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 |
1,772,459 |
A→G |
39.4% |
R99R (CGT→CGC) |
tyrA ← |
fused chorismate mutase T and prephenate dehydrogenase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,772,459 | 0 | A | G | 39.4%
| 30.9
/ 51.2
| 76 | R99R (CGT→CGC) | tyrA | fused chorismate mutase T and prephenate dehydrogenase |
| Reads supporting (aligned to +/- strand): ref base A (29/17); new base G (17/13); total (46/30) |
| Fisher's exact test for biased strand distribution p-value = 6.36e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.38e-01 |
TTCTCGAACAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTGGAGTAAGATTCACGC > minE/1772409‑1772519
|
ttctCGAACAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAgt > 1:2288347/1‑69 (MQ=255)
ttctCGAACAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAgt > 1:1638920/1‑69 (MQ=255)
ttctCGAACAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAgt > 1:1519772/1‑69 (MQ=255)
ttctCGAACAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAgt > 1:1483091/1‑69 (MQ=255)
ttctCGAACAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAgt > 1:447387/1‑69 (MQ=255)
ttctCGAACAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAgt > 1:3250301/1‑69 (MQ=255)
ttctCGAACAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAgt > 1:1825571/1‑69 (MQ=255)
aCAGACGTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGttt < 1:3325458/66‑1 (MQ=255)
aCAGACGTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGttt < 1:2230251/66‑1 (MQ=255)
aCAGACGTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGttt < 1:1691392/66‑1 (MQ=255)
aCAGACGTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGttt < 1:3283072/66‑1 (MQ=255)
aCAGACGTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGttt < 1:1437001/66‑1 (MQ=255)
aCAGACGTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGttt < 1:320310/66‑1 (MQ=255)
aCAGACGTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGttt < 1:3101652/66‑1 (MQ=255)
aCAGACGTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGttt < 1:3048140/66‑1 (MQ=255)
aCAGACGTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGttt < 1:2985776/66‑1 (MQ=255)
aCAGACGTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGttt < 1:604311/66‑1 (MQ=255)
aCAGACGTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGttt < 1:2934321/66‑1 (MQ=255)
cAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTaaa > 1:2500988/1‑69 (MQ=255)
cAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTaaa > 1:3207910/1‑69 (MQ=255)
cAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTaaa > 1:689157/1‑69 (MQ=255)
cAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTaaa > 1:1968670/1‑69 (MQ=255)
cAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTaaa > 1:2251576/1‑69 (MQ=255)
cAGACGTCCCATCTGACCGCCACCTCCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGttt < 1:467429/65‑1 (MQ=255)
cAGACGTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGttt < 1:160625/65‑1 (MQ=255)
gTCCCATCTGACCGCCCCCACCGACGATAACCACCGGGCGCAGTGCCGGACAAAg > 1:293356/1‑55 (MQ=255)
gTCCCATCTGACCGCCACCGCCGACGATATCCCCCGGACGCAGTGACGGACAAAGTGTTTTAAATCCt > 1:3322194/1‑68 (MQ=255)
gTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTg > 1:2979957/1‑45 (MQ=255)
gTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCtt > 1:2043645/1‑69 (MQ=255)
gTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCtt > 1:1426030/1‑69 (MQ=255)
gTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTCACCGACAAAg > 1:2729880/1‑55 (MQ=255)
gTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGTTTTAAATCCtt > 1:3252035/1‑69 (MQ=255)
gTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGTTTTAAATCCtt > 1:2729556/1‑69 (MQ=255)
gTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGTTTTAAATCCtt > 1:2759034/1‑69 (MQ=255)
gTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGTTTTAAATCCtt > 1:3139814/1‑69 (MQ=255)
gTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGTTTTAAATCCtt > 1:3317455/1‑69 (MQ=255)
gTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGTTTTAAATCCtt > 1:1764543/1‑69 (MQ=255)
gTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGTTTTAAATCCtt > 1:1700192/1‑69 (MQ=255)
gTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGTTTTAAATCCtt > 1:1066031/1‑69 (MQ=255)
gTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGTTTTAAATCCtt > 1:1512809/1‑69 (MQ=255)
gTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGTTTTAAATCCtt > 1:1139743/1‑69 (MQ=255)
gTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGTTTTAAATCCtt > 1:1187600/1‑69 (MQ=255)
gTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGTTTTAAATCCtt > 1:1453420/1‑69 (MQ=255)
gTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGTTTTAAATCCtt > 1:1450815/1‑69 (MQ=255)
gTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGTTTTAAATCCtt > 1:472808/1‑69 (MQ=255)
gTCCCATCTGACCGCCACCACCGACGATAACCACCGGGCGCAGTGACGGACAAAGCGTTTTAAATCCtt > 1:1355197/1‑69 (MQ=255)
gTCCCATCTGACCGCCACCACCGACGATAACCAACGGGCGCAGTGACGGACAAAGCGTTTTAAATCCtt > 1:249395/1‑69 (MQ=255)
tGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGtt > 1:1115328/1‑68 (MQ=255)
ccaccgccGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTg < 1:199141/69‑1 (MQ=255)
ccaccgccGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTg < 1:1024337/69‑1 (MQ=255)
ccaccgccGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTg < 1:1212789/69‑1 (MQ=255)
ccaccgccGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTg < 1:1492463/69‑1 (MQ=255)
ccaccgccGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTg < 1:2328144/69‑1 (MQ=255)
ccaccgccGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTg < 1:46402/69‑1 (MQ=255)
ccaccgccGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTg < 1:2117597/69‑1 (MQ=255)
gccgACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTgg > 1:1255177/1‑65 (MQ=255)
gccgACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTGGa > 1:1163903/1‑66 (MQ=255)
gccgACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTGGa > 1:1161377/1‑66 (MQ=255)
gccgACGATAACCACCGGACGCAGTGACGCACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTGGa > 1:2438299/1‑66 (MQ=255)
gaTAACCACCGGACGCAGTGATGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTGGAGt < 1:1041551/62‑1 (MQ=255)
gaTAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCTTTTTCACTGGAGt < 1:2324528/62‑1 (MQ=255)
gaTAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTGGAGt < 1:257355/62‑1 (MQ=255)
gaTAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTGGAGt < 1:2037172/62‑1 (MQ=255)
gaTAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTGGAGt < 1:1778403/62‑1 (MQ=255)
gaTAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTGGAGt < 1:177340/62‑1 (MQ=255)
gaTAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTGGAGt < 1:1539840/62‑1 (MQ=255)
gaTAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTGGAGt < 1:1418679/62‑1 (MQ=255)
gaTAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTGGAGt < 1:1159960/62‑1 (MQ=255)
gaTAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTGGAGt < 1:853273/62‑1 (MQ=255)
aaCCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTGGAGTAAGATTCACg > 1:2941610/1‑69 (MQ=255)
aaCCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTGGAGTAAGATTCACg > 1:2890905/1‑69 (MQ=255)
aaCCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTGGAGTAAGATTCACg > 1:2624874/1‑69 (MQ=255)
aaCCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTGGAGTAAGATTCACg > 1:1962828/1‑69 (MQ=255)
accaccGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTGGAGTAAGATTCACGc > 1:1698863/1‑69 (MQ=255)
accaccGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTGGAGTAAGATTCACGc > 1:1392471/1‑69 (MQ=255)
accaccGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTGGAGTAAGATTCACGc > 1:76180/1‑69 (MQ=255)
|
TTCTCGAACAGGCGTCCCATCTGACCGCCACCGCCGACGATAACCACCGGACGCAGTGACGGACAAAGTGTTTTAAATCCTTTGTCGTTTTCACTGGAGTAAGATTCACGC > minE/1772409‑1772519
|
| 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
