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Arabidopsis thaliana vs Marchantia polymorpha LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Marchantia polymorpha (Marchantia polymorpha str. Tak-1, Marchanta_polymorpha_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 97. Arabidopsis thaliana 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

ParameterArabidopsis thalianaMarchantia 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 68,816 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 104,497,256 out of 119,667,750
Covered: 15,170,494 out of 119,667,750

Uncovered: 21,845,918 out of 33,775,569
Matches: 7,595,808 out of 33,775,569
Mismatches: 4,147,250 out of 33,775,569
Insertions: 186,593 out of 33,775,569
Identity over aligned base-pairs: 63.7%

Marchantia polymorpha

Uncovered: 214,832,521 out of 225,760,816
Covered: 10,928,295 out of 225,760,816

Uncovered: 15,857,889 out of 23,498,831
Matches: 4,852,043 out of 23,498,831
Mismatches: 2,607,762 out of 23,498,831
Insertions: 181,137 out of 23,498,831
Identity over aligned base-pairs: 63.5%

Block size distribution

Size range All 68,816 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
392
2.1 kb
10 bp - 100 bp
14,069
1.0 Mb
1,862
135.7 kb
100 bp - 1 kb
52,598
15.0 Mb
12,784
5.5 Mb
1 kb - 10 kb
1,736
2.5 Mb
6,593
12.6 Mb
10 kb - 100 kb
21
338.9 kb
33
552.2 kb