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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,839,920 |
A→T |
40.0% |
P229P (CCT→CCA) |
ampC ← |
beta‑lactamase/D‑alanine carboxypeptidase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,839,920 | 0 | A | T | 40.0%
| 36.9
/ 58.9
| 65 | P229P (CCT→CCA) | ampC | beta‑lactamase/D‑alanine carboxypeptidase |
| Reads supporting (aligned to +/- strand): ref base A (30/9); new base T (11/15); total (41/24) |
| Fisher's exact test for biased strand distribution p-value = 8.12e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CCCAGCGGGCCATATCTTCAATGGTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGATATCCCCAGGCGTAATTCTTTTCTTCTGCGGGCGG > minE/2839859‑2839985
|
cccAGCGGGCCATATCTTCAATGGTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCTGGCGaaa > 1:368745/1‑69 (MQ=255)
cccAGCGGGCCATATCTTCAATGGTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCTGGCGaaa > 1:500308/1‑69 (MQ=255)
cccAGCGGGCCATATCTTCAATGGTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCTGGCGaaa > 1:1183/1‑69 (MQ=255)
cccAGCGGGCCATATCTTCAATGGTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCTGGCGaaa > 1:1226949/1‑69 (MQ=255)
cccAGCGGGCCATATCTTCAATGGTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCTGGCGaaa > 1:861743/1‑69 (MQ=255)
cccAGCGGGCCATATCTTCAATGGTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCTGGCGaaa > 1:849674/1‑69 (MQ=255)
cccAGCGGGCCATATCTTCAATGGTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCTGGCGaaa > 1:823672/1‑69 (MQ=255)
cccAGCGGGCCATATCTTCAATGGTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCTGGCGaaa > 1:1540138/1‑69 (MQ=255)
cccAGCGGGCCATATCTTCAATGGTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCTGGCGaaa > 1:2904326/1‑69 (MQ=255)
cccAGCGGGCCATATCTTCAATGGTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCTGGCGaaa > 1:2885432/1‑69 (MQ=255)
cccAGCGGGCCATATCTTCAATGGTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCTGGCGaaa > 1:689893/1‑69 (MQ=255)
gCCATATGTTCAATGGTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCTGGCGAAACATGTACt < 1:1648632/69‑1 (MQ=255)
gCCATATCTTCAATGGTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCTGGCGAAACATGTACt < 1:2385697/69‑1 (MQ=255)
gCCATATCTTCAATGGTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCTGGCGAAACATGTACt < 1:2161283/69‑1 (MQ=255)
gCCATATCTTCAATGGTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCTGGCGAAACATGTACt < 1:2739615/69‑1 (MQ=255)
gCCATATCTTCAATGGTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCTGGCGAAACATGTACt < 1:882215/69‑1 (MQ=255)
gCCATATCTTCAATGGTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCTGGCGAAACATGTACt < 1:2663624/69‑1 (MQ=255)
gCCATATCTTCAATGGTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCTGGCGAAACATGTACt < 1:2658398/69‑1 (MQ=255)
gCCATATCTTCAATGGTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCTGGCGAAACATGTACt < 1:3207552/69‑1 (MQ=255)
gCCATATCTTCAATGGTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCTGGCGAAACATGTACt < 1:725788/69‑1 (MQ=255)
gCCATATCTTCAATGGTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCTGGCGAAACATGTACt < 1:1623956/69‑1 (MQ=255)
gCCATATCTTCAATGGTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCTGGCGAAACATGTACt < 1:874876/69‑1 (MQ=255)
ccATATCTTCAATGGTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCTGGCGAAACATGTACt < 1:2880394/68‑1 (MQ=255)
tCTTCAATGGTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCAGGCGAAACATGCACTGCCTTa > 1:2986882/1‑69 (MQ=255)
tCTTCAATGGTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCAGGCGAAACATGCACTGCCTTa > 1:1772009/1‑69 (MQ=255)
tCTTCAATGGTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCAGGCGAAACATGCACTGCCTTa > 1:1755216/1‑69 (MQ=255)
tCTTCAATGGTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCAGGCGAAACATGCACTGCCTTa > 1:542139/1‑69 (MQ=255)
tGGTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCAGGCGAAACATGCACTGCCTTACCTTcgc > 1:2821272/1‑69 (MQ=255)
gTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGa > 1:920421/1‑69 (MQ=255)
gTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGa > 1:1084983/1‑69 (MQ=255)
gTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGa > 1:1499439/1‑69 (MQ=255)
aCTTCACACCATAAGCTTCAGCATCTAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGATATc < 1:1075816/69‑1 (MQ=255)
cTTCACACCATAAGCTTCAGCATCTAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGATATc < 1:1090042/68‑1 (MQ=255)
cTTCACACCATAAGCTTCAGCATCTAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGATATc < 1:728645/68‑1 (MQ=255)
cTTCACACCATAAGCTTCAGCATCTAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGATATc < 1:2837002/68‑1 (MQ=255)
cTTCACACCATAAGCTTCAGCATCTAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGATATc < 1:2169277/68‑1 (MQ=255)
cTTCACACCATAAGCTTCAGCATCTAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGATATc < 1:398969/68‑1 (MQ=255)
acCATAAGCTTCAGCATCTAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGATATc < 1:1947195/62‑1 (MQ=255)
aGCTTCAGCATCTAACGCCCCAGGCGAAACATGCACTGCCt > 1:163619/1‑41 (MQ=255)
aGCTTCAGCATCTAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGATATCCCCAGGCGt > 1:2891729/1‑65 (MQ=255)
aGCTTCAGCATCTAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGATATCCCCAGGCGt > 1:2286185/1‑65 (MQ=255)
aGCTTCAGCATCTAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGATATCCCCAGGCGt < 1:2737927/65‑1 (MQ=255)
aGCTTCAGCATCTAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGATATCCCCAGGCGt > 1:163306/1‑65 (MQ=255)
aGCTTCAGCATCTAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGATATCCCCAGGCGt > 1:168466/1‑65 (MQ=255)
aGCTTCAGCATCTAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGATATCCCCAGGCGt > 1:181291/1‑65 (MQ=255)
aGCTTCAGCATCTAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGATATCCCCAGGCGt > 1:434257/1‑65 (MQ=255)
aGCTTCAGCATCTAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGATATCCCCAGGCGTAAtt > 1:80919/1‑69 (MQ=255)
aGCTTCAGCATCTAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGATATCCCCAGGCGTAAtt > 1:481864/1‑69 (MQ=255)
aGCTTCAGCATCTAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGATATCCCCAGGCGTAAtt > 1:2644750/1‑69 (MQ=255)
aGCTTCAGCATCTAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGATATCCCCAGGCGTAAtt > 1:878737/1‑69 (MQ=255)
aGCTTCAGCATCTAACGCCACAGGCGAAACATGCACTGCCTTACCTTCGCGATATCCCCAGGCGt > 1:2337863/1‑65 (MQ=255)
aGCTTCAGCATCTAACG‑‑CCAGGCGAAACATGCACTGc > 1:3181685/1‑37 (MQ=37)
aGCTTCAGAATCTAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGATATCCCCAGGCGt > 1:2810250/1‑65 (MQ=255)
cTTCAGCATCTAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGATATCCCCAGGCGTAAttct > 1:562358/1‑69 (MQ=255)
cATCTAACGCCCCTGGCGAAACATGTACTGCCTTACCTTCGCGATATCCCCAGGCGTAGttcttttct < 1:1342711/68‑1 (MQ=255)
cATCTAACGCCCCTGGCGAAACATGTACTGCCTTACCTTCGCGATATCCCCAGGCGTAGttcttttct < 1:1329760/68‑1 (MQ=255)
cATCTAACGCCCCTGGCGAAACATGTACTGCCTTACCTTCGCGATATCCCCAGGCGTAGttcttttct < 1:2936132/68‑1 (MQ=255)
tAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGATATCCCCAGGCGTAATTCTTTTCTTCTgc > 1:242054/1‑69 (MQ=255)
tAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGATATCCCCAGGCGTAATTCTTTTCTTCTgc > 1:205310/1‑69 (MQ=255)
tAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGATATCCCCAGGCGTAATTCTTTTCTTCTgc > 1:3391155/1‑69 (MQ=255)
tAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGATATCCCCAGGCGTAATTCTTTTCTTCTgc > 1:1962194/1‑69 (MQ=255)
tAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGATATCCCCAGGCGTAATTCTTTTCTTCTgc > 1:3091183/1‑69 (MQ=255)
tAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGATATCCCCAGGCGTAATTCTTTTCTTCTgc > 1:2034749/1‑69 (MQ=255)
tAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGATATCCCCAGGCGTAATTCTTTTCTTCAgc > 1:2042325/1‑69 (MQ=255)
cccAGGCGAAACATGCACTGCCTTACCTTCGCGATATCCCCAGGCGTAATTCTTTTCTTCTgcgggcgg < 1:3122210/69‑1 (MQ=255)
|
CCCAGCGGGCCATATCTTCAATGGTCGACTTCACACCATAAGCTTCAGCATCTAACGCCCCAGGCGAAACATGCACTGCCTTACCTTCGCGATATCCCCAGGCGTAATTCTTTTCTTCTGCGGGCGG > minE/2839859‑2839985
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
