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 F4 I96 R1
|
227 |
23.3 |
882352 |
98.0% |
864704 |
126.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
928,200 |
T→C |
R50R (CGT→CGC) |
lrp → |
leucine‑responsive transcriptional regulator Lrp |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 928,200 | 0 | T | C | 100.0%
| 56.3
/ NA
| 18 | R50R (CGT→CGC) | lrp | leucine‑responsive transcriptional regulator Lrp |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (6/12); total (6/12) |
GAAGCGCCCTGGCAAAGATCTCGACCGTATCGATCGTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTG‑CCTTGAGCGTGTGCGTCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACTCTGAATCGTGGCGCACCGGATGTGTTTGAACAATTCAATA > NZ_CP009273/928065‑928333
|
gaagCGCCCTGGCAAAGATCTCGACCGTATCGATCGTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTG‑CCTTGAGCGTGTGCGCCgg < 1:351722/139‑1 (MQ=255)
gCAAAGATCTCGACCGTATCGATCGTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTG‑CCTTGAGCGTGTGCGCCGGCTGGAAAGACa < 1:163089/139‑1 (MQ=255)
gATCTCGACCGTATCGATCGTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTG‑CCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGt < 1:130348/139‑1 (MQ=255)
gATCTCGACCGTATCGATCGTAACATTCTTAATGAGGTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTG‑CCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGt < 2:298918/139‑1 (MQ=255)
aCCGTATCGATCGTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTG‑CCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCa < 2:417277/139‑1 (MQ=255)
ttAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTG‑CCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTaa > 1:280238/1‑139 (MQ=255)
aGTTTCGAAAGGCTGGCCGTATTTCTAACGTCGAGCTTGCTAAACGAGTGAGGCTTACCTCACGGCCTTGTCAAAGATC‑TGTGCGCCGGTTAGAAAGGCATGGGTTTATTCACGGCTATACTGCGCGGCTTAAcccag < 2:256784/138‑3 (MQ=255)
ttGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTG‑CCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAAccccc < 2:87673/136‑1 (MQ=255)
ttGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTG‑CCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAAccccc > 1:87673/1‑136 (MQ=255)
aaGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTG‑CCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTgg < 2:47598/139‑1 (MQ=255)
ggCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTG‑CCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCAt > 2:403914/1‑138 (MQ=255)
ggCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTG‑CCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGATTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCAt > 2:270591/1‑138 (MQ=255)
cTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTG‑CCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTgaga < 1:403914/139‑1 (MQ=255)
cTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTG‑CCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTgaga < 1:217485/139‑1 (MQ=255)
tgGGACTTTCCCCAACGCCGTG‑CCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACTCTGAATCg > 1:394839/1‑139 (MQ=255)
gACTTTCCCCAACGCCGTG‑CCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACTCTGAATCGTgg < 2:280640/139‑1 (MQ=255)
ccTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACTCTGAATCGTGGCGCACCGGATGTGTTTGaa < 2:204650/139‑1 (MQ=255)
gtgCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACTCTGAATCGTGGCGCACCGGATGTGTTTGAACAATTCAATa > 1:1291/1‑139 (MQ=255)
|
GAAGCGCCCTGGCAAAGATCTCGACCGTATCGATCGTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTG‑CCTTGAGCGTGTGCGTCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACTCTGAATCGTGGCGCACCGGATGTGTTTGAACAATTCAATA > NZ_CP009273/928065‑928333
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ATGGTAGATAGCAAGAAGCGCCCTGGCAAAGATCTCGACCGTATCGATCGTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGTCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACTCTGAATCGTGGCGCACCGGATGTGTTTGAACAATTCAATACCGCTGTAC > NZ_CP009273/928051‑928342
|
ATGGTAGATAGCAAGAAGCGCCCTGGCAAAGATCTCGACCGTATCGATCGTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCC > SRR3722119.352210/1‑151 (MQ=60)
GCAGGAAGCGCCCTGGCAAAGATCTCGACCGTATCGATCGTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAG < SRR3722119.260608/151‑1 (MQ=60)
AGAAGCGCCCTGGCAAAGATCTCGACCGTATCGATCGTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACA < SRR3722119.355296/151‑1 (MQ=60)
ggnnnnnnnnTCNACCGTATCGATCGTAACATTCTTAATGAGTTNNNNNNNNNNNNNNNNATTTCTAACNTCGAGNNNNCTAAACGTGTGGGACTTTCCCCAANGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTC < SRR3722119.417496/141‑1 (MQ=60)
GGCAAAGATCTCGACCGTATCGATCGTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTC < SRR3722119.164756/151‑1 (MQ=60)
AGATCTCGACCGTATCGATCGTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGC < SRR3722119.131660/151‑1 (MQ=60)
TCGTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAAC > SRR3722119.283130/1‑151 (MQ=60)
TTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATT > SRR3722119.88535/1‑150 (MQ=60)
GCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACTCTGAAT < SRR3722119.219819/151‑1 (MQ=60)
GCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACTCTGAAT < SRR3722119.407954/151‑1 (MQ=60)
TTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACTCTGAATCGT > SRR3722119.398778/1‑151 (MQ=60)
GCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACTCTGAATCGTGGCGCACCGGATGTGTTTGAACAATTCAATAC > SRR3722119.1305/1‑151 (MQ=60)
CGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCtgtctcttatacacatctccgagcccacgagactaaggcgaatctcgtatgccgtcttctgcttgaaaaaaaaaaaaacaaacgctaagatgccactacctaat > SRR3722119.140665/1‑47 (MQ=60)
|
ATGGTAGATAGCAAGAAGCGCCCTGGCAAAGATCTCGACCGTATCGATCGTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGTCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACTCTGAATCGTGGCGCACCGGATGTGTTTGAACAATTCAATACCGCTGTAC > NZ_CP009273/928051‑928342
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
