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 |
1,634,474 |
T→C |
41.6% |
T204T (ACT→ACC) |
acrD → |
aminoglycoside/multidrug efflux system |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,634,474 | 0 | T | C | 41.6%
| 18.1
/ 42.7
| 60 | T204T (ACT→ACC) | acrD | aminoglycoside/multidrug efflux system |
| Reads supporting (aligned to +/- strand): ref base T (17/18); new base C (15/10); total (32/28) |
| Fisher's exact test for biased strand distribution p-value = 4.39e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TATTCCATGCGTATCTGGCTGGACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACTGATGCCATTGAGTCACAGAACGCGCAGATTGCGGTTGGGCAACTTGGTGGTACACCT > minE/1634406‑1634531
|
tatTCCATGCGTATCTGGCTGGACCCGGCGAAACTCTACAGTTTCCAGATGACGGCTAAAGATGTCACt < 1:1118177/69‑1 (MQ=255)
tatTCCATGCGTATCTGGCTGGACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTATAGATGTCACt < 1:2466656/69‑1 (MQ=255)
tatTCCATGCGTATCTGGCTGGACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACt < 1:2303234/69‑1 (MQ=255)
tatTCCATGCGTATCTGGCTGGACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACt < 1:2258884/69‑1 (MQ=255)
tatTCCATGCGTATCTGGCTGGACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACt < 1:209465/69‑1 (MQ=255)
tatTCCATGCGTATCTGGCTGGACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACt < 1:3051411/69‑1 (MQ=255)
tatTCCATGCGTATCTGGCTGGACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACt < 1:405067/69‑1 (MQ=255)
tatTCCATGCGTATCTGGCTGGACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACt < 1:1216997/69‑1 (MQ=255)
atTCCATGCGTATCTGGCTGGACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACTg > 1:506302/1‑69 (MQ=255)
atTCCATGCGTATCTGGCTGGACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACTg > 1:3429509/1‑69 (MQ=255)
atTCCATGCGTATCTGGCTGGACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACTg > 1:3027297/1‑69 (MQ=255)
atTCCATGCGTATCTGGCTGGACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACTg > 1:1805219/1‑69 (MQ=255)
atTCCATGCGTATCTGGCTGGACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACTg > 1:1879573/1‑69 (MQ=255)
atTCCATGCGTATCTGGCTGGACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACTg > 1:2652909/1‑69 (MQ=255)
atTCCATGCGTATCTGGCTGGACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACTg > 1:1957578/1‑69 (MQ=255)
atTCCATGCGTATCTGGCTGGACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACTg > 1:1239635/1‑69 (MQ=255)
ccATGCGTATCTGGCTGGACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACTGAt > 1:417389/1‑68 (MQ=255)
cGTATCTGGCTGGACCCGGCGAAACTCAACAGTTTCCAGATGACTGCTAAAGATGTCACTGAt > 1:64562/1‑63 (MQ=255)
cGTATCTGGCTGGACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACTGATGCCa > 1:2981050/1‑67 (MQ=255)
cGTATCTGGCTGGACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACTGATGCCa > 1:2574136/1‑67 (MQ=255)
cGTATCTGGCTGGACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACTGATGCCa > 1:81553/1‑67 (MQ=255)
cGTATCTGGCTGGACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACTGATGCCa > 1:842358/1‑67 (MQ=255)
cGTATCTGGCTGGACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACTGATGCCa > 1:1378472/1‑67 (MQ=255)
tggACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACTGATGCCATTGAGTca < 1:2320532/65‑1 (MQ=255)
tggACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACTGATGCCATTGAGTca < 1:1509189/65‑1 (MQ=255)
tggACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACTGATGCCATTGAGTca < 1:3150310/65‑1 (MQ=255)
tggACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACTGATGCCATTGAGTca < 1:1620831/65‑1 (MQ=255)
tggACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACTGATGCCATTGAGTca < 1:1320911/65‑1 (MQ=255)
tggACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACTGATGCCATTGAGTca < 1:565514/65‑1 (MQ=255)
tggACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACTGATGCCATTGAGTca < 1:2667486/65‑1 (MQ=255)
tggACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACTGATGCCATTGAGTca < 1:2617359/65‑1 (MQ=255)
ggCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACTGATGCCATTGAGTCACAGAACGCGCa < 1:612897/69‑1 (MQ=255)
ggCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACTGATGCCATTGAGTCACAGAACGCGCa < 1:2816398/69‑1 (MQ=255)
ggCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACTGATGCCATTGAGTCACAGAACGCGCa < 1:640212/69‑1 (MQ=255)
ggCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACTGATGCCATTGAGTCACAGAACGCGCa < 1:2612180/69‑1 (MQ=255)
gAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACTGATGCCATTGAGTca < 1:2691793/55‑1 (MQ=255)
cAACAGTTTCCAGATGACGGCTAAAGATGTCACTGATGCCATTGAGTCACAGAACgcgc > 1:717054/1‑59 (MQ=255)
cAACAGCTTCCAGATGACGGCTAAAGATGTCACTGATGCCATTGAGTCACAGAACGCGCa > 1:435103/1‑60 (MQ=255)
aaCAGTTTCCAGATGACGGCTAAAGATGTCACCGATGCCAt > 1:3072097/1‑41 (MQ=255)
aaCAGTTTCCAGATGACGGCTAAAGATGTCACCGATGCCATTg > 1:621145/1‑43 (MQ=255)
aaCAGTTTCCAGATGACGGCTAAAGATGTCACCGATGCCATTg > 1:571131/1‑43 (MQ=255)
aaCAGTTTCCAGATGACGGCTAAAGATGTCACCGATGCCATTg > 1:420765/1‑43 (MQ=255)
aaCAGTTTCCAGATGACGGCTAAAGATGTCACCGATGCCATTg > 1:753954/1‑43 (MQ=255)
aaCAGTTTCCAGATGACGGCTAAAGATGTCACCGATGCCATTg > 1:367819/1‑43 (MQ=255)
aaCAGTTTCCAGATGACGGCTAAAGATGTCACCGATGCCATTg > 1:2274140/1‑43 (MQ=255)
aaCAGTTTCCAGATGACGGCTAAAGATGTCACCGATGCCATTg > 1:2075702/1‑43 (MQ=255)
aaCAGTTTCCAGATGACGGCTAAAGATGTCACCGATGCCATTg > 1:1752816/1‑43 (MQ=255)
aaCAGTTTCCAGATGACGGCTAAAGATGTCACCGATGCCATTg > 1:2971704/1‑43 (MQ=255)
aaCAGTTTCCAGATGACGGCTAAAGATGTCACCGATGCCATTg > 1:2630214/1‑43 (MQ=255)
aaCAGTTTCCAGATGACGGCTAAAGATGTCACCGATGCCATTg > 1:2793260/1‑43 (MQ=255)
aaCAGTTTCCAGATGACGGCTAAAGATGTCACCGATGCCATTg > 1:2911202/1‑43 (MQ=255)
aaCAGTTTCCAGATGACGGCTAAAGATGTCACCGATGCCATTg > 1:2816401/1‑43 (MQ=255)
aaCAGTTTCCAGATGACGGCT‑AAGATGTCACCGATGCCATTg > 1:66438/1‑42 (MQ=255)
gACGGCTAAAGATGTCACCGATGCCATTGAATCACAGAACGCGCAGATTGCGGTTGGGCAACTtggtgg < 1:1007092/69‑1 (MQ=255)
gACGGCTAAAGATGTCACCGATGCCATTGAATCACAGAACGCGCAGATTGCGGTTGGGCAACTtggtgg < 1:2572060/69‑1 (MQ=255)
gACGGCTAAAGATGTCACCGATGCCATTGAATCACAGAACGCGCAGATTGCGGTTGGGCAACTtggtgg < 1:1268375/69‑1 (MQ=255)
gACGGCTAAAGATGTCACCGATGCCATTGAATCACAGAACGCGCAGATTGCGGTTGGGCAACTtggtgg < 1:464943/69‑1 (MQ=255)
gACGGCTAAAGATGTCACCGATGCCATTGAATCACAGAACGCGCAGATTGCGGTTGGGCAACTtggtgg < 1:1593166/69‑1 (MQ=255)
gACGGCTAAAGATGTCACCGATGCCATTGAATCACAGAACGCGCAGATTGCGGTTGGGCAACTtggtgg < 1:412956/69‑1 (MQ=255)
aCGGCTAAAGATGTCACCGATGCCATTGAATCACAGAACGCGCAGATTGCGGTTGGGCAACTtggtgg < 1:476625/68‑1 (MQ=255)
aCGGCTAAAGATGTCACCGATGCCATTGAATCACAGAACGCGCAGATTGCGGTTGGGCAACTtggtgg < 1:1890727/68‑1 (MQ=255)
aCGGCTAAAGATGTCACCGATGCCATTGAATCACAGAACGCGCAGATTGCGGTTGGGCAACTtggtgg < 1:408148/68‑1 (MQ=255)
aCGGCTAAAGATGTCACCGATGCCATTGAATCACAGAACGCGCAGATTGCGGTTGGGCAACTtggtgg < 1:1161825/68‑1 (MQ=255)
ggCTAAAGATGTCACTGATGCCATTGAGTCACAGAACGCGCAGATTGCGGTTGGGCAACTTGGTGGTa < 1:3201018/68‑1 (MQ=255)
aaaGATGTCACTGATGCCATTGAGTCACAGAACGCGCAGATTGCGGTTGGGCAACTTGGTGGTACACCt < 1:2833979/69‑1 (MQ=255)
aaaGATGTCACTGATGCCATTGAGTCACAGAACGCGCAGATTGCGGTTGGGCAACTTGGTGGTACACCt < 1:724571/69‑1 (MQ=255)
aaaGATGTCACTGATGCCATTGAGTCACAGAACGCGCAGATTGCGGTTGGGCAACTTGGTGGTACACCt < 1:138481/69‑1 (MQ=255)
aaGATGTCACTGATGCCATTGAGTCACAGAACGCGCAGATTGCGGTTGGGCAACTTGGTGGTACACCt < 1:803432/68‑1 (MQ=255)
|
TATTCCATGCGTATCTGGCTGGACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACTGATGCCATTGAGTCACAGAACGCGCAGATTGCGGTTGGGCAACTTGGTGGTACACCT > minE/1634406‑1634531
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
