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Arabidopsis thaliana vs Chlamydomonas reinhardtii LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Chlamydomonas reinhardtii (Chlamydomonas reinhardtii, Chlamydomonas_reinhardtii_v5.5) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 93. 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)3000
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 thalianaChlamydomonas reinhardtii
Chunk size50,000,000100,100,000
Overlap0100,000
Group set size0100,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 13,751 alignment blocks

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

Uncovered: 118,025,804 out of 119,667,750
Covered: 1,641,946 out of 119,667,750

Uncovered: 32,241,041 out of 33,775,569
Matches: 1,012,062 out of 33,775,569
Mismatches: 510,244 out of 33,775,569
Insertions: 12,222 out of 33,775,569
Identity over aligned base-pairs: 66.0%

Chlamydomonas reinhardtii

Uncovered: 110,094,124 out of 111,098,438
Covered: 1,004,314 out of 111,098,438

Uncovered: 38,241,832 out of 39,157,072
Matches: 599,595 out of 39,157,072
Mismatches: 307,063 out of 39,157,072
Insertions: 8,582 out of 39,157,072
Identity over aligned base-pairs: 65.5%

Block size distribution

Size range All 13,751 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
62
359.0 bp
10 bp - 100 bp
5,897
431.1 kb
970
71.0 kb
100 bp - 1 kb
7,778
1.4 Mb
3,440
1.3 Mb
1 kb - 10 kb
14
15.4 kb
327
476.4 kb