SGA Preqc Results : fig1

Est. Genome Size bird : 1094.4 fish : 923.7 human : 2914.6 oyster : 529.5 snake : 1451.7 yeast : 12.5 0

1000

1500

Size (Mbp)

2000

2500

Simulated contig lengths vs k Frequency of repeat branches

25000 20000 15000 10000 5000 0 20

30

40

50

60

k

70

80

90

10-4

20

0.6 0.4 0.2 0.2

0.4

0.6

0.8

1.0

40

50

k

60

70

80

repeat branches in k-de Bruijn graph

10-3 10-4 10-5 20

30

40

50

k

60

70

80

error branches in k-de Bruijn graph

10-2

0.8

30

10-2

10-6

100

1.0

0.0 0.0

10-3

10-1

30000

variant branches in k-de Bruijn graph

10-2

10-5

3000

Frequency of error branches

Simulated contig length N50

35000

500

Frequency of variant branches

FCC4L5DACXX-WHAIPI005073-13_L5 : 644.8

10-1

10-3

10-4

10-5

20

30

40

50

k

60

70

80

SGA Preqc Results : fig2

Est. PCR Duplicate Proportion FCC4L5DACXX-WHAIPI005073-13_L5

35

Mean Phred Score

bird fish human oyster snake

30 25 20

yeast

15

0.00 0.02 0.04 0.06 0.08 0.10 0.12 0.14 0.16

Duplicate proportion

Estimated Fragment Size Histogram

0.040

20

40

60

80

100

Base position

120

140

160

Fraction of bases at least Q30

0.9

Fraction at least Q30

0.030

Proportion

0

1.0

0.035

0.025 0.020 0.015 0.010

0.8 0.7 0.6 0.5 0.4

0.005 0.000

Mean quality score by position

40

0

200

400

600

0.3

800 1000 1200 1400

Fragment Size (bp)

k-mer position of first error

0.025

0

20

40

60

80

100

Base position

120

140

160

140

160

Per-position error rate

0.035 0.030

0.020 0.015

Error rate

Proportion

0.025

0.010

0.020 0.015 0.010

0.005 0.000

0.005 0

20

40

60

80

k-mer position

100

120

0.000

0

20

40

60

80

100

Base position

120

SGA Preqc Results : fig3

1600 1400

80

k-mer coverage

FCC4L5DACXX-WHAIPI005073-13_L5 bird fish human oyster snake yeast

FCC4L5DACXX-WHAIPI005073-13_L5 GC Bias 100

1200 1000

60

800 40

600 400

20 0

51-mer count distribution

0.25

0

20

40

GC %

60

80

100

bird GC Bias

100

0.15 0.10 0.05

0

2000 1750

80

k-mer coverage

0.20

1500 1250

60

1000 40

750 500

20

250 0.00

0

20

40

60

51-mer count

80

0

100

1.0

0

20

40

GC %

60

80

100

0

fish GC Bias

100

1400 0.8

80

k-mer coverage

Proportion

200

0.6 0.4 0.2 0.0 0.0

1200 1000

60

800

40

600 400

20 0.2

0.4

0.6

0.8

1.0

0

200 0

20

40

GC %

60

80

100

0

human GC Bias

100

SGA Preqc Results : fig4 1200 1000

60

800 40

600 400

20

900

150

k-mer coverage

k-mer coverage

1050

1400

80

0

oyster GC Bias

200

750 600

100

450 300

50

150

200 0

20

40

GC %

60

80

100

0

0

snake GC Bias

200

0

20

40

GC %

60

80

100

yeast GC Bias

100

3200

2700 2400 2100 1800 1500

100

1200 900

50

600

2800

80

k-mer coverage

k-mer coverage

150

2400 60

2000 1600

40

1200 800

20

400

300 0

0

20

40

GC %

60

80

100

0

0

1.0

1.0

0.8

0.8

0.6

0.6

0.4

0.4

0.2

0.2

0.0 0.0

0.2

0.4

0.6

0.8

1.0

0

0

0.0 0.0

20

0.2

40

GC %

0.4

60

0.6

80

100

0.8

0

1.0

SGA Preqc Results : fig1 -

100 k. 0. 5000. 10000. 15000. 20000. 25000. 30000. 35000. Simulated contig length N50. Simulated contig lengths vs k. 20. 30. 40. 50. 60. 70. 80 k. 10-6. 10-5.
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