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 |
|
A6 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,608,105:1 |
+C |
20.6% |
intergenic (‑215/+95) |
pitA ← / ← nikR |
phosphate transporter, low‑affinity/DNA‑binding transcriptional regulator, Ni‑binding |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,608,105 | 1 | . | C | 20.6%
| 66.2
/ 31.6
| 34 | intergenic (‑215/+95) | pitA/nikR | phosphate transporter, low‑affinity/DNA‑binding transcriptional regulator, Ni‑binding |
| Reads supporting (aligned to +/- strand): ref base . (13/14); new base C (3/4); total (16/18) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.85e-01 |
TTCCTTTTAGTAATATTGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGATAGGGTATTTAGAGAGGAATCAGGTGTGCTAGTGGCCCTTTGTTGA > minE/2608040‑2608171
|
ttCCTTTTAGTAATATTGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGTCCGTTTTTT‑Taa < 1:3823549/69‑1 (MQ=255)
ccTTTTAGTAATATTGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGTCCGTTTTTT‑TAagag < 1:3135682/70‑1 (MQ=255)
ttAGTAATATTGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGTCCGTTTTTT‑TAAgaggag < 1:1210578/69‑1 (MQ=255)
ttAGTAATATTGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGTCCGTTTTTT‑TAAGAGGAgc < 1:563309/70‑1 (MQ=255)
ttAGTAATATTGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGCCCGTTTTTTCTAAgagga < 1:857298/69‑1 (MQ=255)
tAATATTGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGTCCGTTTTTT‑TAagag > 1:1042874/1‑62 (MQ=255)
atatTGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGCCCGTTTTTTCTAAGAGGAGCGCAAcg < 1:2252254/71‑2 (MQ=255)
tatTGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGCCCGTTTTTTCTAAGAGGAGCGCAAcg < 1:1581266/70‑2 (MQ=255)
ttGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGCCCGTTTTTTCTAAGAGGAGCGCAAcgtg > 1:3525982/1‑67 (MQ=255)
gATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGCCCGTTTTTTCTAAgagg < 1:183097/57‑1 (MQ=255)
cTGGTGCGACCACTGAGGAATCTTTACAATTCACGCCCGTTTTTTCTAAGAGGAGCGCAACGTGGAAAggt > 1:687266/1‑70 (MQ=255)
cTGGTGCGACCACTGAGGAATCTTTACAATTCACGCCCGTTTTTTCTAAGAGGAGCGCAACGTGGAAAggt > 1:2967704/1‑70 (MQ=255)
tGGTGCGACCACTGAGGAATCTTTACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGATAGGGTa > 1:419066/1‑71 (MQ=255)
gTGCGACCACTGAGGAATCTTTACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGATAGGGTAt < 1:2763547/70‑1 (MQ=255)
gACCACTGAGGAATCTTTACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGATAGGGTATTTaga < 1:2232496/71‑1 (MQ=255)
ccACTGAGGAATCTTTACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGATAGGGTATTTaga > 1:170219/1‑69 (MQ=255)
ctcTGAGGAATCTTTACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGATAGGGTATTTagagag < 1:3577709/69‑1 (MQ=255)
cTGAGGAATCTTTACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAAc < 1:810081/48‑1 (MQ=255)
tGAGGAATCTTTACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGATAGGGTATTTAGAGAGGaa > 1:2410538/1‑71 (MQ=255)
tGAGGAATCTTTACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGATAGGGTATTTAGAGAGGa > 1:2146907/1‑70 (MQ=255)
gAGGAATCTTTACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGATAGGGTATTTAGAGAGGAAt > 1:2999092/1‑71 (MQ=255)
gAATCTTTACAATTCACGTCCGTTTTTT‑TAAgaggag < 1:478477/37‑1 (MQ=255)
gAATCTTTACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGATAGGGTATTTAGAGAGGAATCAg < 1:1887432/71‑1 (MQ=255)
gAATCTTTACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAAATCGGATAGGGTATTTAGAGAGGAATCAg > 1:2107823/1‑71 (MQ=255)
aaTCTTTACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGATAGGGTATTTAGAGAGGAATCAgg < 1:1628187/71‑1 (MQ=255)
tttACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGa > 1:398495/1‑43 (MQ=255)
ttACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGATAGGGTATTTAGAGAGGAATCAg < 1:126788/65‑1 (MQ=255)
tACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGATAGGGTATTTAGAGAGGAATCAg > 1:1249411/1‑64 (MQ=255)
aCAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGATAGGGTATTTAGAGAGGAATCAGgt > 1:3401170/1‑65 (MQ=255)
aaTTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGATAg > 1:516944/1‑41 (MQ=255)
ttCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGATAGGGTATTTAGAGAGGAATCAGGTGTGCTAGTgg > 1:2380378/1‑71 (MQ=255)
cACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGATAGGGTATTTAGAGAGGAATCAGGTGTGCTAGTGGcc > 1:3325786/1‑71 (MQ=255)
aCGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGATAGGGTATTTa < 1:2252844/44‑1 (MQ=255)
gTTTTTT‑TAAGAGGAGCGCAACTCGGATAGGGTATTTAGAGAGGAATCAGGTGTGCTAGTGGccc < 1:2256775/65‑1 (MQ=255)
ttttt‑tAAGAGGAGCGCAACTCGGATAGGGTATTTAGAGAGGAATCAGGTGTGCTAGTGGCCCTTTGTTGa > 1:3807672/1‑71 (MQ=255)
|
TTCCTTTTAGTAATATTGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGATAGGGTATTTAGAGAGGAATCAGGTGTGCTAGTGGCCCTTTGTTGA > minE/2608040‑2608171
|
| 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
