Skip to main content

Table 1 Sequencing and variant calling statistics for SAS-AP samples

From: Extremely low-coverage whole genome sequencing in South Asians captures population genomics information

Group

Populations

# of samples

Depth of Coverage

Total SNVs

Avg SNVs

Ti/Tv

Novel 1000G-SAS

Novel dbSNP 141

aUpper

Brahmins

16

1.81

4,443,583

2,571,972

2.09

97,022

5632

aMiddle

Kapu

37

1.57

4,457,414

2,582,833

2.09

97,303

5701

aMiddle

Yadava

32

1.65

4,457,237

2,575,646

2.09

97,300

5699

aLower

Mala

23

1.56

4,455,626

2,615,726

2.09

97,261

5701

aLower

Madiga

24

1.35

4,455,972

2,583,914

2.09

97,271

5699

aLower

Relli

15

1.69

4,455,972

2,586,868

2.09

96,908

5639

Tribal

Irula

22

1.86

4,439,932

2,570,388

2.09

97,024

5674

Tribal

Khonda Dora

16

1.82

4,403,761

2,574,472

2.09

96,340

5523

Total

 

185

1.64

4,457,475

2,583,004

2.09

97,309

5701

  1. Only SNVs with minor allele frequency (MAF) ≥10% are included. Total SNVs: the total number of SNVs in a population. Avg SNVs: the average number of SNVs in an individual. Ti/Tv: transition/transversion SNV ratio. Novel 1000G-SAS: the number of SNVs that are not in the 1000G-SAS dataset. Novel dbSNP 141: the number of SNVs that are not in dbSNP 141. aCaste Populations