Supplemental materials
Table S1. Assemblathon2 statistics for genome assembly, assuming a genome
size of 448Mb.
Number of scaffolds
551923
Total size of scaffolds
564011865
Total scaffold length as percentage of known genome size
125.90%
Longest scaffold
398841
Shortest scaffold
81
Number of scaffolds > 500 nt
75763
Percentage of scaffolds > 500 nt
13.70%
Number of scaffolds > 1K nt
46831
Percentage of scaffolds > 1K nt
8.50%
Number of scaffolds > 10K nt
12078
Percentage of scaffolds > 10K nt
2.20%
Number of scaffolds > 100K nt
288
Percentage of scaffolds > 100K nt
0.10%
Number of scaffolds > 1M nt
0
Percentage of scaffolds > 1M nt
0.00%
Mean scaffold size
1022
Median scaffold size
151
N50 scaffold length
18689
L50 scaffold count
6810
NG50 scaffold length
27577
LG50 scaffold count
4257
N50 scaffold - NG50 scaffold length difference
8888
scaffold %A
28.76
scaffold %C
17.4
scaffold %G
17.36
scaffold %T
28.69
scaffold %N
7.78
scaffold N nt
43891042
scaffold %non-ACGTN
0
Number of scaffold non-ACGTN nt
0
Percentage of assembly in scaffolded contigs
73.40%
Percentage of assembly in unscaffolded contigs
26.60%
Average number of contigs per scaffold
1.2
Average length of breaks (20 or more Ns) between contigs
460
Number of contigs
647121
Number of contigs in scaffolds
125686
Number of contigs not in scaffolds
521435
Total size of contigs
520210681
Longest contig
85582
Shortest contig
2
Number of contigs > 500 nt
133203
Percentage of contigs > 500 nt
20.60%
Number of contigs > 1K nt
84301
Percentage of contigs > 1K nt
13.00%
Number of contigs > 10K nt
9510
Percentage of contigs > 10K nt
1.50%
Number of contigs > 100K nt
0
Percentage of contigs > 100K nt
0.00%
Number of contigs > 1M nt
0
Percentage of contigs > 1M nt
0.00%
Mean contig size
804
Median contig size
167
N50 contig length
5078
L50 contig count
22857
NG50 contig length
6730
LG50 contig count
16683
N50 contig - NG50 contig length difference
1652
contig %A
31.18
contig %C
18.87
contig %G
18.82
contig %T
31.11
contig %N
0.02
contig N nt
89858
contig %non-ACGTN
0
Number of contig non-ACGTN nt
0
Explanatory notes on statistics from http://assemblathon.org/:
Each scaffold is split on runs of 25 or more ‘N’ characters to form ‘contigs’. Any contigs that could
be split in this way are regarded as ‘scaffolded contigs’. Scaffolds that don’t have runs of 25 or
more ‘N’ characters are also counted as ‘unscaffolded contigs’. N50 scaffold/contig length is
calculated by summing lengths of scaffolds/contigs from the longest to the shortest and
determining at what point you reach 50% of the total assembly size. The length of the
scaffold/contig at that point is the N50 length. The L50 measure is the number of
scaffolds/contigs that are greater than, or equal to, the N50 length. The NG50 and LG50 measures
are the same as the N50 and L50 measures except that rather than compare against the total
assembly size, we compare against the estimated genome sizes of the three species.
425
574
582
583
605
1045
1123
1124
1153
1158
1183
1184
1578
97
325
97
Table S2. Sequenced RAD loci shared between each pair of samples, expressed as
a percentage of the total number of loci in the RAD locus catalog from the sample
listed in the left-hand edge column.
44
43
45
53
45
41
39
45
41
36
40
42
41
42
50
47
40
51
46
43
51
46
39
44
48
47
47
51
42
54
49
46
54
49
42
47
51
50
50
48
56
52
49
56
51
45
51
53
54
53
46
41
39
43
41
37
40
42
42
42
37
33
41
36
30
35
38
37
37
50
56
52
46
51
54
54
54
59
56
51
56
58
58
58
45
37
43
46
46
46
46
51
53
53
53
58
60
59
60
55
55
55
52
52
325
42
425
45
53
574
50
55
55
582
56
44
43
45
583
34
40
39
37
33
605
48
56
55
54
45
57
1045
52
59
59
58
50
60
57
1123
42
49
48
46
38
50
44
41
1124
48
56
55
53
46
56
52
49
57
1153
54
60
61
61
52
61
59
57
61
59
1158
49
57
56
56
47
58
54
51
57
54
48
1183
47
54
54
52
44
55
51
48
55
50
44
49
1184
47
55
55
54
45
56
52
49
56
51
45
51
54
1578
47
54
54
52
44
55
51
48
55
50
44
49
53
53
52
Figure S1. Photograph of Betula nana individual 097-10 used for genome
sequencing
Figure S2. Flow chart outlining analysis pipelines used in this study