Vitis vinifera vs Cyanidioschyzon merolae LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Cyanidioschyzon merolae (Cyanidioschyzon merolae strain 10D, ASM9120v1) 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 viniferaCyanidioschyzon merolae
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 6,154 alignment blocks

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

Uncovered: 485,025,682 out of 486,265,422
Covered: 1,239,740 out of 486,265,422

Uncovered: 31,715,644 out of 32,794,161
Matches: 671,781 out of 32,794,161
Mismatches: 387,836 out of 32,794,161
Insertions: 18,900 out of 32,794,161
Identity over aligned base-pairs: 62.3%

Cyanidioschyzon merolae

Uncovered: 16,086,401 out of 16,728,945
Covered: 642,544 out of 16,728,945

Uncovered: 6,869,453 out of 7,493,795
Matches: 381,908 out of 7,493,795
Mismatches: 227,457 out of 7,493,795
Insertions: 14,977 out of 7,493,795
Identity over aligned base-pairs: 61.2%

Block size distribution

Size range All 6,154 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
9
56.0 bp
10 bp - 100 bp
1,574
115.7 kb
394
28.7 kb
100 bp - 1 kb
4,478
1.1 Mb
2,522
896.7 kb
1 kb - 10 kb
93
123.2 kb
306
429.0 kb