Vitis vinifera vs Theobroma cacao Matina 1-6 LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Theobroma cacao Matina 1-6 (Theobroma cacao, Theobroma_cacao_20110822) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 100. 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 viniferaTheobroma cacao Matina 1-6
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options

Statistics over 182,734 alignment blocks

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

Uncovered: 419,868,641 out of 486,265,422
Covered: 66,396,781 out of 486,265,422

Uncovered: 3,411,321 out of 32,794,161
Matches: 21,383,281 out of 32,794,161
Mismatches: 7,521,745 out of 32,794,161
Insertions: 477,814 out of 32,794,161
Identity over aligned base-pairs: 72.8%

Theobroma cacao Matina 1-6

Uncovered: 292,657,403 out of 345,993,675
Covered: 53,336,272 out of 345,993,675

Uncovered: 6,601,058 out of 34,800,751
Matches: 20,369,885 out of 34,800,751
Mismatches: 7,295,151 out of 34,800,751
Insertions: 534,657 out of 34,800,751
Identity over aligned base-pairs: 72.2%

Block size distribution

Size range All 182,734 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,291
6.6 kb
10 bp - 100 bp
29,522
2.0 Mb
9,494
689.9 kb
100 bp - 1 kb
133,406
47.3 Mb
45,283
15.3 Mb
1 kb - 10 kb
18,463
30.9 Mb
12,830
30.8 Mb
10 kb - 100 kb
52
1.0 Mb
500
11.4 Mb
100 kb - 1 Mb
68
20.6 Mb
1 Mb - 10 Mb
2
2.4 Mb