Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A1 F1 I1 R1
|
150 |
26.0 |
2053212 |
90.0% |
1847890 |
107.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260479 |
1,112,158 |
Δ1 bp |
coding (2295/2469 nt) |
xdhB1 ← |
xanthine dehydrogenase, subunit B |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 1,112,156 | 0 | C | . | 100.0%
| 58.2
/ NA
| 14 | coding (2297/2469 nt) | xdhB1 | xanthine dehydrogenase, subunit B |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base . (7/7); total (7/7) |
CATGCCCGTCAACGCGGCCAAGGGGGGAAAGTCCGGGGGCGCCCGCAGGCGCGCGCTTCCTGCGATCGTTCCGCCAGCTCAGGCTGGCTGCGCCGCGGCTTCGCGCACGGCGTCGACGGCGTCCAGGATCGCCCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGCGGTAGTCGCCAACGGCAGCCACGGCGTCGCGGATCGCGAAGAACACCGAGAACGGCAGCAGCAGCGGCGGCTCGCCCACGGCCTTG > AM260479/1112025‑1112281
|
cATGCCCGTCAACGCGGCCAAGGGGGGAAAGTCCGGGGGCGCCCGCAGGCGCGCGCTTCCTGCGATCGTTCCGCCAGCTCAGGCTGGCTGCGCCGCGGCTTCGCGCACGGCGTCGACGGCGTCCAGGATCGcct > 1:140877/1‑133 (MQ=255)
tCCGGGGGCGCCCGCAGGCGCGCGCTTCCTGCGATCGTTCCGCCAGCTCAGGCTGGCTGCGCCGCGGCTTCGCGCACGGCGTCGACGGCGTCCAGGATCG‑CCTCGCTGGTGGc < 1:874780/113‑1 (MQ=255)
tCCGGGGGCGCCCGCAGGCGCGCGCTTCCTGCGATCGTTCCGCCAGCTCAGGCTGGCTGCGCCGCGGCTTCGCGCACGGCGTCGACGGCGTCCAGGATCG‑CCTCGCTGGTGGc > 2:874780/1‑113 (MQ=255)
cAGGCGCGCGCTTCCTGCGATCGTTCCGCCAGCTCAGGCTGGCTGCGCCGCGGCTTCGCGCACGGCGTCGACGGCGTCCAGGATCG‑CCTCGCTGGTGGCCGGGGCCTTc > 1:467393/1‑109 (MQ=255)
cAGGCGCGCGCTTCCTGCGATCGTTCCGCCAGCTCAGGCTGGCTGCGCCGCGGCTTCGCGCACGGCGTCGACGGCGTCCAGGATCG‑CCTCGCTGGTGGCCGGGGCCTTc < 2:467393/109‑1 (MQ=255)
gcgcgcgcTTCCTGCGATCGTTCCGCCAGCTCAGGCTGGCTGCGCCGCGGCTTCGCGCACGGCGTCGACGGCGTCCAGGATCG‑CCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGCGGTAGTCGCCaa < 2:140877/134‑1 (MQ=255)
cgcTTCCTGCGATCGTTCCGCCAGCTCAGGCTGGCTGCGCCGCGGCTTCGCGCACGGCGTCGACGGCGTCCAGGATCG‑CCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGCGGTAGTCGCCAACGGCa < 1:888319/134‑1 (MQ=255)
tCCTGCGATCGTTCCGCCAGCTCAGGCTGGCTGCGCCGCGGCTTCGCGCACGGCGTCGACGGCGTCCAGGATCG‑CCTCGCTGGTGGCCGGGGCCTTCa > 1:634591/1‑98 (MQ=255)
tCCTGCGATCGTTCCGCCAGCTCAGGCTGGCTGCGCCGCGGCTTCGCGCACGGCGTCGACGGCGTCCAGGATCG‑CCTCGCTGGTGGCCGGGGCCTTCa < 2:634591/98‑1 (MQ=255)
ccTGCGATCGTTCCGCCAGCTCAGGCTGGCTGCGCCGCGGCTTCGCGCACGGCGTCGACGGCGTCCAGGATCG‑CCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGCGGTAGTCGCCAACGGCAGCCAc > 2:1004768/1‑134 (MQ=255)
cgccgcGGCTTCGCGCACGGCGTCGACGGCGTCCAGGATCG‑CCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGCGGTAGTCGCCAACGGCAGCCACGGCGTCGCGGATcgc < 1:1004041/117‑1 (MQ=255)
cgccgcGGCTTCGCGCACGGCGTCGACGGCGTCCAGGATCG‑CCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGCGGTAGTCGCCAACGGCAGCCACGGCGTCGCGGATcgc > 2:1004041/1‑117 (MQ=255)
tCGACGGCGTCCAGGATCG‑CCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGCGGTAGTCGCCAACGGCAGCCACGGCGTCGCGGATCGCGAAGAACACCGAGAACGGCAGCAGCAGCGGCGGCTCGcc > 1:829390/1‑134 (MQ=255)
gACGGCGTCCAGGATCG‑CCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGCGGTAGTCGCCAACGGCAGCCACGGCGTCGCGGATCGCGAAGAACACCGAGAACGGCAGCAGCAGCGGCGGCTCGCCCa > 2:545656/1‑134 (MQ=255)
cAGGATCG‑CCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGCGGTAGTCGCCAACGGCAGCCACGGCGTCGCGGATCGCGAAGAACACCGAGAACGGCAGCAGCAGCGGCGGCTCGCCCACGGCCTTg < 1:545656/133‑1 (MQ=255)
|
CATGCCCGTCAACGCGGCCAAGGGGGGAAAGTCCGGGGGCGCCCGCAGGCGCGCGCTTCCTGCGATCGTTCCGCCAGCTCAGGCTGGCTGCGCCGCGGCTTCGCGCACGGCGTCGACGGCGTCCAGGATCGCCCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGCGGTAGTCGCCAACGGCAGCCACGGCGTCGCGGATCGCGAAGAACACCGAGAACGGCAGCAGCAGCGGCGGCTCGCCCACGGCCTTG > AM260479/1112025‑1112281
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CAACGCGGCCAAGGGGGGAAAGTCCGGGGGCGCCCGCAGGCGCGCGCTTCCTGCGATCGTTCCGCCAGCTCAGGCTGGCTGCGCCGCGGCTTCGCGCACGGCGTCGACGGCGTCCAGGATCGCCCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGCGGTAGTCGCCAACGGCAGCCACGGCGTCGCGGATCGCGAAGAACACCGAGAACGGCAGCAGCAGCGGCGGCTCGCCCACGGCCTTGGAGCGGTGGATGCTG > AM260479/1112034‑1112296
|
gagacaGGCCAAGGGGGGAAAGTCCGGGGGCGCCCGCAGGCGCGCGCTTCCTGCGATCGTTCCGCCAGCTCAGGCTGGCTGCGCCGCGGCTTCGCGCACGGCGTCGACGGCGTCCAGGATCG‑CCTCGCTGGTGGCCGGGGCCTTCAGCGG < GWNJ‑0478:712:GW2002102894th:2:2207:6962:10590/144‑1 (MQ=60)
tttatgttttatttttttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaGGCGTCCAGGATCG‑CCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGCGGTAG < GWNJ‑0478:712:GW2002102894th:2:2210:6360:50554/58‑1 (MQ=60)
GTCCGGGGGCGCCCGCAGGCGCGCGCTTCCTGCGATCGTTCCGCCAGCTCAGGCTGGCTGCGCCGCGGCTTCGCGCACGGCGTCGACGGCGTCCAGGATCG‑CCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGCtgtctcttat > GWNJ‑0478:712:GW2002102894th:2:1215:19731:34166/1‑140 (MQ=60)
CCGCAGGCGCGCGCTTCCTGCGATCGTTCCGCCAGCTCAGGCTGGCTGCGCCGCGGCTTCGCGCACGGCGTCGACGGCGTCCAGGATCG‑CCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGCctgtctcttatacacatctccg > GWNJ‑0478:712:GW2002102894th:2:2109:16003:14481/1‑128 (MQ=60)
GCGCTTCCTGCGATCGTTCCGCCAGCTCAGGCTGGCTGCGCCGCGGCTTCGCGCACGGCGTCGACGGCGTCCAGGATCG‑CCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGCGGTAGTCGCCAACGGCAGCCACGGCGTCGCGG < GWNJ‑0478:712:GW2002102894th:2:2207:12106:93809/150‑1 (MQ=60)
cagAGCTCAGGCTGGCTGCGCCGCGGCTTCGCGCACGGCGTCGACGGCGTCCAGGATCG‑CCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGCGGTAGTCGCCAACGGCAGCCACGGCGTCGCGGATCGCGAAGAACACCGAGAA < GWNJ‑0478:712:GW2002102894th:2:2215:19829:67614/147‑1 (MQ=60)
CGCCGCGGCTTCGCGCACGGCGTCGACGGCGTCCAGGATCG‑CCTCGCTGGTGctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaaaaaaaaaaaaacaaacaagcggaga > GWNJ‑0478:712:GW2002102894th:2:1106:9006:13697/1‑52 (MQ=60)
GCTTCGCGCACGGCGTCGACGGCGTCCAGGATCG‑CCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGCGGTAGTCGCCAACGGCAGCCACGGCGTCGCGGATCGCGAAGAACACCGAGAACGGCAGCAGCAGCGGCGGCTCGCCC > GWNJ‑0478:712:GW2002102894th:2:2205:20371:24735/1‑150 (MQ=60)
CCAGGATCG‑CCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGCGGTAGTCGCCAACGGCAGCCACGGCGTCGCGGATCGCGAAGAACACCGAGAACGGCAGCAGCAGCGGCGGCTCGCCCACGGCCTTGGAGCGGTGGATGCTG < GWNJ‑0478:712:GW2002102894th:2:2102:20228:21348/149‑1 (MQ=60)
|
CAACGCGGCCAAGGGGGGAAAGTCCGGGGGCGCCCGCAGGCGCGCGCTTCCTGCGATCGTTCCGCCAGCTCAGGCTGGCTGCGCCGCGGCTTCGCGCACGGCGTCGACGGCGTCCAGGATCGCCCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGCGGTAGTCGCCAACGGCAGCCACGGCGTCGCGGATCGCGAAGAACACCGAGAACGGCAGCAGCAGCGGCGGCTCGCCCACGGCCTTGGAGCGGTGGATGCTG > AM260479/1112034‑1112296
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
