import numpy as np
from IPython.display import HTML
from bokeh.plotting import output_notebook, show
import genomes_dnj.lct_interval.series_plots as dm
import genomes_dnj.lct_interval.chrom_plots as cp
output_notebook(hide_banner=True)

Dense Series

The studies of SNP series statistics showed large variations in the number of active series at different positions of the autosomal chromosomes, the number of SNPs in those series and lengths of the series in DNA bases. These studies also showed that chromosomes could be partitioned into regions between positions where the number of active series went to zero. The studies in these notebooks focus on one of these regions of chromosome 2 where the gene lct is located.

For chromosome 2, the mean number of SNPs in a series is 10 and the mean length of a series is 55,000 DNA bases. But, the lactase persistence region of chromosome 2 includes many series with SNP counts and lengths that far exceed these means and are expressed by large numbers of the 1000 genomes chromosome 2 samples. Four of the most exceptional series are 117_1685, 123_1561, 62_1265, and 193_843. Those series include a total of 495 SNPs Each of them covers a large part the first 600,000 bases of the studied region of chromosome 2. That DNA segment includes the genes rab3gap1, zranb3 and the lower half of r3hdm1. Over 2,000 of the 5,008 1000 genomes chromosome 2 samples express at least one of these four series. All four of them are expressed by 842 of those samples.

There is no obvious process for generating series that include these large numbers of SNPs simply from some event that selects for the functional role of a single SNP. The problem posed by the varying combinations of the series expressed by different chromosome 2 samples is even more difficult. But, the series do tend to be part of hierarchies where some series is specific for the hierarchy and appears to have played some kind of role in the process that selected that hierarchy for overexpression. For example the series 193_843 is the selector series for the hierarchies that are associated with the SAS tree.

The series 28_434 is an example of a more complex selector series. It acts as a selector series for multiple hierarchies with varying combinations of the series 117_1685 and 123_1561. Those hierarchies have been generated by processes that include fragmentation of series, recombination events, and appearance of new series that selected some 28_434 subtree for overexpression.

This notebook provides an introduction to these four series and some of the events that appear to have caused them to be so widely expressed.

Series 193_843

The 843 chromosome 2 samples that express the 193 SNPs in the 628,000 DNA base series 193_843 all also express the overlapping series 123_1561 and 62_1265. All but one of them express 117_1685. The series 193_843 is a major part of the root of the SAS tree. But, no samples express just the root of that tree. The large number of samples expressing 193_843 appear to be the result of processes during the human expansion from Africa that generated an hierarchy of overexpressed new series. But, the process that generated 193_843 itself has not left any obvious trace.

plt_obj = dm.superset_yes_no([dm.di_193_843], min_match=0.5)
plt = plt_obj.do_plot()
show(plt)

<Bokeh Notebook handle for In[2]>

HTML(plt_obj.get_html())

index	first	length	snps	alleles		matches		afr		afx		amr		eas		eur		sas		sax
353244	135,758,231	618,284	117	1685	0.50	842	1.00	79	0.47	26	0.49	143	1.23	167	0.99	83	0.49	116	1.90	228	2.21
353478	135,933,921	434,642	123	1561	0.54	843	1.00	79	0.47	26	0.49	143	1.22	167	0.98	83	0.49	117	1.91	228	2.21
353814	136,406,646	31,432	5	1460	0.50	731	0.87	74	0.50	24	0.52	138	1.36	139	0.94	81	0.55	88	1.66	187	2.09
353269	135,766,890	509,095	62	1265	0.67	843	1.00	79	0.47	26	0.49	143	1.22	167	0.98	83	0.49	117	1.91	228	2.21
353790	136,393,157	48,253	10	1218	0.62	750	0.89	76	0.50	26	0.55	138	1.33	141	0.93	81	0.54	92	1.69	196	2.13
353906	136,496,493	57,432	9	1170	0.51	592	0.70	45	0.38	16	0.43	126	1.54	138	1.16	49	0.41	68	1.58	150	2.07
353849	136,447,707	42,559	4	1149	0.62	711	0.84	50	0.35	20	0.45	134	1.36	144	1.01	78	0.55	90	1.74	195	2.24
353907	136,496,805	55,824	9	1023	0.58	595	0.71	45	0.38	15	0.40	128	1.55	140	1.17	49	0.41	68	1.57	150	2.06
353984	136,556,805	190,280	39	1014	0.51	518	0.61	31	0.30	15	0.46	121	1.69	99	0.95	45	0.43	72	1.91	135	2.13
353935	136,511,874	21,321	5	976	0.48	468	0.56	44	0.47	13	0.44	77	1.19	129	1.37	18	0.19	61	1.79	126	2.20
353504	135,964,764	136,368	6	946	0.88	832	0.99	78	0.47	26	0.50	141	1.22	165	0.99	82	0.49	114	1.89	226	2.22
353807	136,403,994	81,102	13	911	0.77	703	0.83	45	0.32	17	0.39	134	1.38	142	1.00	79	0.56	91	1.78	195	2.26
353248	135,759,095	628,204	193	843	1.00	843	1.00	79	0.47	26	0.49	143	1.22	167	0.98	83	0.49	117	1.91	228	2.21
353938	136,514,709	28,438	6	820	0.57	467	0.55	44	0.47	12	0.41	77	1.19	129	1.37	18	0.19	61	1.80	126	2.20
353384	135,839,805	84,662	4	815	0.82	667	0.79	47	0.35	18	0.43	135	1.46	147	1.09	71	0.53	79	1.63	170	2.08
353521	135,989,333	275,298	6	713	0.94	668	0.79	47	0.35	18	0.43	135	1.46	146	1.09	73	0.54	79	1.63	170	2.08

Series 62_1265

The identity of 62_1265, the 62 SNP series expressed by 1265 samples as a series independent of 193_843 is primarily due to chromosome 2 samples that express the series 67_329. The 371 samples that express 67_329, 123_1561, and 117_1685 without 193_843 include 309 that express 67_329.

plt_obj = dm.superset_yes_no([dm.di_62_1265, dm.di_117_1685, dm.di_123_1561], [dm.di_193_843], min_match=0.5)
plt = plt_obj.do_plot()
show(plt)

<Bokeh Notebook handle for In[4]>

HTML(plt_obj.get_html())

index	first	length	snps	alleles		matches		afr		afx		amr		eas		eur		sas		sax
353921	136,501,840	53,819	10	2206	0.13	279	0.75	150	2.41	44	2.28	19	0.51	41	0.73	20	0.32	4	0.24	1	0.04
353244	135,758,231	618,284	117	1685	0.22	371	1.00	214	2.59	62	2.42	24	0.49	44	0.59	21	0.26	4	0.18	2	0.06
353478	135,933,921	434,642	123	1561	0.24	371	1.00	214	2.59	62	2.42	24	0.49	44	0.59	21	0.26	4	0.18	2	0.06
353814	136,406,646	31,432	5	1460	0.16	235	0.63	114	2.17	35	2.15	16	0.51	44	0.93	21	0.40	3	0.22	2	0.09
353269	135,766,890	509,095	62	1265	0.29	371	1.00	214	2.59	62	2.42	24	0.49	44	0.59	21	0.26	4	0.18	2	0.06
353729	136,309,239	52,321	9	887	0.42	369	0.99	213	2.59	62	2.43	24	0.49	44	0.59	21	0.26	4	0.18	1	0.03
353312	135,784,351	117,869	8	718	0.43	312	0.84	172	2.47	50	2.32	19	0.46	44	0.70	21	0.30	4	0.22	2	0.07
353851	136,448,855	17,976	4	612	0.36	218	0.59	105	2.16	33	2.19	16	0.55	40	0.91	20	0.41	3	0.23	1	0.05
353349	135,810,535	87,488	9	545	0.68	369	0.99	213	2.59	62	2.43	24	0.49	44	0.59	21	0.26	4	0.18	1	0.03
353904	136,495,815	46,924	9	378	0.55	208	0.56	100	2.16	29	2.02	14	0.51	41	0.98	20	0.43	3	0.24	1	0.05
353804	136,402,778	90,652	21	332	0.64	214	0.58	106	2.22	31	2.09	12	0.42	41	0.95	20	0.42	3	0.24	1	0.05
353331	135,795,222	587,478	67	329	0.94	309	0.83	170	2.47	50	2.34	19	0.46	44	0.71	21	0.31	4	0.22	1	0.03
354064	136,605,402	19,284	8	328	0.63	207	0.56	101	2.19	29	2.03	14	0.51	40	0.96	19	0.41	3	0.24	1	0.05
353263	135,764,184	345,934	100	279	0.97	271	0.73	142	2.35	40	2.13	19	0.53	44	0.80	21	0.35	4	0.25	1	0.04
353281	135,771,350	569,467	35	240	1.00	239	0.64	120	2.25	36	2.18	13	0.41	44	0.91	21	0.40	4	0.28	1	0.05
353780	136,388,934	198,304	28	231	0.84	193	0.52	92	2.14	27	2.02	11	0.43	40	1.03	19	0.44	3	0.26	1	0.06

The overexpression of the 209 SNP series 209_56 expressed by 56 chromosome 2 samples appears to have resulted from an indepdent selection process for chromosome 2 samples that express 62_1265, 123_1561, and 117_1685 but not 193_843. This process appears to have started with a more extended series that included 209_56 and 14_48. The full series of selected SNPs also included 117_1685, 123_1561, 62_1265, 26_1414 and 10_2206. All of these series have participated in other independent selection processes that formed different hierarchies.

plt_obj = dm.superset_yes_no([dm.di_209_56], min_match=0.5)
plt = plt_obj.do_plot()
show(plt)

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HTML(plt_obj.get_html())

index	first	length	snps	alleles		matches		afr		afx		amr		eas		eur		sas		sax
353921	136,501,840	53,819	10	2206	0.02	51	0.91	36	3.51	10	3.13	5	0.71	0	0.00	0	0.00	0	0.00	0	0.00
353244	135,758,231	618,284	117	1685	0.03	56	1.00	40	3.55	11	3.13	5	0.64	0	0.00	0	0.00	0	0.00	0	0.00
353478	135,933,921	434,642	123	1561	0.04	56	1.00	40	3.55	11	3.13	5	0.64	0	0.00	0	0.00	0	0.00	0	0.00
354130	136,653,925	107,928	24	1504	0.02	37	0.66	26	3.49	6	2.59	5	0.98	0	0.00	0	0.00	0	0.00	0	0.00
353797	136,398,174	75,924	26	1414	0.04	51	0.91	37	3.60	10	3.13	4	0.57	0	0.00	0	0.00	0	0.00	0	0.00
353269	135,766,890	509,095	62	1265	0.04	56	1.00	40	3.55	11	3.13	5	0.64	0	0.00	0	0.00	0	0.00	0	0.00
353729	136,309,239	52,321	9	887	0.06	56	1.00	40	3.55	11	3.13	5	0.64	0	0.00	0	0.00	0	0.00	0	0.00
353764	136,364,916	22,977	5	588	0.10	56	1.00	40	3.55	11	3.13	5	0.64	0	0.00	0	0.00	0	0.00	0	0.00
353349	135,810,535	87,488	9	545	0.10	56	1.00	40	3.55	11	3.13	5	0.64	0	0.00	0	0.00	0	0.00	0	0.00
354189	136,704,466	27,748	5	212	0.17	36	0.64	26	3.59	6	2.66	4	0.80	0	0.00	0	0.00	0	0.00	0	0.00
354143	136,658,238	19,681	6	167	0.22	36	0.64	26	3.59	6	2.66	4	0.80	0	0.00	0	0.00	0	0.00	0	0.00
353486	135,946,660	156,668	5	96	0.58	56	1.00	40	3.55	11	3.13	5	0.64	0	0.00	0	0.00	0	0.00	0	0.00
353276	135,769,240	617,518	209	56	1.00	56	1.00	40	3.55	11	3.13	5	0.64	0	0.00	0	0.00	0	0.00	0	0.00
353833	136,428,402	221,239	14	48	0.96	46	0.82	33	3.56	9	3.12	4	0.63	0	0.00	0	0.00	0	0.00	0	0.00
353347	135,809,270	491,372	10	43	1.00	43	0.77	31	3.58	8	2.97	4	0.67	0	0.00	0	0.00	0	0.00	0	0.00
354128	136,652,918	133,712	80	38	0.95	36	0.64	26	3.59	6	2.66	4	0.80	0	0.00	0	0.00	0	0.00	0	0.00

There are 43 samples that express 62_1265 and 117_1685 but not 123_1561 or 193_843. Those samples include 39 that are the result of the appearance of the series 9_39. The hierarchy selected by this series is rooted in a genetic event that recombined series 8_267 that is part of the SAS tree with the series 32_1361 and 81_857 that are part of the EAS tree root. Fragments of the series 193_843 and 123_1561 are still visible in the chromosme samples that express series that derive from this event.

plt_obj = dm.superset_yes_no([dm.di_117_1685, dm.di_62_1265], [dm.di_123_1561], min_match=0.5)
plt = plt_obj.do_plot()
show(plt)

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HTML(plt_obj.get_html())

index	first	length	snps	alleles		matches		afr		afx		amr		eas		eur		sas		sax
354033	136,588,031	5,647	7	1760	0.02	35	0.81	2	0.42	0	0.00	9	1.71	0	0.00	21	2.30	0	0.00	3	0.78
353244	135,758,231	618,284	117	1685	0.03	43	1.00	2	0.35	0	0.00	13	2.01	0	0.00	25	2.22	0	0.00	3	0.64
354130	136,653,925	107,928	24	1504	0.02	32	0.74	2	0.46	0	0.00	9	1.87	0	0.00	18	2.15	0	0.00	3	0.85
353925	136,506,375	32,564	4	1442	0.02	35	0.81	2	0.42	0	0.00	9	1.71	0	0.00	21	2.30	0	0.00	3	0.78
353791	136,393,658	92,684	32	1361	0.03	43	1.00	2	0.35	0	0.00	13	2.01	0	0.00	25	2.22	0	0.00	3	0.64
353958	136,535,876	19,014	7	1303	0.03	35	0.81	2	0.42	0	0.00	9	1.71	0	0.00	21	2.30	0	0.00	3	0.78
354129	136,652,953	108,222	5	1296	0.02	32	0.74	2	0.46	0	0.00	9	1.87	0	0.00	18	2.15	0	0.00	3	0.85
353269	135,766,890	509,095	62	1265	0.03	43	1.00	2	0.35	0	0.00	13	2.01	0	0.00	25	2.22	0	0.00	3	0.64
353919	136,500,475	42,085	13	1227	0.03	35	0.81	2	0.42	0	0.00	9	1.71	0	0.00	21	2.30	0	0.00	3	0.78
354127	136,652,491	80,281	6	1114	0.03	32	0.74	2	0.46	0	0.00	9	1.87	0	0.00	18	2.15	0	0.00	3	0.85
353504	135,964,764	136,368	6	946	0.04	42	0.98	1	0.18	0	0.00	13	2.06	0	0.00	25	2.28	0	0.00	3	0.65
353902	136,494,985	278,653	81	857	0.04	32	0.74	2	0.46	0	0.00	9	1.87	0	0.00	18	2.15	0	0.00	3	0.85
353384	135,839,805	84,662	4	815	0.05	42	0.98	1	0.18	0	0.00	13	2.06	0	0.00	25	2.28	0	0.00	3	0.65
353521	135,989,333	275,298	6	713	0.06	42	0.98	1	0.18	0	0.00	13	2.06	0	0.00	25	2.28	0	0.00	3	0.65
353358	135,818,487	471,078	8	267	0.16	42	0.98	1	0.18	0	0.00	13	2.06	0	0.00	25	2.28	0	0.00	3	0.65
353559	136,028,572	409,893	9	39	1.00	39	0.91	1	0.19	0	0.00	13	2.22	0	0.00	22	2.16	0	0.00	3	0.70

Series 117_1685

The identity of 117_1685 as a distinct series is largely the result of the 210 chromosomes that express the 74 SNP series 74_210. Those chromosomes all express 117_1685 but not 123_1561, 62_1265, or 193_843. Nor is there any pattern of residual fragments of any of those series that might provide some trace of an history of series SNP remodling events.

plt_obj = dm.superset_yes_no([dm.di_117_1685, dm.di_74_210], [dm.di_28_434, dm.di_123_1561], min_match=0.5)
plt = plt_obj.do_plot()
show(plt)

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HTML(plt_obj.get_html())

index	first	length	snps	alleles		matches		afr		afx		amr		eas		eur		sas		sax
353244	135,758,231	618,284	117	1685	0.12	210	1.00	61	2.66	12	1.67	29	0.89	3	0.06	66	1.15	14	0.92	25	1.04
353906	136,496,493	57,432	9	1170	0.16	188	0.90	48	2.34	10	1.55	28	0.96	3	0.07	64	1.25	13	0.96	22	1.02
353907	136,496,805	55,824	9	1023	0.19	190	0.90	47	2.27	10	1.54	28	0.95	3	0.07	65	1.25	14	1.02	23	1.06
353984	136,556,805	190,280	39	1014	0.16	167	0.80	30	1.65	9	1.57	28	1.08	3	0.07	63	1.38	13	1.08	21	1.10
353935	136,511,874	21,321	5	976	0.13	131	0.62	48	3.36	10	2.23	21	1.03	3	0.10	30	0.84	7	0.74	12	0.80
353938	136,514,709	28,438	6	820	0.16	130	0.62	47	3.31	10	2.25	21	1.04	3	0.10	30	0.84	7	0.75	12	0.81
353312	135,784,351	117,869	8	718	0.29	210	1.00	61	2.66	12	1.67	29	0.89	3	0.06	66	1.15	14	0.92	25	1.04
353249	135,759,145	604,162	74	210	1.00	210	1.00	61	2.66	12	1.67	29	0.89	3	0.06	66	1.15	14	0.92	25	1.04
353325	135,790,329	493,075	18	131	0.99	130	0.62	0	0.00	2	0.45	26	1.28	3	0.10	60	1.69	14	1.49	25	1.68

The series 290_16 is another case of chromosomes expressing only 117_1685. The number of chromosomes expressing this series is modest. But its 290 SNPs are a particularly large number.

plt_obj = dm.superset_yes_no([dm.di_290_16], min_match=0.5)
plt = plt_obj.do_plot()
show(plt)

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HTML(plt_obj.get_html())

index	first	length	snps	alleles		matches		afr		afx		amr		eas		eur		sas		sax
353244	135,758,231	618,284	117	1685	0.01	16	1.00	14	4.35	1	1.00	1	0.45	0	0.00	0	0.00	0	0.00	0	0.00
353906	136,496,493	57,432	9	1170	0.01	10	0.62	9	4.47	0	0.00	1	0.72	0	0.00	0	0.00	0	0.00	0	0.00
353907	136,496,805	55,824	9	1023	0.01	10	0.62	9	4.47	0	0.00	1	0.72	0	0.00	0	0.00	0	0.00	0	0.00
353984	136,556,805	190,280	39	1014	0.01	10	0.62	9	4.47	0	0.00	1	0.72	0	0.00	0	0.00	0	0.00	0	0.00
353935	136,511,874	21,321	5	976	0.01	10	0.62	9	4.47	0	0.00	1	0.72	0	0.00	0	0.00	0	0.00	0	0.00
353729	136,309,239	52,321	9	887	0.02	16	1.00	14	4.35	1	1.00	1	0.45	0	0.00	0	0.00	0	0.00	0	0.00
353938	136,514,709	28,438	6	820	0.01	10	0.62	9	4.47	0	0.00	1	0.72	0	0.00	0	0.00	0	0.00	0	0.00
353312	135,784,351	117,869	8	718	0.02	16	1.00	14	4.35	1	1.00	1	0.45	0	0.00	0	0.00	0	0.00	0	0.00
353764	136,364,916	22,977	5	588	0.03	16	1.00	14	4.35	1	1.00	1	0.45	0	0.00	0	0.00	0	0.00	0	0.00
353349	135,810,535	87,488	9	545	0.03	16	1.00	14	4.35	1	1.00	1	0.45	0	0.00	0	0.00	0	0.00	0	0.00
353388	135,841,328	88,121	4	21	0.76	16	1.00	14	4.35	1	1.00	1	0.45	0	0.00	0	0.00	0	0.00	0	0.00
353480	135,938,537	309,346	6	18	0.89	16	1.00	14	4.35	1	1.00	1	0.45	0	0.00	0	0.00	0	0.00	0	0.00
353922	136,504,541	23,683	4	17	0.59	10	0.62	9	4.47	0	0.00	1	0.72	0	0.00	0	0.00	0	0.00	0	0.00
353261	135,762,824	682,468	290	16	1.00	16	1.00	14	4.35	1	1.00	1	0.45	0	0.00	0	0.00	0	0.00	0	0.00

Series 28_434

The 434 chromosomse 2 samples that express the series 28_434 provide some insight into the history that generated the four different hierarchies rooted in that series. Those hierarchies include varying combinations of 117_1685 and 123_1561. That selection process included extensive remodling of series 117_1685 and 123_1561 SNPs, two recombination events, and four significant selection processes. Each of those processes has selected an independent subtree of 28_434 for overexpression. This plot shows the results of one of those selection processes. It generated the hiearchy that incudes the 25 SNP series 25_27 that is associated with a combination of the series 28_434, 123_1561, and 117_1685.

plt_obj = dm.superset_yes_no([dm.di_123_1561, dm.di_117_1685], [dm.di_62_1265], min_match=0.5)
plt = plt_obj.do_plot()
show(plt)

<Bokeh Notebook handle for In[14]>

HTML(plt_obj.get_html())

index	first	length	snps	alleles		matches		afr		afx		amr		eas		eur		sas		sax
354170	136,682,274	93,624	7	1868	0.01	17	0.55	10	3.10	6	5.85	1	0.43	0	0.00	0	0.00	0	0.00	0	0.00
354033	136,588,031	5,647	7	1760	0.01	20	0.65	11	2.90	8	6.62	1	0.36	0	0.00	0	0.00	0	0.00	0	0.00
353244	135,758,231	618,284	117	1685	0.02	31	1.00	21	3.57	8	4.27	2	0.47	0	0.00	0	0.00	0	0.00	0	0.00
353478	135,933,921	434,642	123	1561	0.02	31	1.00	21	3.57	8	4.27	2	0.47	0	0.00	0	0.00	0	0.00	0	0.00
353814	136,406,646	31,432	5	1460	0.02	30	0.97	20	3.51	8	4.42	2	0.49	0	0.00	0	0.00	0	0.00	0	0.00
353729	136,309,239	52,321	9	887	0.03	30	0.97	20	3.51	8	4.42	2	0.49	0	0.00	0	0.00	0	0.00	0	0.00
353851	136,448,855	17,976	4	612	0.05	30	0.97	20	3.51	8	4.42	2	0.49	0	0.00	0	0.00	0	0.00	0	0.00
353764	136,364,916	22,977	5	588	0.05	29	0.94	19	3.45	8	4.57	2	0.50	0	0.00	0	0.00	0	0.00	0	0.00
354061	136,603,638	28,487	16	511	0.03	16	0.52	9	2.96	6	6.21	1	0.46	0	0.00	0	0.00	0	0.00	0	0.00
353614	136,115,507	269,773	28	434	0.07	29	0.94	19	3.45	8	4.57	2	0.50	0	0.00	0	0.00	0	0.00	0	0.00
353804	136,402,778	90,652	21	332	0.08	26	0.84	17	3.44	7	4.46	2	0.56	0	0.00	0	0.00	0	0.00	0	0.00
354057	136,602,291	27,696	7	226	0.07	16	0.52	9	2.96	6	6.21	1	0.46	0	0.00	0	0.00	0	0.00	0	0.00
353931	136,509,361	28,756	11	173	0.09	16	0.52	9	2.96	6	6.21	1	0.46	0	0.00	0	0.00	0	0.00	0	0.00
353538	136,008,173	373,078	70	166	0.16	26	0.84	17	3.44	7	4.46	2	0.56	0	0.00	0	0.00	0	0.00	0	0.00
354036	136,589,521	52,491	17	127	0.13	16	0.52	9	2.96	6	6.21	1	0.46	0	0.00	0	0.00	0	0.00	0	0.00
353910	136,497,006	91,732	19	77	0.21	16	0.52	9	2.96	6	6.21	1	0.46	0	0.00	0	0.00	0	0.00	0	0.00
353581	136,056,699	377,203	5	69	0.36	25	0.81	16	3.37	7	4.64	2	0.58	0	0.00	0	0.00	0	0.00	0	0.00
353563	136,033,448	378,721	7	34	0.76	26	0.84	17	3.44	7	4.46	2	0.56	0	0.00	0	0.00	0	0.00	0	0.00
354101	136,633,976	108,844	6	27	0.59	16	0.52	9	2.96	6	6.21	1	0.46	0	0.00	0	0.00	0	0.00	0	0.00
353496	135,956,166	528,513	25	27	0.93	25	0.81	16	3.37	7	4.64	2	0.58	0	0.00	0	0.00	0	0.00	0	0.00

The next plot shows another hierarchy expressed by a subset of the 28_434 samples. The selection process for this hierarchy worked with the 180 SNP series 180_251. The 251 samples that express 180_251 and 28_434 also express 123_1561 and 13_1696 but not 117_1685. They are almost all of the samples that express 28_434 but not 117_1685. They are a large part of the samples that express 123_1561 but not 117_1685, 62_1265, or 193_843.

plt_obj = dm.superset_yes_no([dm.di_123_1561, dm.di_28_434], [dm.di_117_1685], min_match=0.5)
plt = plt_obj.do_plot()
show(plt)

<Bokeh Notebook handle for In[16]>

HTML(plt_obj.get_html())

index	first	length	snps	alleles		matches		afr		afx		amr		eas		eur		sas		sax
354033	136,588,031	5,647	7	1760	0.11	186	0.73	145	5.17	37	4.13	4	0.15	0	0.00	0	0.00	0	0.00	0	0.00
353240	135,757,320	20,184	13	1696	0.15	251	0.98	191	5.05	56	4.63	4	0.11	0	0.00	0	0.00	0	0.00	0	0.00
353478	135,933,921	434,642	123	1561	0.16	256	1.00	195	5.05	56	4.54	5	0.14	0	0.00	0	0.00	0	0.00	0	0.00
353790	136,393,157	48,253	10	1218	0.20	244	0.95	185	5.03	55	4.68	4	0.11	0	0.00	0	0.00	0	0.00	0	0.00
353906	136,496,493	57,432	9	1170	0.12	138	0.54	100	4.81	36	5.42	2	0.10	0	0.00	0	0.00	0	0.00	0	0.00
353935	136,511,874	21,321	5	976	0.14	138	0.54	100	4.81	36	5.42	2	0.10	0	0.00	0	0.00	0	0.00	0	0.00
353729	136,309,239	52,321	9	887	0.29	256	1.00	195	5.05	56	4.54	5	0.14	0	0.00	0	0.00	0	0.00	0	0.00
353851	136,448,855	17,976	4	612	0.37	225	0.88	168	4.95	52	4.80	5	0.15	0	0.00	0	0.00	0	0.00	0	0.00
353764	136,364,916	22,977	5	588	0.43	255	1.00	194	5.05	56	4.56	5	0.14	0	0.00	0	0.00	0	0.00	0	0.00
353614	136,115,507	269,773	28	434	0.59	256	1.00	195	5.05	56	4.54	5	0.14	0	0.00	0	0.00	0	0.00	0	0.00
353288	135,773,319	720,812	180	251	1.00	251	0.98	190	5.02	56	4.63	5	0.14	0	0.00	0	0.00	0	0.00	0	0.00
353300	135,778,464	608,500	23	226	1.00	225	0.88	171	5.04	50	4.62	4	0.12	0	0.00	0	0.00	0	0.00	0	0.00
353909	136,496,875	51,331	18	148	0.89	132	0.52	96	4.82	34	5.35	2	0.11	0	0.00	0	0.00	0	0.00	0	0.00

The next plot shows another hierarchy expressed by 73 of the 28_434 samples. This hierarchy is formed by samples that express 28_434 and 117_1685 but not 123_1561 or 13_1696. It is expressed by 67 of the 6_68 samples and all 40 of the 14_40 samples.

plt_obj = dm.superset_yes_no([dm.di_117_1685, dm.di_28_434], [dm.di_13_1696, dm.di_123_1561], min_match=0.5)
plt = plt_obj.do_plot()
show(plt)

<Bokeh Notebook handle for In[18]>

HTML(plt_obj.get_html())

index	first	length	snps	alleles		matches		afr		afx		amr		eas		eur		sas		sax
354033	136,588,031	5,647	7	1760	0.03	44	0.60	33	8.04	10	6.08	1	0.13	0	0.00	0	0.00	0	0.00	0	0.00
353244	135,758,231	618,284	117	1685	0.04	73	1.00	56	8.23	15	5.49	2	0.15	0	0.00	0	0.00	0	0.00	0	0.00
353814	136,406,646	31,432	5	1460	0.04	53	0.73	38	7.69	14	7.06	1	0.11	0	0.00	0	0.00	0	0.00	0	0.00
353729	136,309,239	52,321	9	887	0.08	73	1.00	56	8.23	15	5.49	2	0.15	0	0.00	0	0.00	0	0.00	0	0.00
353312	135,784,351	117,869	8	718	0.10	71	0.97	54	8.16	15	5.65	2	0.16	0	0.00	0	0.00	0	0.00	0	0.00
353851	136,448,855	17,976	4	612	0.08	49	0.67	38	8.32	10	5.46	1	0.11	0	0.00	0	0.00	0	0.00	0	0.00
353764	136,364,916	22,977	5	588	0.12	73	1.00	56	8.23	15	5.49	2	0.15	0	0.00	0	0.00	0	0.00	0	0.00
353349	135,810,535	87,488	9	545	0.12	68	0.93	53	8.36	14	5.51	1	0.08	0	0.00	0	0.00	0	0.00	0	0.00
353614	136,115,507	269,773	28	434	0.17	73	1.00	56	8.23	15	5.49	2	0.15	0	0.00	0	0.00	0	0.00	0	0.00
353804	136,402,778	90,652	21	332	0.13	44	0.60	33	8.04	10	6.08	1	0.13	0	0.00	0	0.00	0	0.00	0	0.00
353538	136,008,173	373,078	70	166	0.40	66	0.90	49	7.96	15	6.08	2	0.17	0	0.00	0	0.00	0	0.00	0	0.00
353304	135,780,924	236,215	49	136	0.46	62	0.85	47	8.13	14	6.04	1	0.09	0	0.00	0	0.00	0	0.00	0	0.00
353581	136,056,699	377,203	5	69	0.64	44	0.60	32	7.80	12	7.29	0	0.00	0	0.00	0	0.00	0	0.00	0	0.00
353247	135,758,713	19,520	6	68	0.99	67	0.92	53	8.48	13	5.19	1	0.08	0	0.00	0	0.00	0	0.00	0	0.00
353354	135,814,021	610,527	14	40	1.00	40	0.55	30	8.04	10	6.69	0	0.00	0	0.00	0	0.00	0	0.00	0	0.00

This plot shows the hierarchy rooted in the 28_434, 117_1685, and 13_1696 association. This hierarchy appears to have resulted from the appearance of the series 22_73.

plt_obj = dm.superset_yes_no([dm.di_117_1685, dm.di_28_434, dm.di_13_1696], [dm.di_123_1561], min_match=0.5)
plt = plt_obj.do_plot()
show(plt)

<Bokeh Notebook handle for In[20]>

HTML(plt_obj.get_html())

index	first	length	snps	alleles		matches		afr		afx		amr		eas		eur		sas		sax
353240	135,757,320	20,184	13	1696	0.04	74	1.00	47	4.72	26	7.86	1	0.09	0	0.00	0	0.00	0	0.00	0	0.00
353244	135,758,231	618,284	117	1685	0.04	74	1.00	47	4.72	26	7.86	1	0.09	0	0.00	0	0.00	0	0.00	0	0.00
354130	136,653,925	107,928	24	1504	0.04	64	0.86	41	4.76	22	7.69	1	0.10	0	0.00	0	0.00	0	0.00	0	0.00
353925	136,506,375	32,564	4	1442	0.05	66	0.89	42	4.73	23	7.80	1	0.10	0	0.00	0	0.00	0	0.00	0	0.00
353958	136,535,876	19,014	7	1303	0.05	66	0.89	42	4.73	23	7.80	1	0.10	0	0.00	0	0.00	0	0.00	0	0.00
354129	136,652,953	108,222	5	1296	0.05	64	0.86	41	4.76	22	7.69	1	0.10	0	0.00	0	0.00	0	0.00	0	0.00
354127	136,652,491	80,281	6	1114	0.06	64	0.86	41	4.76	22	7.69	1	0.10	0	0.00	0	0.00	0	0.00	0	0.00
353504	135,964,764	136,368	6	946	0.07	62	0.84	37	4.43	24	8.66	1	0.11	0	0.00	0	0.00	0	0.00	0	0.00
353729	136,309,239	52,321	9	887	0.08	74	1.00	47	4.72	26	7.86	1	0.09	0	0.00	0	0.00	0	0.00	0	0.00
353312	135,784,351	117,869	8	718	0.10	74	1.00	47	4.72	26	7.86	1	0.09	0	0.00	0	0.00	0	0.00	0	0.00
353764	136,364,916	22,977	5	588	0.12	71	0.96	45	4.71	25	7.88	1	0.09	0	0.00	0	0.00	0	0.00	0	0.00
353349	135,810,535	87,488	9	545	0.14	74	1.00	47	4.72	26	7.86	1	0.09	0	0.00	0	0.00	0	0.00	0	0.00
353614	136,115,507	269,773	28	434	0.17	74	1.00	47	4.72	26	7.86	1	0.09	0	0.00	0	0.00	0	0.00	0	0.00
353788	136,392,700	158,106	55	180	0.34	62	0.84	38	4.55	23	8.30	1	0.11	0	0.00	0	0.00	0	0.00	0	0.00
353538	136,008,173	373,078	70	166	0.45	74	1.00	47	4.72	26	7.86	1	0.09	0	0.00	0	0.00	0	0.00	0	0.00
353304	135,780,924	236,215	49	136	0.54	74	1.00	47	4.72	26	7.86	1	0.09	0	0.00	0	0.00	0	0.00	0	0.00
354125	136,651,969	124,016	24	113	0.54	61	0.82	38	4.63	22	8.07	1	0.11	0	0.00	0	0.00	0	0.00	0	0.00
353915	136,499,188	132,236	26	96	0.62	60	0.81	37	4.58	22	8.21	1	0.11	0	0.00	0	0.00	0	0.00	0	0.00
354037	136,589,701	51,567	4	80	0.75	60	0.81	36	4.46	23	8.58	1	0.11	0	0.00	0	0.00	0	0.00	0	0.00
353259	135,761,470	609,610	22	73	1.00	73	0.99	46	4.68	26	7.97	1	0.09	0	0.00	0	0.00	0	0.00	0	0.00
353806	136,403,061	84,783	4	67	0.96	64	0.86	40	4.64	23	8.04	1	0.10	0	0.00	0	0.00	0	0.00	0	0.00
353379	135,837,488	509,187	7	49	0.98	48	0.65	31	4.80	16	7.46	1	0.14	0	0.00	0	0.00	0	0.00	0	0.00

The plot below shows the series hierarchy for the 35 samples that express the 22 SNP series 22_35. This hierarchy is the result of an independent process that has selected the series 123_1561 for overexpression without 117_1685, 62_1265, or 193_843.

plt_obj = dm.superset_yes_no([dm.di_22_35], min_match=0.5)
plt = plt_obj.do_plot()
show(plt)

<Bokeh Notebook handle for In[22]>

HTML(plt_obj.get_html())

index	first	length	snps	alleles		matches		afr		afx		amr		eas		eur		sas		sax
353240	135,757,320	20,184	13	1696	0.02	35	1.00	21	2.98	4	1.82	1	0.21	0	0.00	0	0.00	5	1.97	4	0.93
353478	135,933,921	434,642	123	1561	0.02	35	1.00	21	2.98	4	1.82	1	0.21	0	0.00	0	0.00	5	1.97	4	0.93
353814	136,406,646	31,432	5	1460	0.02	26	0.74	21	4.01	4	2.45	1	0.28	0	0.00	0	0.00	0	0.00	0	0.00
353729	136,309,239	52,321	9	887	0.04	35	1.00	21	2.98	4	1.82	1	0.21	0	0.00	0	0.00	5	1.97	4	0.93
353851	136,448,855	17,976	4	612	0.04	26	0.74	21	4.01	4	2.45	1	0.28	0	0.00	0	0.00	0	0.00	0	0.00
353483	135,939,427	422,689	22	35	1.00	35	1.00	21	2.98	4	1.82	1	0.21	0	0.00	0	0.00	5	1.97	4	0.93
353326	135,791,020	702,063	219	26	1.00	26	0.74	21	4.01	4	2.45	1	0.28	0	0.00	0	0.00	0	0.00	0	0.00