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 F17 I0 R2
|
159 |
90.8 |
4763082 |
92.7% |
4415377 |
60.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,714,239 |
C→A |
8.4% |
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 | 8.4%
| 196.1
/ 3.7
| 59 | R41L (CGC→CTC) | nirB | nitrite reductase, large subunit, NAD(P)H‑binding |
| Reads supporting (aligned to +/- strand): ref base C (20/34); new base A (3/2); total (23/36) |
| Fisher's exact test for biased strand distribution p-value = 3.69e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.25e-01 |
CCAGCGACAGCTCTTCGGCGGTGTGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTATCAAGAAGATCTTCGA > minE/2714171‑2714305
|
ccAGCGACAGCTCTTCGGCGGTGTGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATgcgc < 1:1961186/71‑1 (MQ=255)
cAGCTCTTCGGCGGTGTGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGttctt < 1:249699/71‑1 (MQ=255)
aGCTCTTCGGCGGTGTGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGttctt > 1:1103338/1‑70 (MQ=255)
aGCTCTTCGGCGGTGTGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGttctt > 1:4342326/1‑70 (MQ=255)
aGCTCTTCGGCGGTGTGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGttctt > 1:2187564/1‑70 (MQ=255)
ctctTCGGCGGTGTGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGAGCGGTTCTTca > 1:3989097/1‑70 (MQ=255)
ctTCGGCGGTGTGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTca > 1:2444233/1‑68 (MQ=255)
ttCGGCGGTGTGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTcaca < 1:512233/69‑1 (MQ=255)
ttCGGCGGTGTGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTcaca < 1:3094619/69‑1 (MQ=255)
cggcggTGTGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGaa < 1:222980/70‑1 (MQ=255)
cggcggTGTGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGaa < 1:3238156/70‑1 (MQ=255)
cggcggTGTGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGaa < 1:3390558/70‑1 (MQ=255)
gtgtGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATgc < 1:3064577/49‑1 (MQ=255)
gtggtgAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATgcgc > 1:2741894/1‑49 (MQ=255)
gtggtgAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATgcgc > 1:3418854/1‑49 (MQ=255)
gtggtgAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATgcgc > 1:3627277/1‑49 (MQ=255)
gtggtgAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATgcgc > 1:4011222/1‑49 (MQ=255)
gtggtgAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATgcgc > 1:669618/1‑49 (MQ=255)
gtgAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGaaaa > 1:3122950/1‑62 (MQ=255)
gtgAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGaaaa > 1:4564758/1‑62 (MQ=255)
agagaAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGaa < 1:1972748/57‑1 (MQ=255)
agagaAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCa > 1:1768867/1‑70 (MQ=255)
agagaAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCa > 1:962234/1‑70 (MQ=255)
agaAGTAAGACGAGAGGTGTACGCGGTCATAAGCGAAGAGCGGTTCTTCACAGAAAACGGTAATATCAAAg > 1:3350470/1‑71 (MQ=255)
aaGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGtt < 1:865153/71‑1 (MQ=255)
aaGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGtt < 1:4658361/71‑1 (MQ=255)
aGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTg > 1:4338632/1‑71 (MQ=255)
aGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTg > 1:3981127/1‑71 (MQ=255)
tAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGc < 1:919989/71‑1 (MQ=255)
tAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGc < 1:2189300/71‑1 (MQ=255)
tAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGc < 1:1061651/71‑1 (MQ=255)
tAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGc < 1:395385/71‑1 (MQ=255)
tAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGc < 1:3437901/71‑1 (MQ=255)
tAAGACGAGAGGTGTACGCGGTCATAAGCGATGAGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGc > 1:570157/1‑71 (MQ=255)
aaGACGAGAGGTGTACGCGGTCATAAGCGATGcgcg > 1:2648838/1‑36 (MQ=255)
aGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCg > 1:4425477/1‑71 (MQ=255)
cGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCAt < 1:4015/71‑1 (MQ=255)
gagaGGTGTACGCGGTCATAAGCGATGAGCGGTTCTTCACAGAAAACGGt < 1:2941942/50‑1 (MQ=255)
agGTGTACGCGGTCATAAGCGATGCTCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCAt < 1:4720213/67‑1 (MQ=255)
gtgtACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGt > 1:2142678/1‑56 (MQ=255)
gtgtACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCa > 1:2106836/1‑67 (MQ=255)
tACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCaa < 1:1775050/50‑1 (MQ=255)
tACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTa < 1:46269/70‑1 (MQ=255)
tACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTa < 1:998575/70‑1 (MQ=255)
tACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTa < 1:1855812/70‑1 (MQ=255)
cgGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTATCaag < 1:4470569/71‑1 (MQ=255)
cgGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTATCaag < 1:177149/71‑1 (MQ=255)
cgGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTATCaag < 1:1750855/71‑1 (MQ=255)
tCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGa < 1:4561215/59‑1 (MQ=255)
cATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCaaa > 1:334187/1‑43 (MQ=255)
cATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTATCaag > 1:4424750/1‑67 (MQ=255)
cATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTATCaag > 1:758019/1‑67 (MQ=255)
aTAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTATCaag > 1:1412926/1‑66 (MQ=255)
aTAAGCGATGAGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTATCAagaaga < 1:626106/70‑1 (MQ=255)
tAAGCGATTCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTATCAAGAAGATc < 1:2173392/71‑1 (MQ=255)
tAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATc < 1:1351960/53‑1 (MQ=255)
tAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATc < 1:4555411/53‑1 (MQ=255)
aGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTATCAAGAAGATCt < 1:2442472/70‑1 (MQ=255)
aGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTATCAAGAAGATCt < 1:3243456/70‑1 (MQ=255)
aGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTATCAAGAAGATCt < 1:3312184/70‑1 (MQ=255)
aGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTATCAAGAAGATCt < 1:3332848/70‑1 (MQ=255)
aGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTATCAAGAAGATCt < 1:4547196/70‑1 (MQ=255)
aGCGATGCGCGGTTCTTCACAGAAAACGGTAATATAAAAGTTGGCCGCATCAGATTTATCAAGAAGATCt < 1:2441508/70‑1 (MQ=255)
gCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTATCAAGAAGATCTTc > 1:4349892/1‑71 (MQ=255)
cGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTATCAAGAAGATCTTCg < 1:1774634/71‑1 (MQ=255)
aTGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTATCAAGAAGATCTTCGa > 1:3744804/1‑70 (MQ=255)
aTGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTATCAAGAAGATCTTCGa > 1:945788/1‑70 (MQ=255)
|
CCAGCGACAGCTCTTCGGCGGTGTGGTGAGAGAAGTAAGACGAGAGGTGTACGCGGTCATAAGCGATGCGCGGTTCTTCACAGAAAACGGTAATATCAAAGTTGGCCGCATCAGATTTATCAAGAAGATCTTCGA > minE/2714171‑2714305
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
