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Table 6 Sequence and Quast metrics for the initial synthetic data version

From: Global exact optimisations for chloroplast structural haplotype scaffolding

   

Successful

Quast

Instance

ILPs

Total

\(\textsf{SOC}\)

\(\textsf{SOR}\)

%gnm

#mis

Abies_alba

dr-sc

1

0

0

99.879

3

0

ir-sc

2

1

2

100.0

0

0

Acorus_americanus

ir-sc

2

1

2

99.987

0

0

Agathis_dammara

dr-ir-sc

10

0

2

80.509

1

2

ir-dr-sc

6

0

0

80.935

2

2

Azima_tetracantha

ir-sc

2

1

2

99.987

0

0

Begonia_pulchrifolia

Carpodetus_serratus

ir-sc

2

0

2

99.998

2

0

Circaeaster_agrestis

ir-sc

2

1

2

99.987

0

0

Clematis_repens

ir-sc

2

1

2

100.0

0

0

Commiphora_foliacea

ir-sc

4

1

4

98.82

0

5

Cucumis_hystrix

ir-sc

2

0

0

100.0

0

0

Eucommia_ulmoides

ir-sc

2

1

2

99.988

0

2

Jasminum_tortuosum

ir-sc

2

0

2

99.992

2

0

Juniperus_scopulorum

sc

1

1

1

99.722

0

1

Lamprocapnos_spectabilis

dr-sc

1

0

0

35.86

3

0

Lathyrus_pubescens

dr-sc

1

0

0

98.471

2

2

ir-sc

2

0

2

98.496

0

2

Lophocereus_schottii

sc

1

0

1

99.884

1

0

Musa_ornata

ir-sc

2

1

2

99.97

0

2

Oenothera_glazioviana

ir-sc

2

1

2

100.0

0

0

Pelargonium_nanum

ir-sc

2

0

2

96.44

4

0

Podocarpus_totara

sc

1

0

1

99.712

4

0

Porphyra_purpura

dr-sc

1

1

1

100.0

0

0

Sagittaria_trifolia

ir-sc

2

1

2

100.0

0

0

Sciadopitys_verticillata

dr-sc

1

0

0

98.989

6

3

ir-sc

2

1

2

98.997

1

4

Sciaphila_densiflora

sc

1

1

1

100.0

0

0

Selaginella_kraussiana

dr-sc

1

1

1

100.0

0

0

Selaginella_vardei

dr-sc

1

1

1

100.0

0

0

Taxus_baccata

sc

1

1

1

99.767

0

2

Triosteum_pinnatifidum

ir-dr-sc

2

0

2

99.278

0

2

Uvaria_macrophylla

ir-sc

2

1

2

99.896

0

0

Welwitschia_mirabilis

ir-sc

2

1

2

100.0

0

1

Wolffia_australiana

ir-sc

4

1

4

99.988

0

0

  1. For each instance in the column Instance: ILPs provides the optimal (at most two) hierarchical problem successions; Total reports the number of eulerian circuits in the region graph (genome forms); \(\textsf{SOC}\) is the number of oriented contig sequences that equal to the reference oriented contig sequence; \(\textsf{SOR}\) is the number of oriented region sequences in bijection with the reference oriented region sequence; %gnm is the genome fraction of the best sequence produced by one of the genome forms; #mis are the number of misassemblies (left) and of local misassemblies (right)