Vitis vinifera vs Marchantia polymorpha LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Marchantia polymorpha (Marchantia polymorpha str. Tak-1, Marchanta_polymorpha_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 97. 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 viniferaMarchantia polymorpha
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 85,039 alignment blocks

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

Uncovered: 468,576,503 out of 486,265,422
Covered: 17,688,919 out of 486,265,422

Uncovered: 20,080,431 out of 32,794,161
Matches: 8,122,335 out of 32,794,161
Mismatches: 4,390,621 out of 32,794,161
Insertions: 200,774 out of 32,794,161
Identity over aligned base-pairs: 63.9%

Marchantia polymorpha

Uncovered: 214,368,456 out of 225,760,816
Covered: 11,392,360 out of 225,760,816

Uncovered: 15,267,310 out of 23,498,831
Matches: 5,237,752 out of 23,498,831
Mismatches: 2,805,485 out of 23,498,831
Insertions: 188,284 out of 23,498,831
Identity over aligned base-pairs: 63.6%

Block size distribution

Size range All 85,039 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
355
1.6 kb
10 bp - 100 bp
18,129
1.3 Mb
4,282
320.7 kb
100 bp - 1 kb
64,884
17.1 Mb
24,859
9.2 Mb
1 kb - 10 kb
1,643
2.4 Mb
6,170
11.2 Mb
10 kb - 100 kb
28
440.5 kb
34
593.2 kb