Arabidopsis thaliana vs Hordeum vulgare LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Hordeum vulgare (Hordeum vulgare subsp. vulgare, IBSC_v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 94. 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 thalianaHordeum vulgare
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 165,915 alignment blocks

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

Uncovered: 92,861,049 out of 119,667,750
Covered: 26,806,701 out of 119,667,750

Uncovered: 14,177,475 out of 33,775,569
Matches: 12,474,087 out of 33,775,569
Mismatches: 6,731,462 out of 33,775,569
Insertions: 392,545 out of 33,775,569
Identity over aligned base-pairs: 63.6%

Hordeum vulgare

Uncovered: 4,788,489,275 out of 4,834,432,680
Covered: 45,943,405 out of 4,834,432,680

Uncovered: 21,702,856 out of 44,420,163
Matches: 14,435,720 out of 44,420,163
Mismatches: 7,665,119 out of 44,420,163
Insertions: 616,468 out of 44,420,163
Identity over aligned base-pairs: 63.5%

Block size distribution

Size range All 165,915 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
932
4.9 kb
10 bp - 100 bp
26,068
1.8 Mb
7,054
522.7 kb
100 bp - 1 kb
129,577
42.5 Mb
50,302
19.7 Mb
1 kb - 10 kb
9,338
14.1 Mb
19,403
37.7 Mb
10 kb - 100 kb
26
383.2 kb