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Arabidopsis thaliana vs Marchantia polymorpha LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Marchantia polymorpha (Marchantia polymorpha, MpTak1_v7.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 113. 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 size10,100,00010,100,000
Masking options

Statistics over 58,033 alignment blocks

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

Uncovered: 106,870,597 out of 119,667,750
Covered: 12,797,153 out of 119,667,750

Uncovered: 23,654,133 out of 33,775,569
Matches: 6,506,879 out of 33,775,569
Mismatches: 3,457,763 out of 33,775,569
Insertions: 156,794 out of 33,775,569
Identity over aligned base-pairs: 64.3%

Marchantia polymorpha

Uncovered: 238,591,362 out of 248,042,680
Covered: 9,451,318 out of 248,042,680

Uncovered: 16,421,071 out of 23,102,497
Matches: 4,245,943 out of 23,102,497
Mismatches: 2,279,564 out of 23,102,497
Insertions: 155,919 out of 23,102,497
Identity over aligned base-pairs: 63.5%

Block size distribution

Size range All 58,033 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
325
1.8 kb
10 bp - 100 bp
11,895
856.6 kb
1,380
101.4 kb
100 bp - 1 kb
44,397
12.6 Mb
10,042
4.4 Mb
1 kb - 10 kb
1,416
1.9 Mb
5,615
10.8 Mb
10 kb - 100 kb
11
130.5 kb