Vitis vinifera vs Citrullus lanatus LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Citrullus lanatus (Citrullus lanatus, Cla97_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 101. 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 viniferaCitrullus lanatus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 185,313 alignment blocks

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

Uncovered: 431,296,328 out of 486,265,422
Covered: 54,969,094 out of 486,265,422

Uncovered: 6,047,543 out of 32,794,161
Matches: 18,692,305 out of 32,794,161
Mismatches: 7,566,705 out of 32,794,161
Insertions: 487,608 out of 32,794,161
Identity over aligned base-pairs: 69.9%

Citrullus lanatus

Uncovered: 320,732,892 out of 365,450,462
Covered: 44,717,570 out of 365,450,462

Uncovered: 3,734,725 out of 26,302,942
Matches: 15,921,232 out of 26,302,942
Mismatches: 6,229,165 out of 26,302,942
Insertions: 417,820 out of 26,302,942
Identity over aligned base-pairs: 70.5%

Block size distribution

Size range All 185,313 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,324
6.4 kb
10 bp - 100 bp
32,309
2.2 Mb
12,925
915.0 kb
100 bp - 1 kb
138,014
45.8 Mb
51,463
17.5 Mb
1 kb - 10 kb
13,586
22.3 Mb
17,072
39.9 Mb
10 kb - 100 kb
79
1.4 Mb
494
10.9 Mb
100 kb - 1 Mb
1
139.4 kb
14
2.5 Mb