coccidioides_pangenome / immitis_in_posadasii_out

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250 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 146, content_variants 61, swap_candidate 18, monomorphic 14, presence_absence 6, rare_content 4, absent_in_focal 1

All loci: carrier fraction against locus type.

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

Strips for all loci (PDF)

Swap candidates (TSV)

key	type	size	n_strains	content_n	content_frac	n_states	tier	pair
L001	swap_candidate	7	169	148	0.876	8	contig_end	PPPPPPP(44) vs PPAAAPP(104)
L002	swap_candidate	11	169	146	0.864	21	short_flanks	PPPPPPPPPPP(54) vs AAAAAPPPPPP(53)
L003	monomorphic	7	169	158	0.935	9	full
L004	monomorphic	7	169	158	0.935	9	full
L005	monomorphic	7	169	158	0.935	9	full
L006	swap_candidate	8	169	166	0.982	10	full	PPPPPPPP(43) vs AAAPPPPP(103)
L007	swap_candidate	8	169	166	0.982	9	full	PPPPPPPP(46) vs PPPPPAAA(103)
L008	monomorphic	10	169	165	0.976	4	contig_end
L009	monomorphic	9	169	165	0.976	4	full
L010	rare_content	13	169	4	0.024	11	full
L011	monomorphic	11	169	158	0.935	6	full
L012	monomorphic	11	169	158	0.935	6	full
L013	content_variants	6	169	151	0.893	17	full
L014	content_variants	6	169	152	0.899	16	full
L015	content_variants	10	169	141	0.834	5	contig_end
L016	unresolved	12	169	68	0.402	16	contig_end
L017	swap_candidate	12	169	88	0.521	10	contig_end	PPPPPPPPPPPP(80) vs AAAAAAAAAAPP(77)
L018	swap_candidate	12	169	88	0.521	10	contig_end	PPPPPPPPPPPP(80) vs PPAAAAAAAAAA(77)
L019	swap_candidate	12	169	87	0.515	11	full	PPPPPPPPPPPP(80) vs PPAAAAAAAAAA(77)
L020	swap_candidate	9	169	118	0.698	11	full	PPPPPPPAA(89) vs APPPPPPAA(29)
L021	swap_candidate	9	169	118	0.698	11	full	AAPPPPPPP(89) vs AAPPPPPPA(29)
L022	content_variants	17	169	107	0.633	16	full
L023	content_variants	17	169	107	0.633	10	contig_end
L024	content_variants	17	169	107	0.633	9	contig_end
L025	content_variants	9	169	103	0.609	7	short_flanks
L026	content_variants	8	169	107	0.633	6	full
L027	content_variants	8	169	108	0.639	6	full
L028	content_variants	8	169	101	0.598	17	full
L029	content_variants	8	169	107	0.633	9	full
L030	content_variants	8	169	107	0.633	8	full
L031	content_variants	7	169	151	0.893	12	full
L032	content_variants	9	169	93	0.550	23	full
L033	content_variants	10	169	140	0.828	15	full
L034	swap_candidate	7	169	109	0.645	6	full	PPPPPPP(37) vs PPPPPPA(72)
L035	unresolved	12	169	49	0.290	10	contig_end
L036	unresolved	12	169	28	0.166	12	contig_end
L037	unresolved	10	169	73	0.432	17	short_flanks
L038	presence_absence	9	169	71	0.420	14	contig_end	PPPPPPPPP(67) vs AAAAAAAAA(18)
L039	presence_absence	9	169	67	0.396	14	full	PPPPPPPPP(67) vs AAAAAAAAA(18)
L040	swap_candidate	16	169	45	0.266	29	full	PPPPPPPPPPPPPPPP(41) vs PPAAAAAAAAAPPPPP(55)
L041	content_variants	7	169	123	0.728	15	contig_end
L042	content_variants	7	169	106	0.627	6	contig_end
L043	unresolved	21	169	67	0.396	51	full
L044	rare_content	13	169	13	0.077	17	short_flanks
L045	unresolved	16	169	88	0.521	63	full
L046	swap_candidate	8	169	105	0.621	35	contig_end	PPPPPPPP(51) vs PAAPPPPP(22)
L047	swap_candidate	8	169	93	0.550	41	full	PPPPPPPP(47) vs PPPAPPPP(23)
L048	swap_candidate	8	169	92	0.544	44	full	PPPPPPPP(45) vs PPPAPPPP(22)
L049	swap_candidate	25	169	41	0.243	34	contig_end	AAAAAAAPPPPPPPPPPPPPPPPPP(26) vs AAAAAAAAAAAAAAAAAAPPPPPPP(46)
L050	presence_absence	10	169	26	0.154	13	contig_end	PPPPPPPPPP(26) vs PAAAAAAAAA(129)
L051	swap_candidate	13	169	113	0.669	11	contig_end	PPPPPAPPPPPPA(30) vs PPAAAAPPPPPPA(75)
L052	unresolved	21	169	38	0.225	49	short_flanks
L053	unresolved	7	169	38	0.225	23	full
L054	unresolved	13	169	34	0.201	14	full
L055	content_variants	14	169	124	0.734	55	short_flanks
L056	content_variants	10	169	146	0.864	9	full
L057	content_variants	10	169	146	0.864	9	full
L058	content_variants	7	169	96	0.568	15	full
L059	unresolved	10	169	63	0.373	20	full
L060	presence_absence	13	169	48	0.284	29	contig_end	PPPPPPPPPPPPP(19) vs AAAAAPAAAAAAP(60)
L061	unresolved	16	169	71	0.420	81	full
L062	presence_absence	8	169	77	0.456	26	contig_end	PPPPPPPP(67) vs AAAAAAAA(18)
L063	unresolved	10	169	63	0.373	20	full
L064	content_variants	6	169	103	0.609	6	full
L065	unresolved	22	169	65	0.385	77	full
L066	content_variants	16	169	112	0.663	69	full
L067	content_variants	16	169	109	0.645	77	full
L068	content_variants	16	169	98	0.580	73	contig_end
L069	content_variants	16	169	100	0.592	70	full
L070	unresolved	7	169	76	0.450	12	contig_end
L071	unresolved	8	169	75	0.444	30	full
L072	content_variants	8	169	108	0.639	18	full
L073	content_variants	8	169	108	0.639	18	full
L074	content_variants	9	169	129	0.763	13	full
L075	unresolved	6	169	75	0.444	6	full
L076	unresolved	28	169	52	0.308	66	short_flanks
L077	rare_content	35	169	7	0.041	9	full
L078	unresolved	26	169	52	0.308	46	full
L079	unresolved	26	169	52	0.308	47	full
L080	unresolved	26	169	52	0.308	47	full
L081	content_variants	19	169	106	0.627	66	contig_end
L082	rare_content	48	169	9	0.053	23	full
L083	unresolved	79	169	0	0.000	32	full
L084	swap_candidate	19	169	38	0.225	40	full	PPPPPPPPPPPPPPPPPAP(35) vs AAAAAAAAAAAAAAAAAPA(18)
L085	content_variants	33	169	0	0.000	23	full
L086	content_variants	17	169	85	0.503	65	full
L087	content_variants	32	169	0	0.000	16	full
L088	presence_absence	7	169	2	0.012	14	full	AAAAPPA(31) vs AAAAAAA(108)
L089	swap_candidate	11	169	46	0.272	13	full	PPPPAAPPAPP(31) vs PPPAAAAAAPP(119)
L090	absent_in_focal	7	169	0	0.000	2	full
L091	content_variants	50	169	0	0.000	20	full
L092	unresolved	11	169	21	0.124	29	contig_end
L093	content_variants	24	169	0	0.000	19	full
L094	monomorphic	7	169	165	0.976	3	full
L095	monomorphic	7	169	166	0.982	3	contig_end
L096	monomorphic	7	169	166	0.982	3	short_flanks
L097	monomorphic	7	169	165	0.976	3	short_flanks
L098	content_variants	9	169	147	0.870	5	full
L099	content_variants	9	169	147	0.870	4	full
L100	content_variants	39	169	0	0.000	16	full
L101	monomorphic	9	169	154	0.911	6	full
L102	content_variants	7	169	152	0.899	8	full
L103	monomorphic	7	169	153	0.905	6	full
L104	monomorphic	7	169	155	0.917	8	full
L105	content_variants	8	169	108	0.639	17	full
L106	content_variants	8	169	111	0.657	8	contig_end
L107	unresolved	9	169	60	0.355	4	full
L108	unresolved	9	169	60	0.355	4	contig_end
L109	unresolved	9	169	54	0.320	6	short_flanks
L110	unresolved	9	169	54	0.320	6	full
L111	content_variants	7	169	119	0.704	11	full
L112	content_variants	8	169	111	0.657	9	contig_end
L113	content_variants	8	169	111	0.657	8	full
L114	content_variants	10	169	91	0.538	12	full
L115	content_variants	10	169	92	0.544	19	full
L116	content_variants	10	169	91	0.538	13	full
L117	content_variants	7	169	128	0.757	6	full
L118	unresolved	8	169	102	0.604	27	short_flanks
L119	unresolved	7	169	65	0.385	26	full
L120	unresolved	7	169	62	0.367	24	full
L121	unresolved	7	169	55	0.325	22	full
L122	unresolved	11	169	68	0.402	10	full
L123	unresolved	11	169	68	0.402	10	contig_end
L124	unresolved	11	169	68	0.402	7	contig_end
L125	unresolved	10	169	73	0.432	20	full
L126	unresolved	45	169	2	0.012	37	full
L127	unresolved	8	169	54	0.320	17	short_flanks
L128	unresolved	8	169	60	0.355	17	short_flanks
L129	content_variants	51	169	0	0.000	30	full
L130	unresolved	8	169	71	0.420	6	full
L131	unresolved	7	169	47	0.278	9	full
L132	unresolved	7	169	79	0.467	6	short_flanks
L133	unresolved	14	169	12	0.071	16	full
L134	content_variants	11	169	85	0.503	81	short_flanks
L135	unresolved	11	169	46	0.272	13	short_flanks
L136	unresolved	10	169	34	0.201	7	full
L137	content_variants	18	169	122	0.722	71	full
L138	content_variants	18	169	121	0.716	70	contig_end
L139	content_variants	18	169	105	0.621	69	contig_end
L140	content_variants	18	169	111	0.657	72	contig_end
L141	content_variants	12	169	90	0.533	23	contig_end
L142	unresolved	13	169	17	0.101	21	short_flanks
L143	unresolved	36	169	4	0.024	14	short_flanks
L144	unresolved	23	169	0	0.000	9	full
L145	unresolved	10	169	0	0.000	5	contig_end
L146	unresolved	18	169	7	0.041	14	full
L147	unresolved	7	169	4	0.024	12	short_flanks
L148	unresolved	10	169	0	0.000	8	full
L149	unresolved	10	169	0	0.000	5	full
L150	unresolved	8	169	1	0.006	10	contig_end
L151	unresolved	7	169	0	0.000	6	full
L152	content_variants	15	169	112	0.663	66	full
L153	unresolved	11	169	0	0.000	9	full
L154	unresolved	10	169	0	0.000	2	short_flanks
L155	unresolved	13	169	31	0.183	60	short_flanks
L156	unresolved	11	169	2	0.012	6	full
L157	unresolved	9	169	82	0.485	50	full
L158	unresolved	7	169	3	0.018	12	full
L159	unresolved	12	169	17	0.101	12	full
L160	unresolved	7	169	21	0.124	29	full
L161	unresolved	14	169	0	0.000	6	short_flanks
L162	unresolved	16	169	0	0.000	8	full
L163	unresolved	8	169	0	0.000	8	full
L164	unresolved	26	169	2	0.012	16	full
L165	unresolved	10	169	26	0.154	41	short_flanks
L166	content_variants	9	169	91	0.538	42	full
L167	unresolved	11	169	0	0.000	7	contig_end
L168	unresolved	43	169	0	0.000	18	contig_end
L169	unresolved	10	169	0	0.000	4	contig_end
L170	unresolved	25	169	0	0.000	7	contig_end
L171	unresolved	8	169	17	0.101	12	contig_end
L172	unresolved	11	169	0	0.000	6	contig_end
L173	content_variants	8	169	129	0.763	54	contig_end
L174	unresolved	18	169	28	0.166	43	contig_end
L175	unresolved	12	169	5	0.030	10	contig_end
L176	unresolved	7	169	11	0.065	22	contig_end
L177	content_variants	9	169	93	0.550	39	contig_end
L178	unresolved	11	169	10	0.059	54	contig_end
L179	unresolved	10	169	0	0.000	6	contig_end
L180	unresolved	9	169	65	0.385	35	contig_end
L181	unresolved	16	169	5	0.030	45	contig_end
L182	unresolved	16	169	79	0.467	56	contig_end
L183	unresolved	14	169	0	0.000	6	contig_end
L184	unresolved	7	169	68	0.402	19	contig_end
L185	unresolved	42	169	5	0.030	13	contig_end
L186	unresolved	17	169	3	0.018	11	contig_end
L187	unresolved	63	169	63	0.373	94	contig_end
L188	unresolved	26	169	2	0.012	29	contig_end
L189	unresolved	18	169	0	0.000	11	contig_end
L190	unresolved	69	169	5	0.030	28	contig_end
L191	unresolved	7	169	0	0.000	4	contig_end
L192	unresolved	16	169	93	0.550	65	contig_end
L193	unresolved	39	169	4	0.024	43	contig_end
L194	unresolved	74	169	6	0.036	31	contig_end
L195	unresolved	48	169	20	0.118	31	contig_end
L196	content_variants	15	169	92	0.544	90	contig_end
L197	unresolved	22	169	2	0.012	35	contig_end
L198	unresolved	28	169	0	0.000	10	contig_end
L199	unresolved	11	169	0	0.000	16	contig_end
L200	unresolved	10	169	31	0.183	17	contig_end
L201	unresolved	19	169	2	0.012	11	contig_end
L202	unresolved	13	169	27	0.160	87	contig_end
L203	unresolved	7	169	78	0.462	26	contig_end
L204	unresolved	48	169	59	0.349	67	contig_end
L205	unresolved	8	169	13	0.077	24	contig_end
L206	unresolved	16	169	0	0.000	8	contig_end
L207	unresolved	7	169	21	0.124	11	contig_end
L208	unresolved	33	169	9	0.053	24	contig_end
L209	unresolved	32	169	61	0.361	103	contig_end
L210	unresolved	8	169	3	0.018	6	contig_end
L211	content_variants	16	169	144	0.852	108	contig_end
L212	unresolved	10	169	0	0.000	5	contig_end
L213	unresolved	11	169	0	0.000	16	contig_end
L214	unresolved	8	169	0	0.000	5	contig_end
L215	unresolved	22	169	0	0.000	14	contig_end
L216	unresolved	15	169	9	0.053	23	contig_end
L217	unresolved	13	169	1	0.006	41	contig_end
L218	unresolved	8	169	4	0.024	9	contig_end
L219	unresolved	16	169	0	0.000	7	contig_end
L220	unresolved	33	169	1	0.006	11	contig_end
L221	unresolved	22	169	4	0.024	45	contig_end
L222	unresolved	57	169	1	0.006	40	contig_end
L223	unresolved	22	169	2	0.012	35	contig_end
L224	unresolved	61	169	0	0.000	37	contig_end
L225	unresolved	21	169	0	0.000	13	contig_end
L226	unresolved	8	169	0	0.000	8	contig_end
L227	unresolved	50	169	1	0.006	23	contig_end
L228	unresolved	10	169	7	0.041	29	contig_end
L229	unresolved	13	169	3	0.018	24	contig_end
L230	unresolved	9	169	0	0.000	8	contig_end
L231	unresolved	35	169	8	0.047	12	contig_end
L232	unresolved	32	169	5	0.030	23	contig_end
L233	unresolved	12	169	2	0.012	25	contig_end
L234	unresolved	25	169	5	0.030	17	contig_end
L235	unresolved	7	169	3	0.018	10	contig_end
L236	unresolved	21	169	1	0.006	63	contig_end
L237	unresolved	33	169	0	0.000	18	contig_end
L238	unresolved	11	169	5	0.030	16	contig_end
L239	unresolved	19	169	2	0.012	23	contig_end
L240	unresolved	49	169	0	0.000	29	contig_end
L241	unresolved	30	169	1	0.006	15	contig_end
L242	unresolved	15	169	0	0.000	19	contig_end
L243	unresolved	13	169	8	0.047	37	contig_end
L244	unresolved	78	169	12	0.071	50	contig_end
L245	unresolved	54	169	1	0.006	35	contig_end
L246	unresolved	25	169	8	0.047	19	contig_end
L247	unresolved	19	169	5	0.030	10	contig_end
L248	unresolved	48	169	5	0.030	36	contig_end
L249	unresolved	10	169	76	0.450	23	contig_end
L250	unresolved	34	169	0	0.000	16	contig_end