Table 1 Number of sequencing reads before and after alignment and filtering for base (q ≥ 15), mapping quality (q ≥ 30) and duplicate removal. Sex estimation results and genotyped SNPs in Omni and HGDP datasets. UDD – Urban discard deposit

From: Genetic Evidence of African Slavery at the Beginning of the Trans-Atlantic Slave Trade

Burial Context

Sample

Bone sampled

Total Reads

Hits to hg19*

Fraction of Human Reads (%)

Genome Coverage (x)

Sex Determination**

Genotyped SNPs*

        

Omni

HGDP

Leprosarium

Ind. 5

metatarsal

703096

10740

1.53

0.00018

XX

525

156

Leprosarium

Ind. 7

metatarsal

866232

16300

1.88

0.00027

XX

762

208

Leprosarium

Ind. 34

Left Fibula

616433

3800

0.62

0.00006

XX

191

50

Leprosarium

Ind. 36

metatarsal

595411

9502

1.6

0.00016

XY

390

102

Leprosarium

Ind. 37

4th lumbar vertebra

1459865

8255

0.57

0.00014

XX

383

94

UDD

Ind. 25 ‡

metatarsal

766371

799

0.1

0.00001

n/a

32

12

UDD

Ind. 65 ‡

metatarsal

960013

1657

0.17

0.00002

n/a

60

14

UDD

Ind. 125

metatarsal

597681

45414

7.6

0.00077

XX

2131

551

UDD

Ind. 166

metatarsal

1076124

107507

9.99

0.00182

XX

4961

1331

  1. *Reads were filtered by base quality ≥ 15 and mapping quality ≥ 30. Duplicate reads were excluded and only unambiguously mapped reads were kept.
  2. **Sex determination method11. Results shown in more detail in Supplementary Table S1.
  3. ‡Individuals removed from posterior analysis because of insufficient endogenous DNA read number.
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