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Pythium irregulare vs Pythium iwayamai LastZ results

Pythium irregulare (Globisporangium irregulare DAOM BR486, pir_scaffolds_v1) and Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_scaffolds_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Pythium irregulare 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

ParameterPythium irregularePythium iwayamai
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 45,403 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Pythium irregulare

Uncovered: 13,403,530 out of 42,968,084
Covered: 29,564,554 out of 42,968,084

Uncovered: 1,366,521 out of 20,543,058
Matches: 14,483,329 out of 20,543,058
Mismatches: 4,114,656 out of 20,543,058
Insertions: 578,552 out of 20,543,058
Identity over aligned base-pairs: 75.5%

Pythium iwayamai

Uncovered: 14,536,585 out of 43,199,174
Covered: 28,662,589 out of 43,199,174

Uncovered: 921,740 out of 19,552,457
Matches: 14,359,289 out of 19,552,457
Mismatches: 3,946,111 out of 19,552,457
Insertions: 325,317 out of 19,552,457
Identity over aligned base-pairs: 77.1%

Block size distribution

Size range All 45,403 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
190
1.0 kb
10 bp - 100 bp
5,425
352.0 kb
2,522
174.3 kb
100 bp - 1 kb
29,682
11.9 Mb
14,962
5.9 Mb
1 kb - 10 kb
10,026
21.5 Mb
6,886
19.7 Mb
10 kb - 100 kb
80
1.1 Mb
588
9.0 Mb