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 F3 I0 R2
|
232 |
76.3 |
4135488 |
90.9% |
3759158 |
60.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
597,552 |
C→T |
27.1% |
intergenic (+133/‑106) |
serS → / → dmsA |
seryl‑tRNA synthetase, also charges selenocysteinyl‑tRNA with serine/dimethyl sulfoxide reductase, anaerobic, subunit A |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 597,552 | 0 | C | T | 27.1%
| 100.8
/ 40.7
| 59 | intergenic (+133/‑106) | serS/dmsA | seryl‑tRNA synthetase, also charges selenocysteinyl‑tRNA with serine/dimethyl sulfoxide reductase, anaerobic, subunit A |
| Reads supporting (aligned to +/- strand): ref base C (21/22); new base T (8/8); total (29/30) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.93e-01 |
CAATAATTACTCCTCACTTACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGAAATAATTACACAATACGGTTTGT > minE/597485‑597619
|
cAATAATTACTCCTCACTTACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTTaaa > 1:3143179/1‑71 (MQ=255)
cAATAATTACTCCTCACTTACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTTaaa > 1:2552731/1‑71 (MQ=255)
cAATAATTACTCCTCACTTACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTTaaa > 1:193431/1‑71 (MQ=255)
ttACTCCTCACTTACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTTAAATTATTc < 1:3813080/71‑1 (MQ=255)
ttACTCCTCACTTACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTTAAATTATTc < 1:2285713/71‑1 (MQ=255)
ttACTCCTCACTTACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTc < 1:3809259/71‑1 (MQ=255)
ttACTCCTCACTTACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTc < 1:1330307/71‑1 (MQ=255)
ctcACTTACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTTAAATTATTCGATGta > 1:2225289/1‑71 (MQ=255)
ctcACTTACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATGta > 1:3448410/1‑71 (MQ=255)
ctcACTTACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATGta < 1:749427/71‑1 (MQ=255)
ctcACTTACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATGta < 1:4113738/71‑1 (MQ=255)
ctcACTTACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATGta < 1:3459538/71‑1 (MQ=255)
tACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTTAAATTATTCGATGTATACAAg > 1:2212598/1‑71 (MQ=255)
cGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTTAAATTATTCGATGTATACAAGCCta < 1:278580/71‑1 (MQ=255)
cGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTTAAATTATTCGATGTATACAAGCCta < 1:128965/71‑1 (MQ=255)
gTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTc > 1:3073716/1‑54 (MQ=255)
gTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCta > 1:2953207/1‑70 (MQ=255)
gTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCta > 1:1617581/1‑70 (MQ=255)
gTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCta > 1:4044263/1‑70 (MQ=255)
tAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCtata < 1:514005/71‑1 (MQ=255)
tAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCtata < 1:904214/71‑1 (MQ=255)
ctactTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCTATATAGc > 1:3014599/1‑70 (MQ=255)
actTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCTATATAGCGaa > 1:1344032/1‑71 (MQ=255)
actTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCTATATAGCGa > 1:492416/1‑70 (MQ=255)
ctTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCTATATAGCGAAc < 1:1038769/71‑1 (MQ=255)
tttCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATGta < 1:3748726/50‑1 (MQ=255)
tCGAGTGAAAATCTACCTATCTCTTTGATTTTTAAATTATTCGATGTATACAAGCCTATATAGCGAAc < 1:1289952/68‑1 (MQ=255)
tGAAAATCTACCTATCTCTTTGATTTTTAAATTATTCGATGta < 1:2526148/43‑1 (MQ=255)
tGAAAATCTACCTATCTCTTTGATTTTTAAATTATTCGATGta < 1:750432/43‑1 (MQ=255)
tGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATg < 1:2434760/41‑1 (MQ=255)
tGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATg < 1:26185/41‑1 (MQ=255)
tGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATg < 1:4098921/41‑1 (MQ=255)
tGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATg < 1:3088674/41‑1 (MQ=255)
tGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATg < 1:1112977/41‑1 (MQ=255)
aaaaTCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGa > 1:1257684/1‑70 (MQ=255)
aaaTCTACCTATCTCTTTGATTTTTAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGaaa > 1:221203/1‑71 (MQ=255)
tACCTATCTCTTTGATTTTCAAATTATTCGATGta < 1:1043706/35‑1 (MQ=255)
tctcTTTGATTTTTAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGAAATAATTacac < 1:4010155/69‑1 (MQ=255)
tctTTGATTTTTAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGAaataa > 1:1413646/1‑61 (MQ=255)
tctTTGATTTTTAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGAAATAATTACACAATa > 1:405409/1‑71 (MQ=255)
tctTTGATTTTCAAATTATTCGATGTATACAAGCCtata > 1:2761522/1‑39 (MQ=255)
tctTTGATTTTCAAATTATTCGATGTATACAAGCCtata > 1:3724853/1‑39 (MQ=255)
tctTTGATTTTCAAATTATTCGATGTATACAAGCCtata > 1:1306150/1‑39 (MQ=255)
tctTTGATTTTCAAATTATTCGATGTATACAAGCCtata > 1:1869240/1‑39 (MQ=255)
tctTTGATTTTCAAATTATTCGATGTATACAAGCCtata > 1:1944606/1‑39 (MQ=255)
tGATTTTCAAATTATTCGATGTATACAAGCCtata > 1:248540/1‑35 (MQ=255)
gATTTTCAAATTATTCGATGTATACAAGCCTATATAGTGAACTGCTATAGAAATAATTACACAATACGGtt > 1:817532/1‑71 (MQ=255)
gATTTTCAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGAAATAATTACACAATACGGtt > 1:1156192/1‑71 (MQ=255)
gATTTTCAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGAAATAATTACACAATACGGtt > 1:872371/1‑71 (MQ=255)
gATTTTCAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGAAATAATTACACAATACGGtt > 1:17852/1‑71 (MQ=255)
gATTTTCAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGAAATAATTACACAATACGGtt > 1:3712133/1‑71 (MQ=255)
gATTTTCAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGAAATAATTACACAATACGGtt > 1:3126040/1‑71 (MQ=255)
ttCAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGAAATAATTACACAATACGGTTTGt < 1:388500/70‑1 (MQ=255)
ttCAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGAAATAATTACACAATACGGTTTGt < 1:2302970/70‑1 (MQ=255)
ttCAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGAAATAATTACACAATACGGTTTGt < 1:1674863/70‑1 (MQ=255)
ttCAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGAAATAATTACACAATACGGTTTGt < 1:1638214/70‑1 (MQ=255)
ttCAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGAAATAATTACACAATACGGTTTGt < 1:2507193/70‑1 (MQ=255)
ttCAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGAAATAATTACACAATACGGTTTGt < 1:3219015/70‑1 (MQ=255)
tCAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGAAATAATTACACAATACGGTTTGt < 1:3773617/69‑1 (MQ=255)
|
CAATAATTACTCCTCACTTACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGAAATAATTACACAATACGGTTTGT > minE/597485‑597619
|
| 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
