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 |
2,203,791 |
A→G |
75.5% |
R206R (CGT→CGC) |
aaeA ← |
p‑hydroxybenzoic acid efflux system component |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,203,791 | 0 | A | G | 75.5%
| 79.3
/ 20.3
| 65 | R206R (CGT→CGC) | aaeA | p‑hydroxybenzoic acid efflux system component |
| Reads supporting (aligned to +/- strand): ref base A (8/8); new base G (24/25); total (32/33) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.52e-01 |
ATCAACAGTCCCTTTCAGCACTTTGTTACTGCCAAGCGGCGTGATCTCTGCACGATACCCCGGACGCACCCCTTCCAGCTTAGTTTCTTCCATATAGGCCAGTACATAGAAGGAGTTCTGTTTCACCAGCGC > minE/2203728‑2203859
|
aTCAACAGTCCCTTTCAGCACTTTGTTACTGCCAAGCGGCGTGATCTCTGCACGATACCCCGGACGc > 1:368113/1‑67 (MQ=255)
aTCAACAGTCCCTTTCAGCACTTTGTTACTGCCAAGCGGCGTGATCTCTGCACGATACCCCGGACGc > 1:1794730/1‑67 (MQ=255)
aTCAACAGTCCCTTTCAGCACTTTGTTACTGCCAAGCGGCGTGATCTCTGCACGATACCCCGGACGc > 1:1730831/1‑67 (MQ=255)
aTCAACAGTCCCTTTCAGCACTTTGTTACTGCCAAGCGGCGTGATCTCTGCACGATACCCCGGACGc > 1:1272594/1‑67 (MQ=255)
cAGTCCCTTTCAGCACTTTGTTACTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCt < 1:2586016/68‑1 (MQ=255)
cAGTCCCTTTCAGCACTTTGTTACTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCt < 1:2716515/68‑1 (MQ=255)
cAGTCCCTTTCAGCACTTTGTTACTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCt < 1:1906910/68‑1 (MQ=255)
cAGTCCCTTTCAGCACTTTGTTACTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCt < 1:3399794/68‑1 (MQ=255)
cAGTCCCTTTCAGCACTTTGTTACTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCt < 1:1846626/68‑1 (MQ=255)
cAGTCCCTTTCAGCACTTTGTTACTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCt < 1:1800230/68‑1 (MQ=255)
cAGTCCCTTTCAGCACTTTGTTACTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCt < 1:1799692/68‑1 (MQ=255)
cAGTCCCTTTCAGCACTTTGTTACTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCt < 1:1602812/68‑1 (MQ=255)
cAGTCCCTTTCAGCACTTTGTTACTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCt < 1:1583028/68‑1 (MQ=255)
cAGTCCCTTTCAGCACTTTGTTACTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCt < 1:508569/68‑1 (MQ=255)
cAGTCCCTTTCAGCACTTTGTTACTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCt < 1:1099978/68‑1 (MQ=255)
cAGTCCCTTTCAGCACTTTGTTACTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCt < 1:153517/68‑1 (MQ=255)
tttGTTACTGCCAAGCGGCGTGATCTCTGCACGTTACCCCGGACGCACCCCTTCCAGCTTAGTttcttc < 1:2062339/69‑1 (MQ=255)
tttGTTACTGCCAAGCGGCGTGATCTCTGCACGATACCCCGGACGCACCCCTTCCAGCTTAGTttcttc < 1:2812274/69‑1 (MQ=255)
ttACTGCCAAGCGGCGTGATCTCTGCACGATACCCCGGACGCACCCCTTCCAGCTTAGTTTCTTCCa < 1:1600577/67‑1 (MQ=255)
ttACTGCCAAGCGGCGTGATCTCTGCACGATACCCCGGACGCACCCCTTCCAGCTTAGTTTCTTCCa < 1:1241754/67‑1 (MQ=255)
ttACTGCCAAGCGGCGTGATCTCTGCACGATACCCCGGACGCACCCCTTCCAGCTTAGTTTCTTCCa < 1:2959027/67‑1 (MQ=255)
ttACTGCCAAGCGGCGTGATCTCTGCACGATACCCCGGACGCACCCCTTCCAGCTTAGTTTCTTCCa < 1:585671/67‑1 (MQ=255)
ttACTGCCAAGCGGCGTGATCTCTGCACGATACCCCGGACGCACCCCTTCCAGCTTAGTTTCTTCCa < 1:2849249/67‑1 (MQ=255)
tACTGCCAAGCGGCGTGATCTCTGCACGATACCCCGGACGCACCCCTTCCAGCTTAGTTTCTTCCa < 1:1254944/66‑1 (MQ=255)
cTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCCCCCCTTCCAGCTTAGTTTCTTCCata > 1:3066180/1‑66 (MQ=255)
cTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCt > 1:105882/1‑45 (MQ=38)
cTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCata > 1:2804025/1‑66 (MQ=255)
cTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCata > 1:1007569/1‑66 (MQ=255)
cTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCata > 1:2640797/1‑66 (MQ=255)
cTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCata > 1:2625635/1‑66 (MQ=255)
cTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCata > 1:998234/1‑66 (MQ=255)
cTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCata > 1:3068435/1‑66 (MQ=255)
cTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCata > 1:365302/1‑66 (MQ=255)
cTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCata > 1:971643/1‑66 (MQ=255)
cTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCata > 1:568058/1‑66 (MQ=255)
cTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCata > 1:514251/1‑66 (MQ=255)
cTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCata > 1:375299/1‑66 (MQ=255)
cTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCata > 1:47851/1‑66 (MQ=255)
cTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCata > 1:464206/1‑66 (MQ=255)
cTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCata > 1:1108314/1‑66 (MQ=255)
cTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCata > 1:2469986/1‑66 (MQ=255)
cTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCata > 1:229633/1‑66 (MQ=255)
cTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCata > 1:2181733/1‑66 (MQ=255)
cTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCata > 1:118479/1‑66 (MQ=255)
cTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCata > 1:1261897/1‑66 (MQ=255)
cTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCata > 1:1379276/1‑66 (MQ=255)
cTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCata > 1:1458196/1‑66 (MQ=255)
cTGCCAAGCGGCGTGATCTCCGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCat > 1:1114209/1‑65 (MQ=255)
aTCTCTGCACGATACCCCGGACGCACCCCTTCCAGCTTAGTTTCTTCCATATAGGCCAGTACATAGa > 1:2718967/1‑67 (MQ=255)
ctccGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCATATAGGCCAGTACATAGAAgg < 1:261790/68‑1 (MQ=255)
ctccGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCATATAGGCCAGTACATAGAAgg < 1:1118419/68‑1 (MQ=255)
ctccGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCATATAGGCCAGTACATAGAAgg < 1:179602/68‑1 (MQ=255)
ctccGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCATATAGGCCAGTACATAGAAgg < 1:3354799/68‑1 (MQ=255)
ctccGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCATATAGGCCAGTACATAGAAgg < 1:333694/68‑1 (MQ=255)
ctccGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCATATAGGCCAGTACATAGAAgg < 1:2615564/68‑1 (MQ=255)
ctccGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCATATAGGCCAGTACATAGAAgg < 1:2582768/68‑1 (MQ=255)
ctccGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCATATAGGCCAGTACATAGAAgg < 1:2085181/68‑1 (MQ=255)
ctccGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCATATAGGCCAGTACATAGAAgg < 1:2177981/68‑1 (MQ=255)
ctccGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCATATAGGCCAGTACATAGAAgg < 1:2890130/68‑1 (MQ=255)
ctccGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCATATAGGCCAGTACATAGAAgg < 1:2881522/68‑1 (MQ=255)
ctccGCACGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCATATAGGCCAGTACATAGAAgg < 1:2151997/68‑1 (MQ=255)
gctcGATACCCAGGGCGCACCCCTTCCAGCTTAGTTTCTTCCATATAGGCCAGTACATAGAAgg < 1:1706388/61‑1 (MQ=255)
ccccGGACGCACCCCTTCCAGCTTAGTTTCTTCCATATAGGCCAGTACATAGAAGGAGTTCTGTTTc > 1:1870110/1‑67 (MQ=255)
ccccGGACGCACCCCTTCCAGCTTAGTTTCTTCCATATAGGCCAGTACATAGAAGGAGTTCTGTTTc > 1:1855556/1‑67 (MQ=255)
ccccGGACGCACCCCTTCCAGCTTAGTTTCTTCCATATAGGCCAGTACATAGAAGGAGTTCTGTTTc > 1:273780/1‑67 (MQ=255)
aCGCACCCCTTCCAGCTTAGTTTCTTCCATATAGGCCAGTACATAGAAGGAGTTCTGTTTCACCAgcgc < 1:1581803/69‑1 (MQ=255)
aCGCACCCCTTCCAGCTTAGTTTCTTCCATATAGGCCAGTACATAGAAGGAGTTCTGTTTCACCAgcgc < 1:597622/69‑1 (MQ=255)
aCGCACCCCTTCCAGCTTAGTTTCTTCCATATAGGCCAGTACATAGAAGGAGTTCTGTTTCACCAgcgc < 1:3124665/69‑1 (MQ=255)
aCGCACCCCTTCCAGCTTAGTTTCTTCCATATAGGCCAGTACATAGAAGGAGTTCTGTTTCACCAgcgc < 1:2117953/69‑1 (MQ=255)
aCGCACCCCTTCCAGCTTAGTTTCTTCCATATAGGCCAGTACATAGAAGGAGTTCTGTTTCACCAgcgc < 1:3337552/69‑1 (MQ=255)
aCGCACCCCTTCCAGCTTAGTTTCTTCCATATAGGCCAGTACATAGAAGGAGTTCTGTTTCACCAgcgc < 1:1887526/69‑1 (MQ=255)
aCGCAACCCTTCCAGCTTAGTTTCTTCCATATAGGCCAGTACATAGAAGGAGTTCTGTTTCACCAgcgc < 1:3144810/69‑1 (MQ=255)
|
ATCAACAGTCCCTTTCAGCACTTTGTTACTGCCAAGCGGCGTGATCTCTGCACGATACCCCGGACGCACCCCTTCCAGCTTAGTTTCTTCCATATAGGCCAGTACATAGAAGGAGTTCTGTTTCACCAGCGC > minE/2203728‑2203859
|
| 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
