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 I199 R1
|
220 |
57.5 |
3163680 |
97.0% |
3068769 |
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 | 95.5%
| 136.9
/ ‑1.0
| 46 | T208P (ACC→CCC) | proX | glycine betaine/L‑proline ABC transporter substrate‑binding protein ProX |
| Reads supporting (aligned to +/- strand): ref base A (2/0); new base C (26/16); total (29/17) |
| Fisher's exact test for biased strand distribution p-value = 5.26e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.66e-01 |
CGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACACCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCACTGCC > NZ_CP009273/2801027‑2801194
|
cGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTg < 2:96690/90‑1 (MQ=255)
cGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTg < 1:36951/90‑1 (MQ=255)
cGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTg < 1:301933/90‑1 (MQ=255)
gTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTgg > 2:1225246/1‑90 (MQ=255)
gTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTgg > 1:853177/1‑90 (MQ=255)
gTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTgg > 1:298997/1‑90 (MQ=255)
gTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTg < 2:1396409/89‑1 (MQ=255)
gTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTg > 1:1396409/1‑89 (MQ=255)
gACGCATAATCAGGGGAACCACGCAGCCATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGAc < 1:1407204/90‑1 (MQ=255)
aTCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACt < 2:1326056/90‑1 (MQ=255)
cAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTAc > 2:53378/1‑87 (MQ=255)
cAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTAc < 1:53378/87‑1 (MQ=255)
aGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGt < 1:909242/84‑1 (MQ=255)
aGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGt > 2:909242/1‑84 (MQ=255)
ggggAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGt > 2:1371835/1‑90 (MQ=255)
ggggAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACACCTGGACGCCGTACTGGGt > 2:670083/1‑90 (MQ=255)
gggAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTg > 2:614969/1‑90 (MQ=255)
tACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAAc < 2:1292654/90‑1 (MQ=255)
gCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAATCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGaa > 1:1130498/1‑90 (MQ=255)
gCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTAc < 2:601277/75‑1 (MQ=255)
gCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTAc > 1:601277/1‑75 (MQ=255)
gCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTAC‑CCCGGACGCCGTACTGGGTGAGTAAc > 1:455578/1‑86 (MQ=255)
gCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTAC‑CCCGGACGCCGTACTGGGTGAGTAAc < 2:455578/86‑1 (MQ=255)
cAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAAc < 1:1358539/90‑1 (MQ=255)
gCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTg > 2:151008/1‑90 (MQ=255)
atgatgGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAAc > 1:701869/1‑81 (MQ=255)
atgatgGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAAc < 2:701869/81‑1 (MQ=255)
atgatgGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAg > 2:989629/1‑90 (MQ=255)
ggCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACAACTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCggg > 2:710283/1‑90 (MQ=255)
gACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCaaa > 1:1017391/1‑90 (MQ=255)
cTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGtt > 2:1116631/1‑90 (MQ=255)
cTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGtt > 1:1150608/1‑90 (MQ=255)
cTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGtt > 2:791565/1‑90 (MQ=255)
cTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGtt > 2:681950/1‑90 (MQ=255)
cAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCa > 2:1167367/1‑90 (MQ=255)
aaGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAgg > 2:268789/1‑90 (MQ=255)
agagGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACg > 1:271732/1‑53 (MQ=255)
agagGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACg < 2:271732/53‑1 (MQ=255)
ggCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCg > 2:679798/1‑90 (MQ=255)
ggCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCg > 1:1269804/1‑90 (MQ=255)
ggCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCg < 1:681950/90‑1 (MQ=255)
ggCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCg > 2:758627/1‑90 (MQ=255)
ggCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCg > 1:1124748/1‑90 (MQ=255)
aaaCCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTtc < 2:582104/90‑1 (MQ=255)
gtgtTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCa > 1:588362/1‑90 (MQ=255)
ttattaCCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCACTGcc < 2:1073004/90‑1 (MQ=255)
|
CGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACACCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCACTGCC > NZ_CP009273/2801027‑2801194
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 32 ≤ 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 < SRR3722078.454849/100‑1 (MQ=60)
GACCAACACCGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGG > SRR3722078.694212/1‑100 (MQ=60)
GACCAACACCGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGG > SRR3722078.1419000/1‑100 (MQ=60)
GACCAACACCGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGG > SRR3722078.864570/1‑100 (MQ=60)
GACCAACACCGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGG > SRR3722078.302655/1‑100 (MQ=60)
cggcgaccaccgagatctccacgaccgccatcttcggcagcgtcagatgtgtataagagacagGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTAC < SRR3722078.245044/37‑1 (MQ=60)
CGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTAC < SRR3722078.37395/100‑1 (MQ=60)
CGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTAC < SRR3722078.305622/100‑1 (MQ=60)
GACGCATAATCAGGGGAACCACGCAGCCATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACCGG < SRR3722078.1430024/100‑1 (MQ=60)
ATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAG < SRR3722078.921509/100‑1 (MQ=60)
AATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTA < SRR3722078.54009/100‑1 (MQ=60)
GGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAATCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAA > SRR3722078.1147805/1‑100 (MQ=60)
GGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTActgtc > SRR3722078.608229/1‑95 (MQ=60)
GGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTAC‑CCCGGACGCCGTACTGGGTGAGTAACGAAC > SRR3722078.461022/1‑100 (MQ=60)
CTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAG > SRR3722078.710331/1‑100 (MQ=60)
CAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGG < SRR3722078.1380363/100‑1 (MQ=60)
GATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAA > SRR3722078.1032408/1‑100 (MQ=60)
CCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTT > SRR3722078.1168360/1‑100 (MQ=60)
GTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCctgtctcttatacacatctgacgctgc > SRR3722078.275046/1‑73 (MQ=60)
CTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCG > SRR3722078.1141947/1‑100 (MQ=60)
CTACAAAGAGGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCG > SRR3722078.1289952/1‑100 (MQ=60)
GGGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCA > SRR3722078.595205/1‑100 (MQ=60)
GGCAAACCGGTGTTTTATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCAC < SRR3722078.689902/100‑1 (MQ=60)
TATTACCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCACTGCCGGGCGATAAAA > SRR3722078.589301/1‑100 (MQ=60)
CCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCctgtctcttatacacatctgacgctgccgacgatggcggtcgtgt > SRR3722078.364238/1‑55 (MQ=60)
CCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCACTGCCGGGCGATAAAAACGCC > SRR3722078.683330/1‑100 (MQ=60)
CCCCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCACTGCCGGGCGATAAAAACGCC > SRR3722078.1500797/1‑100 (MQ=60)
|
GAACTGACCAACACCGTGACGCATAATCAGGGGAACTACGCAGCGATGATGGCCGACACCATCAGTCGCTACAAAGAGGGCAAACCGGTGTTTTATTACACCTGGACGCCGTACTGGGTGAGTAACGAACTGAAGCCGGGCAAAGATGTCGTCTGGTTGCAGGTGCCGTTCTCCGCACTGCCGGGCGATAAAAACGCC > NZ_CP009273/2801013‑2801210
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
