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 F2 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,801,112 |
A→C |
T208P (ACC→CCC) |
proX → |
glycine betaine/L‑proline ABC transporter substrate‑binding protein ProX |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,801,112 | 0 | A | C | 94.4%
| 112.0
/ ‑0.8
| 36 | T208P (ACC→CCC) | proX | glycine betaine/L‑proline ABC transporter substrate‑binding protein ProX |
| Reads supporting (aligned to +/- strand): ref base A (1/1); new base C (15/19); total (16/20) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01 |
CCGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACACCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCA > NZ_CP009273/2801026‑2801189
|
ccGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCt > 2:281242/1‑90 (MQ=255)
cGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTg < 1:575404/90‑1 (MQ=255)
gTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTgg > 2:438917/1‑90 (MQ=255)
gTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTgg > 1:730583/1‑90 (MQ=255)
aCGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACg < 2:799508/90‑1 (MQ=255)
aCGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACg < 2:541280/90‑1 (MQ=255)
aCGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACg < 1:719117/90‑1 (MQ=255)
aCGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACg < 1:351050/90‑1 (MQ=255)
cGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGc < 2:815091/90‑1 (MQ=255)
gCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCTGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGcc > 2:61724/1‑90 (MQ=255)
tAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACACCTGGACGCCGTa > 1:197654/1‑90 (MQ=255)
aaTCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTAc < 1:438917/90‑1 (MQ=255)
aTCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACt < 2:714104/90‑1 (MQ=255)
aTCAGGGGAACTACGAAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACt < 2:152937/90‑1 (MQ=255)
gggAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTg < 1:126877/90‑1 (MQ=255)
gggAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTg < 1:3774/90‑1 (MQ=255)
aCTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTa > 1:392360/1‑90 (MQ=255)
cGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACACCTGGACGCCGTACTGGGTGAGTAACGa < 2:115564/90‑1 (MQ=255)
gCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGaa > 2:49165/1‑90 (MQ=255)
gCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTg > 2:610848/1‑90 (MQ=255)
gatgatGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGaa > 2:612676/1‑90 (MQ=255)
tgatgGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGc < 1:681495/90‑1 (MQ=255)
tgatgGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGc < 2:431162/90‑1 (MQ=255)
gatgGCCGACACCATCTGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGcc < 1:61724/90‑1 (MQ=255)
gatgGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGcc > 2:422262/1‑90 (MQ=255)
gatgGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGcc > 1:631957/1‑90 (MQ=255)
cGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCaa < 1:673633/90‑1 (MQ=255)
gACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCaaa > 1:485030/1‑90 (MQ=255)
cAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCa < 1:293137/90‑1 (MQ=255)
agGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGc > 2:287976/1‑60 (MQ=255)
agGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGc > 2:330258/1‑60 (MQ=255)
agGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGc < 1:287976/60‑1 (MQ=255)
agGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGc < 1:330258/60‑1 (MQ=255)
aaaCCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTtc < 1:267003/90‑1 (MQ=255)
gtgtTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCa > 1:752810/1‑90 (MQ=255)
gtgtTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCa > 1:345479/1‑90 (MQ=255)
|
CCGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACACCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCA > NZ_CP009273/2801026‑2801189
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GAACTGACCAACACCGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACACCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCACTGCCGGGCGATAAAAACGCC > NZ_CP009273/2801013‑2801210
|
GAACTGACCAACACCGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACC < SRR3722079.82386/100‑1 (MQ=60)
AACTGACCAACACCGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACAC < SRR3722079.574005/100‑1 (MQ=60)
GACCAACACCGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGG > SRR3722079.738399/1‑100 (MQ=60)
CCGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACACCTGGACGCCGTA > SRR3722079.199359/1‑100 (MQ=60)
ggcatacgagatcctctctggtctcgtgggctcggagatgtgtataagagacaGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTAC < SRR3722079.98168/47‑1 (MQ=60)
CGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTAC < SRR3722079.581079/100‑1 (MQ=60)
ACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGG < SRR3722079.726795/100‑1 (MQ=60)
ACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGG < SRR3722079.353814/100‑1 (MQ=60)
AATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTA > SRR3722079.395625/1‑100 (MQ=60)
AATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTA < SRR3722079.442725/100‑1 (MQ=60)
GGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAAC < SRR3722079.3805/100‑1 (MQ=60)
GGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAAC < SRR3722079.127922/100‑1 (MQ=60)
ACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCC > SRR3722079.638420/1‑100 (MQ=60)
GATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAA > SRR3722079.489261/1‑100 (MQ=60)
gagatgtgtataagagacagCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGA < SRR3722079.332895/80‑1 (MQ=60)
gagatgtgtataagagacagCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGA < SRR3722079.290357/80‑1 (MQ=60)
TGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGA < SRR3722079.688651/100‑1 (MQ=60)
GATGGCCGACACCATCTGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGAT < SRR3722079.62223/100‑1 (MQ=60)
CGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTC < SRR3722079.680689/100‑1 (MQ=60)
CAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTC < SRR3722079.295548/100‑1 (MQ=60)
GGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCA > SRR3722079.348208/1‑100 (MQ=60)
GGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCA > SRR3722079.760858/1‑100 (MQ=60)
AAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCACTGC < SRR3722079.269241/100‑1 (MQ=60)
TTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCACTGCCGGGCGATAAA > SRR3722079.458400/1‑100 (MQ=60)
TTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCACTGCCGGGCGATAAA > SRR3722079.181544/1‑100 (MQ=60)
CCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCACTGCCGGGCGATAAAAACGCC > SRR3722079.689423/1‑100 (MQ=60)
CCCCTGGACGCCGTACTGGGGGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCACTGCCGGGCGATAAAAACGCC > SRR3722079.564706/1‑100 (MQ=60)
|
GAACTGACCAACACCGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACACCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCACTGCCGGGCGATAAAAACGCC > NZ_CP009273/2801013‑2801210
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
