic	7	293	293	1.000	2	full
L068		monomorphic	8	293	292	0.997	2	full
L069		monomorphic	9	293	293	1.000	1	full
L070		monomorphic	7	293	292	0.997	3	full
L071		rare_content	106	293	6	0.020	26	full	Lamia-h4
L072		monomorphic	7	293	291	0.993	3	full
L073		monomorphic	8	293	291	0.993	3	full
L074		monomorphic	8	293	291	0.993	4	full
L075		monomorphic	8	293	289	0.986	4	full
L076		monomorphic	10	293	291	0.993	5	full
L077		monomorphic	10	293	291	0.993	5	full
L078		monomorphic	7	293	289	0.986	4	full
L079		monomorphic	7	293	289	0.986	4	full
L080		monomorphic	11	293	285	0.973	5	full
L081		monomorphic	9	293	287	0.980	8	contig_end
L082		monomorphic	10	293	285	0.973	4	full
L083		monomorphic	9	293	287	0.980	7	full
L084		monomorphic	8	293	282	0.962	8	full
L085		monomorphic	9	293	284	0.969	7	full
L086		monomorphic	9	293	284	0.969	2	full
L087		monomorphic	8	293	290	0.990	7	full
L088		monomorphic	8	293	283	0.966	8	full
L089		monomorphic	8	293	281	0.959	5	full
L090		monomorphic	8	293	288	0.983	9	full
L091		monomorphic	10	293	293	1.000	11	full
L092		monomorphic	8	293	284	0.969	10	full
L093		monomorphic	10	293	280	0.956	9	full
L094		monomorphic	8	293	278	0.949	4	full
L095		monomorphic	8	293	276	0.942	7	full
L096		monomorphic	13	293	277	0.945	12	full
L097		monomorphic	8	293	279	0.952	8	full
L098		monomorphic	11	293	274	0.935	7	full
L099		monomorphic	11	293	272	0.928	7	full
L100		monomorphic	10	293	279	0.952	6	full
L101		monomorphic	8	293	276	0.942	9	full
L102		monomorphic	9	293	270	0.922	10	full
L103		monomorphic	8	293	265	0.904	7	full
L104		monomorphic	8	293	264	0.901	4	full
L105		content_variants	11	293	263	0.898	6	full
L106		content_variants	8	293	260	0.887	3	full
L107		content_variants	9	293	262	0.894	11	full
L108		content_variants	10	293	255	0.870	10	contig_end
L109		content_variants	11	293	262	0.894	9	full
L110		content_variants	9	293	253	0.863	9	full
L111		content_variants	8	293	239	0.816	10	full
L112		content_variants	11	293	236	0.805	12	full
L113		content_variants	11	293	229	0.782	7	full
L114		content_variants	8	293	223	0.761	11	full
L115		content_variants	8	293	217	0.741	9	full
L116		content_variants	8	293	211	0.720	6	full
L117		swap_candidate	70	293	1	0.003	81	full		AAPPAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAPPPP(32) vs AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAPPPP(108)
L118		content_variants	8	293	207	0.706	6	full
L119		rare_content	46	293	20	0.068	116	full	Osiris-h3
L120		content_variants	27	293	2	0.007	23	full	Nebuchadnezzar-h2
L121		content_variants	11	293	196	0.669	41	full
L122		content_variants	9	293	165	0.563	13	full
L123		content_variants	8	293	155	0.529	7	full
L124		content_variants	9	293	152	0.519	25	full
L125		unresolved	8	293	149	0.509	16	full
L126		content_variants	29	293	2	0.007	34	full	Lamia-h4
L127		content_variants	7	293	225	0.768	22	full
L128		unresolved	9	293	140	0.478	12	full
L129		unresolved	146	293	1	0.003	170	full	Osiris-h3
L130		unresolved	8	293	133	0.454	7	full
L131		unresolved	10	293	139	0.474	20	full
L132		unresolved	10	293	140	0.478	19	full
L133		content_variants	10	293	184	0.628	15	full
L134		unresolved	22	293	6	0.020	15	full
L135		swap_candidate	51	293	34	0.116	48	full		??????????????????????????????????????????????PP???(32) vs PAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAPPP(87)
L136		unresolved	31	293	0	0.000	31	full
L137		unresolved	8	293	247	0.843	8	full
L138		unresolved	13	293	134	0.457	49	full
L139		content_variants	7	293	160	0.546	10	full
L140		unresolved	8	293	152	0.519	21	full
L141		unresolved	8	293	134	0.457	15	full
L142		unresolved	8	293	162	0.553	27	full
L143		unresolved	39	293	5	0.017	110	full	Osiris-h3
L144		unresolved	14	293	31	0.106	22	full
L145		unresolved	17	293	7	0.024	56	full	Osiris-h3
L146		unresolved	8	293	180	0.614	18	full
L147		unresolved	8	293	106	0.362	16	full
L148		unresolved	8	293	98	0.334	7	full
L149		unresolved	8	293	99	0.338	8	full
L150		unresolved	10	293	99	0.338	19	full
L151		unresolved	8	293	89	0.304	9	full
L152		unresolved	8	293	85	0.290	14	full
L153		unresolved	20	293	6	0.020	25	full
L154		unresolved	11	293	92	0.314	24	full
L155		unresolved	8	293	111	0.379	15	full
L156		unresolved	10	293	167	0.570	31	full
L157		unresolved	12	293	82	0.280	20	full
L158		unresolved	13	293	80	0.273	21	full
L159		unresolved	11	293	77	0.263	25	full
L160		unresolved	9	293	75	0.256	25	contig_end
L161		unresolved	28	293	2	0.007	35	full	Gnosis-h1
L162		unresolved	8	293	58	0.198	33	full
L163		unresolved	10	293	37	0.126	7	full
L164		unresolved	23	293	4	0.014	12	full
L165		unresolved	148	293	14	0.048	219	full
L166		unresolved	23	293	12	0.041	75	full
L167		unresolved	160	293	3	0.010	222	full
L168		unresolved	13	293	7	0.024	28	full
L169		unresolved	12	293	9	0.031	34	full
L170		unresolved	19	293	0	0.000	8	full
L171		unresolved	51	293	4	0.014	12	contig_end	Nebuchadnezzar-h1
L172		unresolved	16	293	19	0.065	38	full	Tardis-h1
L173		unresolved	58	293	3	0.010	54	full	Tardis-h1
L174		unresolved	79	293	3	0.010	95	full	Lamia-h4
L175		unresolved	14	293	15	0.051	16	contig_end
L176		unresolved	26	293	0	0.000	9	full
L177		unresolved	11	293	0	0.000	7	full
L178		unresolved	11	293	2	0.007	7	contig_end	Nebuchadnezzar-h1
L179		unresolved	9	293	5	0.017	9	contig_end
L180		unresolved	10	293	5	0.017	7	contig_end
L181		unresolved	15	293	64	0.218	35	contig_end
L182		unresolved	11	293	2	0.007	12	contig_end
L183		unresolved	30	293	25	0.085	96	contig_end
L184		unresolved	11	293	21	0.072	16	contig_end	Gnosis-h1
L185		unresolved	77	293	17	0.058	166	contig_end	Lamia-h4
L186		unresolved	10	293	76	0.259	23	contig_end
L187		unresolved	132	293	16	0.055	186	contig_end	Janus (likely)-h2 (likely)
L188		unresolved	17	293	6	0.020	5	contig_end
L189		unresolved	12	293	4	0.014	19	contig_end	Nebuchadnezzar-h1
L190		unresolved	12	293	3	0.010	21	contig_end	Nebuchadnezzar-h1
L191		unresolved	60	293	4	0.014	219	contig_end	Gnosis-h1
L192		unresolved	44	293	5	0.017	76	contig_end
L193		unresolved	55	293	26	0.089	137	contig_end
L194		unresolved	13	293	3	0.010	51	contig_end
L195		unresolved	12	293	6	0.020	32	contig_end	Nebuchadnezzar-h1
L196		unresolved	14	293	8	0.027	31	contig_end
L197		unresolved	29	293	4	0.014	52	contig_end
L198		unresolved	16	293	29	0.099	14	contig_end
L199		unresolved	19	293	22	0.075	103	contig_end
L200		unresolved	9	293	1	0.003	12	contig_end
L201		unresolved	95	293	1	0.003	205	contig_end	Janus (likely)-h2 (likely)
L202		unresolved	45	293	3	0.010	111	contig_end	Janus (likely)-h2 (likely)
L203		unresolved	24	293	1	0.003	24	contig_end	Lamia-h4
L204		unresolved	24	293	18	0.061	31	contig_end
L205		unresolved	21	293	3	0.010	25	contig_end
L206		unresolved	9	293	31	0.106	29	contig_end
L207		unresolved	10	293	35	0.119	16	contig_end	Lamia-h4
L208		unresolved	34	293	141	0.481	119	contig_end	Gnosis-h1
L209		unresolved	8	293	85	0.290	30	contig_end
L210		unresolved	8	293	146	0.498	32	contig_end
L211		content_variants	10	293	270	0.922	39	contig_end
L212		unresolved	20	293	24	0.082	43	contig_end
L213		unresolved	9	293	2	0.007	21	contig_end
L214		unresolved	15	293	23	0.078	32	contig_end	Lamia-h4
L215		unresolved	19	293	11	0.038	24	contig_end	Janus (likely)-h2 (likely)
L216		unresolved	38	293	3	0.010	32	contig_end	Lamia-h4
L217		unresolved	25	293	82	0.280	105	contig_end	Janus (likely)-h2 (likely)
L218		unresolved	21	293	13	0.044	34	contig_end
L219		unresolved	28	293	1	0.003	59	contig_end
L220		unresolved	28	293	2	0.007	52	contig_end
L221		unresolved	19	293	12	0.041	21	contig_end
L222		unresolved	15	293	3	0.010	7	contig_end
L223		unresolved	24	293	11	0.038	13	contig_end	Lamia-h4
L224		unresolved	43	293	11	0.038	102	contig_end	Janus (likely)-h2 (likely)
L225		unresolved	9	293	3	0.010	9	contig_end
L226		unresolved	9	293	3	0.010	6	contig_end	Lamia-h4
L227		unresolved	37	293	6	0.020	44	contig_end
L228		unresolved	24	293	21	0.072	34	contig_end
L229		unresolved	12	293	3	0.010	12	contig_end
L230		unresolved	33	293	35	0.119	55	contig_end
L231		unresolved	21	293	3	0.010	31	contig_end
L232		unresolved	23	293	25	0.085	51	contig_end
L233		unresolved	55	293	18	0.061	168	contig_end
L234		unresolved	15	293	2	0.007	32	contig_end	Osiris-h3
L235		unresolved	39	293	36	0.123	131	contig_end	Lamia-h4
L236		unresolved	16	293	19	0.065	11	contig_end
L237		unresolved	20	293	16	0.055	59	contig_end	Osiris-h3
L238		unresolved	39	293	5	0.017	117	contig_end
L239		unresolved	12	293	27	0.092	16	contig_end
L240		unresolved	18	293	7	0.024	18	contig_end
L241		unresolved	37	293	6	0.020	85	contig_end
L242		unresolved	9	293	6	0.020	12	contig_end
L243		unresolved	12	293	38	0.130	68	contig_end	Osiris-h3
L244		unresolved	10	293	6	0.020	10	contig_end
L245		unresolved	29	293	5	0.017	42	contig_end
L246		unresolved	23	293	0	0.000	6	contig_end
L247		unresolved	10	293	0	0.000	5	contig_end
L248		unresolved	52	293	0	0.000	5	contig_end	Lamia-h4