Hordeum vulgare vs Aegilops tauschii LastZ results

Hordeum vulgare (Hordeum vulgare subsp. vulgare, IBSC_v2) and Aegilops tauschii (Aegilops tauschii subsp. strangulata, Aet_v4.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 95. Hordeum vulgare 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)
Gap extend penalty (E)
HSP threshold (K)
Threshold for gapped extension (L)
Threshold for alignments between gapped alignment blocks (H)
Masking count (M)
Seed and Transition value (T)
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

ParameterHordeum vulgareAegilops tauschii
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 2,216,922 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Hordeum vulgare

Uncovered: 3,999,755,092 out of 4,834,432,680
Covered: 834,677,588 out of 4,834,432,680

Uncovered: 2,265,301 out of 44,420,163
Matches: 37,854,235 out of 44,420,163
Mismatches: 3,745,134 out of 44,420,163
Insertions: 555,493 out of 44,420,163
Identity over aligned base-pairs: 89.8%

Aegilops tauschii

Uncovered: 3,586,080,388 out of 4,224,915,394
Covered: 638,835,006 out of 4,224,915,394

Uncovered: 2,608,677 out of 53,210,770
Matches: 43,999,234 out of 53,210,770
Mismatches: 5,872,244 out of 53,210,770
Insertions: 730,615 out of 53,210,770
Identity over aligned base-pairs: 87.0%

Block size distribution

Size range All 2,216,922 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
29,829
160.4 kb
10 bp - 100 bp
396,388
24.4 Mb
166,109
11.1 Mb
100 bp - 1 kb
1,434,759
543.6 Mb
707,233
279.7 Mb
1 kb - 10 kb
355,033
697.1 Mb
325,209
853.1 Mb
10 kb - 100 kb
899
21.8 Mb
7,647
128.7 Mb
100 kb - 1 Mb
14
1.8 Mb
89
16.2 Mb