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 R2
|
370 |
72.1 |
3738297 |
91.5% |
3420541 |
62.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,714,239 |
C→A |
48.9% |
R41L (CGC→CTC) |
nirB ← |
nitrite reductase, large subunit, NAD(P)H‑binding |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,714,239 | 0 | C | A | 48.9%
| 23.1
/ 56.0
| 47 | R41L (CGC→CTC) | nirB | nitrite reductase, large subunit, NAD(P)H‑binding |
| Reads supporting (aligned to +/- strand): ref base C (12/12); new base A (11/12); total (23/24) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.60e-01 |
AGCTCTTCGGCGGTGTGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTATCAAGAAGATCTTCGATAA > minE/2714179‑2714308
|
aGCTCTTCGGCGGTGTGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATgcgc > 1:2616183/1‑63 (MQ=255)
aGCTCTTCGGCGGTGTGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGttctt > 1:931059/1‑70 (MQ=255)
aGCTCTTCGGCGGTGTGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGttctt > 1:2717227/1‑70 (MQ=255)
aGCTCTTCGGCGGTGTGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGttctt > 1:2860640/1‑70 (MQ=255)
aGCTCTTCGGCGGTGTGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGttctt > 1:3135195/1‑70 (MQ=255)
aGCTCTTCGGCGGTGTGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGttctt > 1:3154311/1‑70 (MQ=255)
aGCTCTTCGGCGGTGTGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGttctt > 1:1296485/1‑70 (MQ=255)
ctTCGGCGGTGTGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGAGCGGTTCTTca > 1:2801897/1‑68 (MQ=255)
ctTCGGCGGTGTGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGAGCGGTTCTTca > 1:2935090/1‑68 (MQ=255)
ggcggTGTGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGtt < 1:1435502/59‑1 (MQ=255)
ggcggTGTGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGtt < 1:3536905/59‑1 (MQ=255)
ggcggTGTGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGtt < 1:2773235/59‑1 (MQ=255)
ggcggTGTGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGaaaa > 1:2610664/1‑71 (MQ=255)
gcggTGTGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGtt < 1:3704656/58‑1 (MQ=255)
gcggTGTGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGAGCGGTTCTTCACAGAAAAc < 1:1838903/71‑1 (MQ=255)
gtgtGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGAGCGGTTCTTCACAGAAAACgg > 1:2503122/1‑70 (MQ=255)
gtggtgAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTaa > 1:3197604/1‑71 (MQ=255)
agagaTGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGAGCGGTTCTTCACAGAAAACGGTAATATCa < 1:468762/70‑1 (MQ=255)
agagaAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGAGCGGTTCTTCACAGAAAACGGTAATATCa < 1:377969/70‑1 (MQ=255)
agagaAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGAGCGGTTCTTCACAGAAAACGGTAATATCa < 1:1536371/70‑1 (MQ=255)
gagaAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCa > 1:3539199/1‑69 (MQ=255)
agaAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAg < 1:1364965/71‑1 (MQ=255)
agaAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAg > 1:2589207/1‑71 (MQ=255)
agaAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGAGCGGTTCTTca < 1:2986180/50‑1 (MQ=255)
agaAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGAGCGGTTCTTca < 1:2909960/50‑1 (MQ=255)
agaAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGAGCGGTTCTTca < 1:3374875/50‑1 (MQ=255)
gaAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGt < 1:935190/71‑1 (MQ=255)
gaAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGt < 1:1525163/71‑1 (MQ=255)
aaGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGAGCGGTTCTTCACAGAAAACGGTAATATCAAAGtt > 1:3365810/1‑71 (MQ=255)
aGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTg < 1:2173391/71‑1 (MQ=255)
aGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTg < 1:445373/71‑1 (MQ=255)
aGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGAGTGGTTCTTCACAGAAAACGGTAATATCAAAGtt < 1:137717/70‑1 (MQ=255)
gTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTgg < 1:2271085/71‑1 (MQ=255)
tAAGACGAGAGGTGTACGCGGTCATAAGCGATGAGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGc < 1:1716658/71‑1 (MQ=255)
gACGAGAGGTGTACGCGGTCATAAGCGATGAGCGGTTCTTca > 1:3344969/1‑42 (MQ=255)
agagGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGaaaa > 1:1623316/1‑45 (MQ=255)
gagGTGTACGCGGTCATAAGCGATGAGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAg < 1:1967647/71‑1 (MQ=255)
tACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTa < 1:1076827/70‑1 (MQ=255)
cgcgGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTATc > 1:1487704/1‑70 (MQ=255)
cgcgGTCATAAGCGATGAGCGGTTCTTCACAGAAAACGGTAATATCAAGGTTgc > 1:3459390/1‑53 (MQ=255)
cgcgGTCATAAGCGATGAGCGGTTCTTCACAGAAAACGGTAATATCAAAGtt > 1:2435371/1‑52 (MQ=255)
cgcgGTCATAAGCGATGAGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGG‑CGCATCAGATTTATc > 1:1583003/1‑69 (MQ=255)
aaGCGATGAGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGa > 1:2643771/1‑55 (MQ=255)
aGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTATCAAGAAGATCt < 1:3142656/70‑1 (MQ=255)
cGATGAGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTATCAAGAAGATCTTCg < 1:837945/71‑1 (MQ=255)
gATGAGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTATCa < 1:3523530/58‑1 (MQ=255)
aTGAGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTATCaag > 1:1450492/1‑59 (MQ=255)
aTGAGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTATCaag > 1:122803/1‑59 (MQ=255)
cgcgGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTATCAAGAAGATCTTCGATaa < 1:2828941/70‑1 (MQ=255)
cgcgGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTATCAAGAAGATCTTCGATaa < 1:1121440/70‑1 (MQ=255)
|
AGCTCTTCGGCGGTGTGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTATCAAGAAGATCTTCGATAA > minE/2714179‑2714308
|
| 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
