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Arabidopsis thaliana vs Arabidopsis halleri LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Arabidopsis halleri (Arabidopsis halleri subsp. gemmifera, Ahal2.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 95. 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 thalianaArabidopsis halleri
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 193,242 alignment blocks

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

Uncovered: 22,641,739 out of 119,667,750
Covered: 97,026,011 out of 119,667,750

Uncovered: 604,788 out of 33,775,569
Matches: 29,809,064 out of 33,775,569
Mismatches: 3,143,002 out of 33,775,569
Insertions: 218,715 out of 33,775,569
Identity over aligned base-pairs: 89.9%

Arabidopsis halleri

Uncovered: 73,574,711 out of 196,243,198
Covered: 122,668,487 out of 196,243,198

Uncovered: 3,461,504 out of 38,698,211
Matches: 32,236,909 out of 38,698,211
Mismatches: 2,688,048 out of 38,698,211
Insertions: 311,750 out of 38,698,211
Identity over aligned base-pairs: 91.5%

Block size distribution

Size range All 193,242 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,526
15.5 kb
10 bp - 100 bp
36,791
2.2 Mb
14,322
955.3 kb
100 bp - 1 kb
117,730
42.5 Mb
53,756
19.5 Mb
1 kb - 10 kb
35,756
90.3 Mb
13,880
33.3 Mb
10 kb - 100 kb
439
5.5 Mb
449
12.0 Mb
100 kb - 1 Mb
173
53.5 Mb
1 Mb - 10 Mb
15
21.3 Mb