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

SNP Series Statistics

This notebook presents some statistics for all SNPs and series in the autosome analysis data set. Some plots of series data are presented for chromosome 2 and for a smaller region of chromosome 2 that includes the genetic variations responsible for lactase persistence.

Note that recreation of this table requires SNP data for all chromosomes. Other plots in this notebook can be recreated just from data for chromosome 2.

import genomes_dnj.series_anal.chrom_series_stats as cs
stats_obj = cs.autosome_snp_series_stats_cls()
stats_obj.do_stats()
HTML(stats_obj.stats_html())

chr	series	in_snps	not_in_snps	in_ratio	snp_mean	snp_med	snp_std	len_mean	len_med	len_std
1	74,387	796,158	647,635	0.55	10	6	13.53	53,616	23,620	89,920
2	81,160	865,501	682,045	0.56	10	6	13.24	55,164	25,382	84,828
3	68,222	744,533	556,878	0.57	10	6	14.58	58,394	25,487	97,904
4	69,448	784,085	545,117	0.59	11	7	15.20	49,059	25,030	70,950
5	61,476	667,469	502,587	0.57	10	7	13.89	55,855	26,331	87,644
6	61,184	701,990	483,992	0.59	11	7	16.66	57,924	25,325	99,090
7	56,078	607,361	476,403	0.56	10	6	14.92	53,050	22,929	93,440
8	53,578	575,287	451,502	0.56	10	6	14.01	51,636	22,112	96,151
9	41,365	419,307	381,488	0.52	10	6	12.66	43,501	20,065	66,119
10	47,184	509,139	410,134	0.55	10	6	15.83	49,812	21,916	85,663
11	45,800	519,153	387,462	0.57	11	6	20.67	61,728	23,955	128,574
12	45,356	491,595	385,595	0.56	10	6	17.83	56,691	23,884	99,609
13	34,878	371,639	284,268	0.57	10	6	13.55	48,564	22,679	73,631
14	30,811	330,382	267,406	0.55	10	6	14.05	50,916	22,996	83,338
15	27,304	275,859	266,100	0.51	10	6	13.25	50,947	18,936	91,429
16	29,271	281,091	305,987	0.48	9	6	11.79	42,896	15,399	93,677
17	24,686	246,647	257,802	0.49	9	6	17.97	47,597	18,418	77,604
18	27,266	274,494	243,652	0.53	10	6	12.05	41,691	19,793	64,610
19	20,431	208,902	214,023	0.49	10	6	15.50	38,405	14,981	73,496
20	20,845	203,339	200,647	0.50	9	6	11.39	41,315	17,681	73,079
21	13,213	128,139	127,226	0.50	9	6	10.86	31,577	16,380	44,877
22	12,675	121,440	134,968	0.47	9	6	11.40	42,662	14,358	82,520
all	946,618	10,123,510	8,212,917	0.55	10	6	14.79	51,709	22,524	89,020

A simple method was used with the 1000 genomes phase 3 data to group SNPs into series across all of the autosomes. The criteria used to group the SNPs roughly was:

Each chromosome sample expressing the series needed to express 90% of the SNP's in it.

At least 90% of the chromosome samples expressing any SNP in the series had to express the series.

The series had to include at least 4 SNPs.

The table above shows that over 940,000 series were identified and that more then half of the SNPs were grouped into some series. The average series contained 10 SNPs. But there was a substantial amount of variation both in the number of SNPs and the length of the chromosome covered by a series. The median values for both the number of SNPs and the length is significantly lower then the mean because particularly long series with particularly large numbers of SNPs make a large contribution to the averages.

Chromosomes Expressing Active SNP Series

Statistics were accumulated for the active series at each position in a chromosome where a series started or ended. An active series is one that had a start prior to the measurement position and an end after it. The plot below for chromosome 2 shows that it is common for almost all of the 5008 sampled chromosomes in the 1000 genomes phase 3 data to be expressing an active series. The label "LCT" identifies the location in the region of chromosome 2 where the lactase gene and the series of SNP's associated with lactase persistence are located.

plt0 = cp.chrom2_stats('active_series_allele_count')
show(plt0)

<Bokeh Notebook handle for In[3]>

Active SNP Series

This plot shows the number of active series at each measured location of chromosome 2

plt1 = cp.chrom2_stats('active_series')
show(plt1)

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SNPs In Active Series

This plot shows the number of SNPs in active series at each measured location. The region associated with lactase persistence is the one with the largest number on chromosome 2.

plt2 = cp.chrom2_stats('active_series_snp_count')
show(plt2)

<Bokeh Notebook handle for In[5]>

Lactase Region Chromosome Samples Expressing Active Series

This plot shows the count of chromosome samples expressing an active series in a small part of chromosome 2 that includes the region associated with lactase persistence. Note the regular pattern of the count of these samples dropping to or at least near zero. The region associated with lactase persistence is exceptionally long. But, it does appear to have some internal structure.

plt3 = cp.chrom2_intvl_stats('active_series_allele_count')
show(plt3)

<Bokeh Notebook handle for In[6]>

Lactase Region Active Series

This plot shows the number of active series in the same region of chromosome 2.

plt4 = cp.chrom2_intvl_stats('active_series')
show(plt4)

<Bokeh Notebook handle for In[7]>

Lactase Region SNPs In Active Series

This plot shows the count of SNPs in active series for that same part of chromosome 2.

plt5 = cp.chrom2_intvl_stats('active_series_snp_count')
show(plt5) 

<Bokeh Notebook handle for In[8]>