Vitis vinifera vs Selaginella moellendorffii LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Selaginella moellendorffii (Selaginella moellendorffii, v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 94. Vitis vinifera was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

ParameterVitis viniferaSelaginella moellendorffii
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 142,955 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Vitis vinifera

Uncovered: 465,610,271 out of 486,265,422
Covered: 20,655,151 out of 486,265,422

Uncovered: 18,348,328 out of 32,794,161
Matches: 9,054,128 out of 32,794,161
Mismatches: 5,044,352 out of 32,794,161
Insertions: 347,353 out of 32,794,161
Identity over aligned base-pairs: 62.7%

Selaginella moellendorffii

Uncovered: 183,617,123 out of 212,645,483
Covered: 29,028,360 out of 212,645,483

Uncovered: 22,478,841 out of 41,155,148
Matches: 11,720,875 out of 41,155,148
Mismatches: 6,580,321 out of 41,155,148
Insertions: 375,111 out of 41,155,148
Identity over aligned base-pairs: 62.8%

Block size distribution

Size range All 142,955 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
758
3.8 kb
10 bp - 100 bp
24,941
1.8 Mb
6,209
449.2 kb
100 bp - 1 kb
112,762
34.2 Mb
43,230
17.3 Mb
1 kb - 10 kb
4,483
6.3 Mb
14,093
24.2 Mb
10 kb - 100 kb
11
205.2 kb
28
460.9 kb