Table 2 Sequencing and mapping summary.

From: Ancient human mitochondrial genomes from Bronze Age Bulgaria: new insights into the genetic history of Thracians

Sample ID

Raw reads

Merged reads (%)

Mapped reads prior rmdup

Mapped reads after rmdup

Contamination estimate

mtDNA Average Coverage Depth

mtDNA Average Coverage (%)

Deamination pattern

Average fragment length (bp)

Hg

First iteration (%) [low-high]

Final iteration (%) [low-high]

5′ (%)

3′ (%)

SM 4

1042513

975974 (93.62)

14659

10820

0 [0–0.05]

2 [1–3]

35.73

98.36

41.19

40.68

54.7

J1c

SM 8.1

291072

280395 (93.33)

17037

11026

0 [0–1.5]

1 [0–2]

31.01

98.05

46.00

49.32

46.6

U5a1a2b

SM 24.2

138644

133841 (96.54)

8598

7666

0 [0–0.5]

1 [0–2]

20.92

97.63

35.90

35.90

45.2

HV1a’b’c

GM 30.3

140659

133681 (95.04)

4692

4194

5 [2–8]

2 [1–3]

13.61

95.38

42.46

41.33

53.8

K1c1

BM AG

252894

242542 (95.91)

67931

52866

0 [0–0.5]

1 [0–2]

178.75

100

21.10

21.00

56.0

U5b2a1a1

BM 2

1129167

1072135 (94.95)

568403

362803

4.5 [4–5]

2 [1–3]

1299.92

100

20.00

20.00

59.4

N1b1a1

BM 3

455909

398419 (87.39)

125888

76387

0 [0–1]

2 [1–3]

310.93

100

23.33

22.51

67.4

H3ak

BM 5

241044

223147 (92.58)

44418

39517

6.5 [5.5–7.5]

1 [0–2]

155.55

100

25.95

24.28

65.2

H5a1a

BM 6

795728

767050 (96.40)

272955

170311

0 [0–1]

1 [0–2]

557.29

100

32.25

30.10

54.2

H7a1a

BM 9

306514

293319 (95.70)

38873

27053

0 [0–0.05]

1 [0–2]

102.67

99.96

32.74

31.10

62.6

H7

BM 10

1051289

1015983 (96.64)

190927

120090

8 [9–7]

1 [0–2]

411.12

100

24.67

23.51

56.7

U4c2a

BM 15

308266

292881 (95.01)

67093

43783

0 [0–0.05]

1 [0–2]

170.28

100

28.55

26.10

64.4

T2b

BM 24

336874

306128 (90.87)

48355

39312

5.5 [4.5–6.4]

1 [0–2]

136.90

99.98

31.07

27.00

57.5

I2

BM 31

291132

259451 (89.12)

35740

31783

57 [56–58]

16 [15–17]

122.07

97.04

29.24

26.46

63.6

J1c9

BM 36

542629

521894 (96.18)

244787

178811

0 [0–0.1]

1 [0–2]

599.48

100

33.24

31.47

55.6

N1

BM 40

199895

190493 (95.30)

45850

40103

0 [0–0.05]

2 [1–3]

130.67

99.97

28.72

29.12

54.0

T2e2a

BM 44

167444

162418 (97.00)

40293

32973

0 [0–0.05]

2 [1–3]

100.58

99.93

34.99

33.01

50.5

HV0

BM 51A

1025635

971945 (94.77)

27811

289429

46.5 [45.5–47.5]

10 [9–11]

84.19

99.06

35.98

31.63

56.9

K1c1

BM 58A

164453

156982 (95.46)

39604

33144

0 [0–0.05]

2 [1–3]

113.77

99.97

30.82

28.72

56.9

K1c1

BM 59A

319622

303936 (95.09)

95874

77103

0 [0–0.05]

2 [1–3]

258.96

100

30.16

29.86

55.6

T2b

BM 61

240732

230927 (95.93)

63892

56475

7 [6–8]

1 [0–2]

186.98

99.97

29.29

28.74

54.9

J1c6

BM 68

518653

503547 (97.09)

174125

126713

5 [2–8]

3 [4–2]

400.39

99.98

33.31

32.98

52.4

K1c1

BM 69

361277

343403 (95.05)

70252

55118

0 [0–0.05]

1 [0–2]

165.64

100

32.95

30.15

49.8

H5b

BM 73

311752

292048 (93.68)

127325

95877

0 [0–0.05]

1 [0–2]

256.74

100

37.23

35.02

44.4

H76a

BM 76

486546

473556 (97.33)

86904

61483

0 [0–0.05]

1 [0–2]

192.58

100

22.55

23.35

51.9

H4a1

  1. Number of raw reads, number of merged reads, number of mapping reads before and after removing PCR duplicates, contamination estimate (Schmutzi), average depth of coverage, mitochondrial coverage, deamination pattern (Schmutzi), average fragment length and mt haplogroup (assigned with HaploGrep) are reported.