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 I207 R1
|
218 |
45.0 |
2482936 |
97.1% |
2410930 |
86.1 |
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 | 100.0%
| 132.9
/ NA
| 39 | T208P (ACC→CCC) | proX | glycine betaine/L‑proline ABC transporter substrate‑binding protein ProX |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (20/19); total (20/19) |
CGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACACCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCA > NZ_CP009273/2801027‑2801189
|
cGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTg < 1:979361/90‑1 (MQ=255)
cGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTg < 1:445423/90‑1 (MQ=255)
gTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTgg > 2:184437/1‑90 (MQ=255)
gTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTgg > 1:421072/1‑90 (MQ=255)
gTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTg < 2:199420/89‑1 (MQ=255)
gTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTg > 1:199420/1‑89 (MQ=255)
aCGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACg < 2:1021556/90‑1 (MQ=255)
aCGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACg < 1:509518/90‑1 (MQ=255)
cGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGTAAACCGGTGTTTTATTACCCCTGGACGc < 2:921115/90‑1 (MQ=255)
cGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGc < 1:1072281/90‑1 (MQ=255)
cGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGc < 2:281564/90‑1 (MQ=255)
cGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGc < 1:8095/90‑1 (MQ=255)
cGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGc < 2:350215/90‑1 (MQ=255)
cGCATAATCAGGGGAACTACGAAGCGATGATGGCCGACACCATCAGTGGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGc < 1:983422/90‑1 (MQ=255)
aTCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACt < 1:1009049/90‑1 (MQ=255)
ggggAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGt > 2:217236/1‑90 (MQ=255)
aCTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTa > 2:722468/1‑90 (MQ=255)
aCGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACg > 1:1167724/1‑90 (MQ=255)
gCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTg > 2:755219/1‑90 (MQ=255)
gCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTg > 2:771319/1‑90 (MQ=255)
gatgGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGcc > 1:1140156/1‑90 (MQ=255)
ggCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGGGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCggg > 1:1155555/1‑90 (MQ=255)
gTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCt < 1:948752/90‑1 (MQ=255)
cGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTgg > 1:959073/1‑90 (MQ=255)
cTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGtt > 2:321378/1‑90 (MQ=255)
aaGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAgg < 1:1190061/90‑1 (MQ=255)
agGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACTAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGc < 2:1122994/90‑1 (MQ=255)
agGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGc < 1:708558/90‑1 (MQ=255)
gggCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGcc > 2:1191062/1‑90 (MQ=255)
ggCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGc < 1:1069641/88‑1 (MQ=255)
ggCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGc > 2:1069641/1‑88 (MQ=255)
ggCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCg > 2:571857/1‑90 (MQ=255)
ggCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCg < 2:667995/90‑1 (MQ=255)
aaCCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTtct > 2:633217/1‑90 (MQ=255)
gtgtTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGc < 1:86481/49‑1 (MQ=255)
gtgtTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGc > 2:86481/1‑49 (MQ=255)
gtgtTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCa > 1:966097/1‑90 (MQ=255)
gtgtTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCa > 1:851556/1‑90 (MQ=255)
gtgtTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCa > 1:405653/1‑90 (MQ=255)
|
CGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACACCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCA > NZ_CP009273/2801027‑2801189
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ 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
AACTGACCAACACCGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACACCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCACTGCCGGGCGATAAAAACGCC > NZ_CP009273/2801014‑2801210
|
cagcgtcagatgtgtataagagacagCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCC < SRR3722089.1239609/74‑1 (MQ=60)
GACCAACACCGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGG > SRR3722089.426152/1‑100 (MQ=60)
GACCAACACCGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGG > SRR3722089.201937/1‑100 (MQ=60)
CCAACACCGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGAC < SRR3722089.1208844/100‑1 (MQ=60)
CGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTAC < SRR3722089.993852/100‑1 (MQ=60)
CGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTAC < SRR3722089.450767/100‑1 (MQ=60)
ACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGG < SRR3722089.515518/100‑1 (MQ=60)
CGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGT < SRR3722089.8185/100‑1 (MQ=60)
CGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGT < SRR3722089.1088384/100‑1 (MQ=60)
CGCATAATCAGGGGAACTACGAAGCGATGATGGCCGACACCATCAGTGGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGT < SRR3722089.998002/100‑1 (MQ=60)
ATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAA < SRR3722089.1024075/100‑1 (MQ=60)
CAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACG > SRR3722089.1185488/1‑100 (MQ=60)
GAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACctgtctcttatacacatctgacgct > SRR3722089.409703/1‑75 (MQ=60)
ACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCC > SRR3722089.1157497/1‑100 (MQ=60)
CAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGGGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGG > SRR3722089.1173142/1‑100 (MQ=60)
gtcggcagcgtcagatgtgtataagagacagGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGA < SRR3722089.87548/69‑1 (MQ=60)
CACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGG > SRR3722089.973196/1‑100 (MQ=60)
GTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGT < SRR3722089.962682/100‑1 (MQ=60)
AAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTC < SRR3722089.1208159/100‑1 (MQ=60)
AGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGC < SRR3722089.717783/100‑1 (MQ=60)
AGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGC < SRR3722089.1085703/100‑1 (MQ=60)
GGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCA > SRR3722089.410571/1‑100 (MQ=60)
GGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCA > SRR3722089.863677/1‑100 (MQ=60)
GGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCA > SRR3722089.980350/1‑100 (MQ=60)
TTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCACTGCCGGGCGATAA > SRR3722089.944977/1‑100 (MQ=60)
TTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACctgtctcttatacacatctgacgctgccgacgaccatcttagtgtagatctcggtggtcgcc > SRR3722089.995843/1‑38 (MQ=60)
TATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCACTGCCGGGCGATAAAA > SRR3722089.462284/1‑100 (MQ=60)
ACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCACTGCCGGGCGATAAAAACGC < SRR3722089.520323/100‑1 (MQ=60)
CCCCTGGACGCCATACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCACTGCCGGGCGATAAAAACGCC > SRR3722089.1086337/1‑100 (MQ=60)
|
AACTGACCAACACCGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACACCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCACTGCCGGGCGATAAAAACGCC > NZ_CP009273/2801014‑2801210
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
