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 |
836,314 |
T→C |
32.0% |
H344H (CAT→CAC) |
narH → |
nitrate reductase 1, beta (Fe‑S) subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 836,314 | 0 | T | C | 32.0%
| 62.4
/ 40.4
| 50 | H344H (CAT→CAC) | narH | nitrate reductase 1, beta (Fe‑S) subunit |
| Reads supporting (aligned to +/- strand): ref base T (18/16); new base C (11/5); total (29/21) |
| Fisher's exact test for biased strand distribution p-value = 3.65e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.44e-01 |
TTGAAGCCGCACAGCAGTCGCCGGTTTATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCA > minE/836247‑836380
|
ttGAAGCCGCACAGCAGTCGCCGGTTTATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATcc < 1:2929752/70‑1 (MQ=255)
aaGCCGCACAGCAGTCGCCGGTTTATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGaa > 1:45822/1‑71 (MQ=255)
ccGCACAGCAGTCGCCGGTTTATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCAGGAatat < 1:2303493/71‑1 (MQ=255)
gCACAGCAGTCGCCGGTTTGTAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCg < 1:3517377/71‑1 (MQ=255)
acaGCAGTCGCCGGTTTATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGca > 1:2114912/1‑71 (MQ=255)
acaGCAGTCGCCGGTTTATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGca > 1:3552912/1‑71 (MQ=255)
acaGCAGTCGCCGGTTTATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGca > 1:3843525/1‑71 (MQ=255)
tCGCCGGTTTATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGcc < 1:177900/71‑1 (MQ=255)
gCCGGTTTATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCg < 1:1710379/70‑1 (MQ=255)
ggTTTATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCTGAATATCGCacac > 1:1663398/1‑62 (MQ=255)
tttATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTc < 1:2415971/71‑1 (MQ=255)
tataAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTg > 1:1321571/1‑71 (MQ=255)
tacaaaaTGGCGATGGACTGGAAACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTg > 1:1724754/4‑71 (MQ=255)
taAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGt < 1:3414898/66‑1 (MQ=255)
caaaaTGGCGATGGACTGGAAACTGGCACTACCGTTGCACCCTGaa > 1:2648507/2‑46 (MQ=12)
caaaaTGGCGATGGACTGGAAACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCt < 1:3323974/67‑1 (MQ=255)
aaaaTGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCt < 1:760994/67‑1 (MQ=255)
aaaTGGCGATGGACTGGAAACTGGCACTACCGTTGCACCCTGaa > 1:768524/1‑44 (MQ=12)
aaaTGGCGATGGACTGGAAACTGGCACTACCGTTGCACCCTGaa > 1:648273/1‑44 (MQ=12)
aTGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGTACGt < 1:3284045/71‑1 (MQ=255)
gatggactggaAACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTtcct < 1:2973165/69‑2 (MQ=255)
aatggaatggAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGAttg < 1:1455029/56‑3 (MQ=255)
atggaatggaAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGcc > 1:294193/1‑50 (MQ=255)
tggaatggaaACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGcc > 1:3773178/1‑49 (MQ=255)
tggaatggaaACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCct < 1:1179151/71‑1 (MQ=255)
tggaatggaaACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCct > 1:2348671/1‑71 (MQ=255)
ggactggaaACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATgg < 1:124990/53‑1 (MQ=16)
gaatggaaACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCctct > 1:1978771/1‑71 (MQ=255)
aatggaaACTGGCGCTGCCGCTGCATCCGGAATATc > 1:929345/1‑36 (MQ=255)
aatggaaACTGGCGCTGCCGCTGCATCCGGAATATc > 1:1488579/1‑36 (MQ=255)
aatggaaACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTg > 1:702912/1‑55 (MQ=255)
gaaACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTTCCTCCGCTGtcac > 1:2646398/1‑69 (MQ=255)
gaaACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTTCCTCCGCTGtcac > 1:1016794/1‑69 (MQ=255)
aaaCTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTTCCTCCGCTGtcac < 1:351759/70‑3 (MQ=255)
aaaCTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTTCCTCCGCTGTCAcc < 1:1189360/71‑1 (MQ=255)
aaCTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTcc > 1:2183290/1‑70 (MQ=255)
aaCTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCg < 1:468770/71‑1 (MQ=255)
aaCTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTTCGTTCCTCCGCTGTCAcc > 1:1117825/1‑70 (MQ=255)
aaCTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTTCCTCCGCTGTCAcc > 1:2949734/1‑70 (MQ=255)
aaCTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTTCCTCCGCTGTCAcc > 1:193198/1‑70 (MQ=255)
cTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTg > 1:1158093/1‑47 (MQ=255)
cTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTg > 1:605674/1‑47 (MQ=255)
cTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGAt > 1:1096156/1‑71 (MQ=255)
cTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTTCCTCCGCTGTCACCGAt > 1:2563832/1‑71 (MQ=255)
gctctgccgctgcATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCa < 1:1037688/68‑1 (MQ=255)
gcgcTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCa < 1:938035/71‑1 (MQ=255)
ctgccgctgcATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTc < 1:2020396/71‑1 (MQ=255)
taccgttgcACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTTCCTCCGCTGTCACCGATTCAGTcc > 1:2225747/3‑70 (MQ=255)
ccgctgcATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGAtt > 1:3817749/1‑63 (MQ=255)
cATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTgcagca < 1:2173391/69‑1 (MQ=255)
|
TTGAAGCCGCACAGCAGTCGCCGGTTTATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCA > minE/836247‑836380
|
| 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
