Trichoderma virens vs Fusarium oxysporum Translated Blat results
Trichoderma virens (Trichoderma virens Gv29-8, ASM17099v1) and Fusarium oxysporum (Fusarium oxysporum f. sp. lycopersici, FO2) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Fungi release 94. Trichoderma virens was used as the reference species. After running Translated Blat, the raw Translated Blat 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
Parameter | Value |
---|---|
Minimum score (minScore) | 30 |
Database type (t) | dnax |
Query type (q) | dnax |
Mask out repeats (mask) | lower |
Mask out repeats on query (qMask) | lower |
Chunking parameters
Parameter | Trichoderma virens | Fusarium oxysporum |
---|---|---|
Chunk size | 1,000,000 | 25,000 |
Overlap | 10,000 | 10,000 |
Group set size | 100,000,000 | 10,000,000 |
Masking options | {default_soft_masking => 1} | {default_soft_masking => 1} |
Statistics over 55,329 alignment blocks
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Trichoderma virens |
Uncovered: 30,111,443 out of 39,022,666 |
Uncovered: 8,989,831 out of 17,541,951 |
Fusarium oxysporum |
Uncovered: 51,331,519 out of 61,470,697 |
Uncovered: 12,839,362 out of 21,631,774 |
Block size distribution
Size range | All 55,329 alignment blocks | Blocks grouped in nets | |||
---|---|---|---|---|---|
# blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
1 bp - 10 bp | 356 |
1.5 kb |
|||
10 bp - 100 bp | 46,194 |
2.7 Mb |
261 |
20.7 kb |
|
100 bp - 1 kb | 62,296 |
16.2 Mb |
6,093 |
2.4 Mb |
|
1 kb - 10 kb | 1,812 |
2.6 Mb |
2,814 |
6.9 Mb |
|
10 kb - 100 kb | 224 |
7.2 Mb |
|||
100 kb - 1 Mb | 30 |
4.9 Mb |