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 |
|
A1 F3 I0 R1
|
560 |
56.4 |
4650532 |
94.9% |
4413354 |
59.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
4,326,669 |
A→G |
25.0% |
L145S (TTA→TCA) |
phnF ← |
transcriptional regulator of phosphonate uptake and biodegradation |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 4,326,669 | 0 | A | G | 25.0%
| 74.0
/ 25.5
| 44 | L145S (TTA→TCA) | phnF | transcriptional regulator of phosphonate uptake and biodegradation |
| Reads supporting (aligned to +/- strand): ref base A (19/14); new base G (8/3); total (27/17) |
| Fisher's exact test for biased strand distribution p-value = 4.86e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTCCGCGAAGTAGTGGTCGATTAAACAGAGCGCGACGCCGTTGACACGACGCAGGGTGCGCAGGTGGATGACGTTCTCCCCCTCGG > W3110S.gb/4326606‑4326732
|
gAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTCCGCGAAGTAGTGGTCGATTGAACagag > 1:617852/1‑71 (MQ=255)
aGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTCCGCGAAGTAGTGGTCGATTAAACAGAgc > 1:49128/1‑71 (MQ=255)
aGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTCCGCGAAGTAGTGGTCGATTAAACAGAgc > 1:3060003/1‑71 (MQ=255)
ccGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTCCGCGAAGTAGTGGTCGATTAAACAGAgcgc < 1:4220076/71‑1 (MQ=255)
gTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTCCGCGAAGTAGTGGTCGATTAAACAGAGCGCGACGc > 1:1810711/1‑71 (MQ=255)
tCGAAGCGTTGCAGCGTCTGCCAGAGGGTGAGGTCCGCGAAGTAGTGGTCGATTAAACAGAGCGCGACGc < 1:1691064/70‑1 (MQ=255)
gAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTCCGCGAAGTAGTGGTCGATTAAACAGAGCGCGACGCCGt > 1:3043303/1‑71 (MQ=255)
gAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTCCGCGAAGTAGTGGTCGATTAAACAGAGCGCGACGCCGt > 1:4587643/1‑71 (MQ=255)
aaGCGTTGCAGCGTCGGCCAGAGGGTGAGGTCCGCGAAGTAGTGGTCGATTAAACAGAGCGCGACGCCGtt < 1:2801745/71‑1 (MQ=255)
gCGTTGCAGCGTCGGCCAGAGGGTGAGGTCCGCGAAGTAGTGGTCGATTaaa > 1:3421525/1‑52 (MQ=255)
cGTTGCAGCGTCGGCCAGAGGGTGAGGTCCGCGAAGTAGTGGTCGATTaaa < 1:3906550/51‑1 (MQ=255)
ttGCAGCGTCGGCCAGAGGGTGAGGTCCGCGAAGTAGTGGTCGATTGAACAGAGCGCGACGCCGTTGacac > 1:443756/1‑71 (MQ=255)
gCAGCGTCGGCCAGAGGGTGAGGTCCGCGAAGTAGTGGTCGATTAAACAGAGCGCGACGCCGTTGACacga > 1:1744338/1‑71 (MQ=255)
gCGTCGGCCAGAGGGTGAGGTCCGCGAAGTAGTGGTCGATTAAACAGAGCGCGACGCCGTTGACACGACGc < 1:2139709/71‑1 (MQ=255)
cGTCGGCCAGAGGGTGAGGTCCGCGAAGTAGTGGTCGATTAAACAGAGCGCGACGCCGTTGACACGACGCa < 1:409755/71‑1 (MQ=255)
cGTCGGCCAGAGGGTGAGGTCCGCGAAGTAGTGGTCGATTAAACAGAGCGCGACGCCGTTGACACGACGCa < 1:1115198/71‑1 (MQ=255)
gagGGTGAGGTCCGCGAAGTAGTGGTCGATTGAACAGAGCGCGAc > 1:3711724/1‑45 (MQ=255)
gagGGTGAGGTCCGCGAAGTAGTGGTCGATTAAACAGAGCGCGACGCCGTTGACACGACGCAGGGTGCGCa < 1:1219424/71‑1 (MQ=255)
gggTGAGGTCCGCGAAGTAGTGGTCGATTGAACAGAGCGCGACGCCGTTGACACGACGCAGGGTGCGCAgg < 1:769119/71‑1 (MQ=255)
gggTGAGGTCAGCGAAGTAGTGGTCGATTGAACAGAGCGCGACGCCGTTGACACGACGCAgg > 1:1781478/1‑62 (MQ=255)
ggTGAGGTCCGCGAAGTAGTGGTCGATTGAACAGAGCGCGACGCCGTTGACACGACGCAGGGTGCGCAgg < 1:763710/70‑1 (MQ=255)
ggTGAGGTCCGCGAAGTAGTGGTCGATTAAACAGAGCGCGACGCCg < 1:3332504/46‑1 (MQ=255)
ggTGAGGTCCGCGAAGTAGTGGTCGATTAAACAGAGCGCGACGCCGTTGACACGACGCAg < 1:1108658/60‑1 (MQ=255)
tGAGGTCCGCGAAGTAGTGGTCGATTAAACAGAGCGCGACGCCGtt > 1:803047/1‑46 (MQ=255)
tGAGGTCCGCGAAGTAGTGGTCGATTAAACAGAGCGCGACGCCGTTGACACGACGCAGGGTGCGCAgg > 1:2263319/1‑68 (MQ=255)
tGAGGTCCGCGAAGTAGTGGTCGATTAAACAGAGCGCGACGCCGTTGACACGACGCAGGGTGCGCAGGTg > 1:4145056/1‑70 (MQ=255)
gAGGTCCGCGAAGTAGTGGTCGATTAAACAGAGCGCGACGCCGTTGa < 1:4406449/47‑1 (MQ=255)
aGGTCCGCGAAGTAGTGGTCGATTGAACAGAGCGCGACGCCGTTGACACGACGCAGGGTGCGCAgg > 1:3723778/1‑66 (MQ=255)
aGGTCCGCGAAGTAGTGGTCGATTAAACAAAGCGCGACGCCGTTGACACGACGCAGGGTGCGCAGGTGGAt > 1:1777977/1‑71 (MQ=255)
gTCCGCGAAGTAGTGGTCGATTGAACAGAGCGCGACGCCGTTGACACGACGCAGGGTGCGCAGGTGGATGa < 1:1466167/71‑1 (MQ=255)
tCCGCGAAGTAGTGGTCGATTAAACAGAGCGCGACGCCGTTGACACGACGCAGGGTGCGCAGGTGGATGAc < 1:4263665/71‑1 (MQ=255)
tCCGCGAAGTAGTGGTCGATTAAACAGAGCGCGACGCCGTTGACACGACGCAGGGTGCGCAGGTGGATGAc < 1:4580399/71‑1 (MQ=255)
tCCGCGAAGTAGTGGTCGATTAAACAGAGCGCGACGCCGTTGACACGACGCAGGGTGCGCAGGTGGATGAc < 1:4000449/71‑1 (MQ=255)
ccGCGAAGTAGTGGTCGATTAAACAGAGCGCGACGCCGTTGACACGACGCAGGGTgc > 1:4077411/1‑57 (MQ=255)
cgcgAAGTAGTGGTCGATTAAACAGAGCGCGACGCCGTTGACACGACGCAGGGTGCGCa > 1:3922635/1‑59 (MQ=255)
cgAAGTAGTGGTCGATTAAACAGAGCGCGACGCCGTTGACACGACGCAGGGTGCGCAGGTGGATGACGTtc < 1:4553753/71‑1 (MQ=255)
aaGTAGTGGTCGATTAAACAGAGCGCGACGCCGTTGACACGACGCAgg > 1:1021624/1‑48 (MQ=255)
gtagtGGTCGATTAAACAGAGCGCGACGCCGTTGACACGACGCAGGGTGCGCAGGTGGATGACGTTCTccc > 1:4600542/1‑71 (MQ=255)
gTCGATTGAACAGAGCGCGACGCCGTTGACACGACGc > 1:2973466/1‑37 (MQ=255)
gTCGATTGAACAGAGCGCGACGCCGTTGACACGACGCAGGGTGCGCAGGTGGATGACGTTCTCCCCCTCgg > 1:841163/1‑71 (MQ=255)
gTCGATTAAACAGAGCGCGACGCCGTTGACACGACGCAGGGTGCGCAgg > 1:340562/1‑49 (MQ=255)
gTCGATTAAACAGAGCGCGACGCCGTTGACACGACGCAGGGTGCGCAGGTGGa > 1:223056/1‑53 (MQ=255)
gTCGATTAAACAGAGCGCGACGCCGTTGACACGACGCAGGGTGCGCAGGTGGATGat > 1:2260772/1‑56 (MQ=255)
aTTGAACAGAGCGCGACGCCGTTGACACGACGCAGGGTGCGCAgg > 1:334129/1‑45 (MQ=255)
ttAAACAGAGCGCGACGCCGTTGACACGACGCAggg > 1:3661090/1‑36 (MQ=255)
ttAAACAGAGCGCGACGCCGTTGACACGACGCAggg > 1:1023258/1‑36 (MQ=255)
|
GAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTCCGCGAAGTAGTGGTCGATTAAACAGAGCGCGACGCCGTTGACACGACGCAGGGTGCGCAGGTGGATGACGTTCTCCCCCTCGG > W3110S.gb/4326606‑4326732
|
| 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
