Whole genome resequencing revealed genomic variants and functional pathways related to adaptation in Indian yak populations

Figures & data

Table 1. Summary of whole genome sequencing data.

Sr. No.	Population	Sample ID	Total number of sequences (R1 + R2)	Mapped percentage	Average read depth
1	Arunachal yak	1	199411832	98.77	9.66
2	Arunachal yak	2	199071166	98.83	9.54
3	Arunachal yak	3	199664536	99.32	8.95
4	Arunachal yak	4	198515614	99.02	9.25
5	Arunachal yak	5	198884010	98.75	9.62
6	Arunachal yak	6	199933222	98.77	9.78
7	Arunachal yak	7	198716592	98.80	9.594
8	Arunachal yak	9	198788874	98.59	9.57
9	Arunachal yak	10	199793478	98.83	9.52
10	Arunachal yak	16	198139854	98.84	9.58
11	Himachali yak	YAK1	198955078	98.94	9.46
12	Himachali yak	YAK2	199644652	94.31	9.460
13	Himachali yak	YAK3	198087116	99.32	8.94
14	Himachali yak	YAK4	198579582	98.67	9.81
15	Himachali yak	YAK5	198669812	98.92	9.52
16	Himachali yak	YAK6	198970780	94.41	9.44
17	Himachali yak	YAK7	199730404	94.38	9.47
18	Himachali yak	YAK8	198214482	99.03	9.39
19	Himachali yak	YAK9	198336584	94.04	9.44
20	Himachali yak	YAK10	197922834	98.99	9.41
21	Ladakhi yak	1L	198082048	98.91	9.42
22	Ladakhi yak	3L	198406104	93.69	9.74
23	Ladakhi yak	4L	199249608	93.33	9.62
24	Ladakhi yak	5L	198499154	98.85	9.36
25	Ladakhi yak	6L	198422524	93.94	9.45
26	Ladakhi yak	7L	198423912	98.78	9.49
27	Ladakhi yak	8L	198784058	98.89	9.51
28	Ladakhi yak	9L	198153712	99.26	9.02
29	Ladakhi yak	10L	198269176	99.01	9.48
30	Ladakhi yak	14L	198061058	94.23	9.33

Table 2. Chromosome-wise distribution of SNPs and InDels across the genome in Arunachali, Himachali, and Ladakhi yaks.

	Arunachali Yak		Himachali Yak		Ladakhi Yak
Chromosome	SNPs	INDELS	SNPs	INDELS	SNPs	INDELS
1	19,52,593	2,67,216	16,13,078	2,37,296	20,01,699	2,69,813
2	16,50,035	2,25,730	13,96,542	2,03,817	17,03,494	2,29,435
3	14,89,204	2,02,837	12,45,464	1,80,901	14,97,823	2,00,571
4	14,89,233	2,07,917	12,31,159	1,83,910	14,64,339	2,01,798
5	14,85,847	2,07,948	12,88,492	1,92,029	15,45,220	2,12,870
6	14,84,394	2,10,241	12,72,334	1,91,537	15,21,977	2,12,485
7	14,08,177	1,96,112	11,60,249	1,72,089	14,12,237	1,93,253
8	13,62,983	1,91,313	11,34,844	1,70,023	13,61,662	1,88,076
9	12,80,850	1,77,682	10,79,979	1,60,376	13,07,719	1,78,169
10	12,86,280	1,82,749	10,90,354	1,65,094	13,18,726	1,84,130
11	10,93,826	1,50,296	9,29,165	1,36,716	11,08,429	1,50,202
12	9,24,736	3,13,697	7,90,042	3,00,423	9,48,823	3,14,032
13	11,15,808	1,59,886	10,04,916	1,51,724	11,48,110	1,62,138
14	9,87,500	1,38,300	8,43,491	1,25,237	10,34,177	1,42,358
15	10,98,755	1,57,070	9,40,061	1,42,676	11,32,832	1,60,987
16	9,81,463	1,40,320	8,10,222	1,23,955	9,57,817	1,35,237
17	8,57,715	1,19,096	7,31,469	1,08,197	8,96,175	1,21,297
18	8,36,835	1,15,183	7,13,528	1,04,512	8,49,911	1,14,740
19	7,75,230	1,08,692	6,63,688	99,211	7,73,160	1,05,665
20	8,10,843	1,14,949	6,91,797	1,04,141	8,18,538	1,13,358
21	7,47,722	1,02,451	6,25,787	91,553	7,85,519	1,05,158
22	7,29,550	1,02,477	6,17,403	92,627	7,57,769	1,03,234
23	6,84,525	96,030	5,82,406	87,480	6,93,612	96,207
24	8,56,003	1,24,646	7,20,168	1,11,166	7,98,056	1,15,860
25	6,27,652	87,733	5,32,079	79,482	6,33,787	86,848
26	5,66,837	80,149	4,84,970	72,794	5,64,886	78,550
27	5,69,517	81,814	4,85,716	74,063	5,75,897	81,623
28	5,21,672	71,913	4,37,820	64,160	5,35,318	72,414
29	5,81,916	2,19,462	4,95,961	2,10,713	5,61,056	2,15,506
X	13,71,166	2,30,508	11,58,401	2,16,940	13,73,658	2,20,745
Y	3,01,308	49,116	2,65,877	45,736	3,11,874	50,364

Figure 1. Categorization of identified SNPs in Arunachali, Himachali and Ladakhi yaks (SNPs were classified: number of effects by impact (high, low, and moderate); number of effects by functional classes (Missense, Nonsense and Silence)).

Table 3. Annotation of SNPs and InDels detected in Arunachali, Himachali, and Ladakhi yaks.

Sr. No.	Region	Numbers of SNPs			Numbers of InDels
		Arunachali	Himachali	Ladakhi	Arunachali	Himachali	Ladakhi
1.	DOWNSTREAM	2698468	2290849	2742524	436415	398208	432463
2.	EXON	791487	663930	805543	70740	63170	69640
3.	INTERGENIC	20137928	17121126	20410022	3067535	2797270	3060712
4.	INTRON	30607904	25732689	31057780	4408175	3984260	4379726
5.	SPLICE_SITE_ACCEPTOR	6591	5289	6870	3734	3570	3677
6.	SPLICE_SITE_DONOR	6455	5248	7200	1309	1217	1329
7.	SPLICE_SITE_REGION	61414	51155	63063	11832	11094	11655
8.	TRANSCRIPT	1536	1272	1528	276	249	266
9.	UPSTREAM	2671166	2268758	2706422	424340	388999	421722
10.	UTR_3_PRIME	139763	118321	141953	22339	20461	22049
11.	UTR_5_PRIME	67561	57951	68859	9244	8722	9292

Figure 2. The immune related enriched GO terms observed for genes harboring high impact variants. (A) Arunachali yaks. (B) Himachali yaks. (C) Ladakhi yaks.

Figure 3. The hypoxia and stress related enriched GO terms observed for genes harboring high impact variants. (A) Arunachali yaks. (B) Himachali yaks. (C) Ladakhi yaks.

Data availability statement

The raw data and .vcf file have been submitted to Sequence Read Archive (PRJNA803425) and European Variant Archive (PRJEB50815), respectively.