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 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,799,411 |
C→T |
50.7% |
F79F (TTC→TTT) |
proW → |
glycine betaine transporter subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,799,411 | 0 | C | T | 50.7%
| ‑5.7
/ 61.6
| 67 | F79F (TTC→TTT) | proW | glycine betaine transporter subunit |
| Reads supporting (aligned to +/- strand): ref base C (17/16); new base T (13/21); total (30/37) |
| Fisher's exact test for biased strand distribution p-value = 3.30e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TAAAACGCTGATCCCGCTCGACAGTTGGGTCACTGAAGGGATCGACTGGGTCGTTACCCATTTCCGTCCCGTCTTCCAGGGCGTGCGCGTTCCGGTTGATTATATCCTCAACGGTTTCCAGCAATTGCTGC > minE/1799348‑1799478
|
tAAAACGCTGATCCCGCTCGACAGTTGGGTCACTGAAGGGATCGACTGGGTCGTTACCCATTTccgtc < 1:1018469/68‑1 (MQ=255)
tAAAACGCTGATCCCGCTCGACAGTTGGGTCACTGAAGGGATCGACTGGGTCGTTACCCATTTccgtc < 1:3317330/68‑1 (MQ=255)
tAAAACGCTGATCCCGCTCGACAGTTGGGTCACTGAAGGGATCGACTGGGTCGTTACCCATTTccgtc < 1:2786178/68‑1 (MQ=255)
tAAAACGCTGATCCCGCTCGACAGTTGGGTCACTGAAGGGATCGACTGGGTCGTTACCCATTTccgtc < 1:100798/68‑1 (MQ=255)
cccGCTCGACAGTTGGGTCACTGAAGGGATCGACTGGGTCGTTACCCATTTTCGTCCCGTCTTTCAg < 1:2410659/67‑1 (MQ=255)
cccGCTCGACAGTTGGGTCACTGAAGGGATCGACTGGGTCGTTACCCATTTTCGTCCCGTCTTTCAg < 1:84751/67‑1 (MQ=255)
cccGCTCGACAGTTGGGTCACTGAAGGGATCGACTGGGTCGTTACCCATTTTCGTCCCGTCTTTCAg < 1:844553/67‑1 (MQ=255)
cccGCTCGACAGTTGGGTCACTGAAGGGATCGACTGGGTCGTTACCCATTTTCGTCCCGTCTTTCAg < 1:778833/67‑1 (MQ=255)
cccGCTCGACAGTTGGGTCACTGAAGGGATCGACTGGGTCGTTACCCATTTTCGTCCCGTCTTTCAg < 1:506369/67‑1 (MQ=255)
cccGCTCGACAGTTGGGTCACTGAAGGGATCGACTGGGTCGTTACCCATTTTCGTCCCGTCTTTCAg < 1:48207/67‑1 (MQ=255)
cccGCTCGACAGTTGGGTCACTGAAGGGATCGACTGGGTCGTTACCCATTTTCGTCCCGTCTTTCAg < 1:401891/67‑1 (MQ=255)
cccGCTCGACAGTTGGGTCACTGAAGGGATCGACTGGGTCGTTACCCATTTTCGTCCCGTCTTTCAg < 1:3210719/67‑1 (MQ=255)
cccGCTCGACAGTTGGGTCACTGAAGGGATCGACTGGGTCGTTACCCATTTTCGTCCCGTCTTTCAg < 1:2686485/67‑1 (MQ=255)
cccGCTCGACAGTTGGGTCACTGAAGGGATCGACTGGGTCGTTACCCATTTTCGTCCCGTCTTTCAg < 1:2447540/67‑1 (MQ=255)
cccGCTCGACAGTTGGGTCACTGAAGGGATCGACTGGGTCGTTACCCATTTTCGTCCCGTCTTTCAg < 1:2010604/67‑1 (MQ=255)
cccGCTCGACAGTTGGGTCACTGAAGGGATCGACTGGGTCGTTACCCATTTTCGTCCCGTCTTTCAg < 1:18247/67‑1 (MQ=255)
cccGCTCGACAGTTGGGTCACTGAAGGGATCGACTGGGTCGTTACCCATTTTCGTCCCGTCTTTCAg < 1:1328872/67‑1 (MQ=255)
cccGCTCGACAGTTGGGTCACTGAAGGGATCGACTGGGTCGTTACCCATTTTCGTCCCGTCTTTCAg < 1:1053212/67‑1 (MQ=255)
cccGCTCGACAGTTGGGTCACTGAAGGGATCGACTGGGTCGTTACCCATTTTCGTCCCGTCTTTCAg < 1:1500843/67‑1 (MQ=255)
cTCGACAGTTGGGTCACTGAAGGGATCGACTGGGTCGTTACCCATTTCCGTCCCGTCTTCCAGGGCGt > 1:1175239/1‑68 (MQ=255)
cTCGACAGTTGGGTCACTGAAGGGATCGACTGGGTCGTTACCCATTTCCGTCCCGTCTTCCAGGGCGt > 1:2036069/1‑68 (MQ=255)
cTCGACAGTTGGGTCACTGAAGGGATCGACTGGGTCGTTACCCATTTCCGTCCCGTCTTCCAGGGCGt > 1:2362269/1‑68 (MQ=255)
cTCGACAGTTGGGTCACTGAAGGGATCGACTGGGTCGTTACCCATTTCCGTCCCGTCTTCCAGGGCGTg > 1:2587917/1‑69 (MQ=255)
cTCGACAGTTGGGTCACTGAAGGGATCGACTGGGTCGTTACCCATTTCCGTCCCGTCTTCCAGGGCGTg > 1:81080/1‑69 (MQ=255)
cTCGACAGTTGGGTCACTGAAGGGATCGACTGGGTCGTTACCCATTTCCGTCCCGTCTTCCAGGGCGTg > 1:2341496/1‑69 (MQ=255)
cTCGACAGTTGCGTCACTGAAGGGATCGACTGGGTCGTTACCCATTTCCGTCCCGTCTTCCAGGGCGTg > 1:1399301/1‑69 (MQ=255)
gTCACTGAAGGGATCGACTGGGTCGTTACCCATTTTCGTCCCGTCTTTCAg < 1:71253/51‑1 (MQ=255)
tGAAGGGATCGACTGGGTCGTTACCCATTTCCGTCCCGTCTTCCAGGGCGTGCGCGTTCCGGTTGATta < 1:92125/69‑1 (MQ=255)
gAAGGGATCGACTGGGTCGTTACCCATTTCCGTCCCGTCTTCCAGGGCGTGCGCGTTCCGGTTGATtat > 1:2008206/1‑69 (MQ=255)
gAAGGGATCGACTGGGTCGTTACCCATTTCCGTCCCGTCTTCCAGGGCGTGCGCGTTCCGGTTGATta > 1:2355491/1‑68 (MQ=255)
gAAGGGATCGACTGGGTCGTTACCCATTTCCGTCCCGTCTTCCAGGGCGTGCGCGTTCCGGTTGATta < 1:445343/68‑1 (MQ=255)
gggATCGACTGGGTCGTTACCCATTTCCGTCCCGTCTTCCAGGGCGTGCGCGTTCCGGTTGATtata < 1:2160746/67‑1 (MQ=255)
gggATCGACTGGGTCGTTACCCATTTCCGTCCCGTCTTCCAGGGCGTGCGCGTTCCGGTTGATtata < 1:2570272/67‑1 (MQ=255)
gggATCGACTGGGTCGTTACCCATTTCCGTCCCGTCTTCCAGGGCGTGCGCGTTCCGGTTGATtata < 1:1360746/67‑1 (MQ=255)
gggTCGTTACCCATTTCCGTCCCGTCTTCCAGGGCGTGCGCGTTCCGGTTGATTATATCCTCAACGGtt < 1:2145836/69‑1 (MQ=255)
gggTCGTTACCCATTTCCGTCCCGTCTTCCAGGGCGTGCGCGTTCCGGTTGATTATATCCTCAACGGtt < 1:850141/69‑1 (MQ=255)
gggTCGTTACCCATTTCCGTCCCGTCTTCCAGGGCGTGCGCGTTCCGGTTGATTATATCCTCAACGGtt < 1:1753158/69‑1 (MQ=255)
gggTCGTTACCCATTTCCGTCCCGTCTTCCAGGGCGTGCGCGTTCCGGTTGATTATATCATCAACGGtt < 1:366456/69‑1 (MQ=255)
cGTTACCCATTTTCGTCCCGTCTTTCAGGGCGTGCGCGTTCCGGTTGATTACATCCTCAACGGTTTCCa < 1:1231882/69‑1 (MQ=255)
cGTTACCCATTTTCGTCCCGTCTTTCAGGGCGTGCGCGTTCCGGTTGATTACATCCTCAACGGTTTCCa < 1:3426235/69‑1 (MQ=255)
cGTTACCCATTTTCGTCCCGTCTTTCAGGGCGTGCGCGTTCCGGTTGATTACATCCTCAACGGTTTCCa < 1:2840038/69‑1 (MQ=255)
cGTTACCCATTTTCGTCCCGTCTTTCAGGGCGTGCGCGTTCCGGTTGATTACATCCTCAACGGTTTCCa < 1:1361933/69‑1 (MQ=255)
cGTTACCCATTTTCGTCCCGTCTTTCAGGGCGTGCGCGTTCCGGTTGATTACATCCTCAACGGTTTCCa < 1:2070328/69‑1 (MQ=255)
ttACCCATTTTCGTCCCGTCTTTCAGGGCGTGCGCGTTCCGGTTGATTACATCTTCAACGGTTTCCAGc > 1:256411/1‑69 (MQ=255)
ttACCCATTTTCGTCCCGTCTTTCAGGGCGTGCGCGTTCCGGTTGATTACATCCTCAACGGTTTCCAg > 1:3154430/1‑68 (MQ=255)
ttACCCATTTTCGTCCCGTCTTTCAGGGCGTGCGCGTTCCGGTTGATTACATCCTCAACGGTTTCCAGc > 1:1267579/1‑69 (MQ=255)
ttACCCATTTTCGTCCCGTCTTTCAGGGCGTGCGCGTTCCGGTTGATTACATCCTCAACGGTTTCCAGc > 1:1072470/1‑69 (MQ=255)
ttACCCATTTTCGTCCCGTCTTTCAGGGCGTGCGCGTTCCGGTTGATTACATCCTCAACGGTTTCCAGc > 1:381918/1‑69 (MQ=255)
ttACCCATTTTCGTCCCGTCTTTCAGGGCGTGCGCGTTCCGGTTGATTACATCCTCAACGGTTTCCAGc > 1:1726204/1‑69 (MQ=255)
ttACCCATTTTCGTCCCGTCTTTCAGGGCGTGCGCGTTCCGGTTGATTACATCCTCAACGGTTTCCAGc > 1:3267939/1‑69 (MQ=255)
ttACCCATTTTCGTCCCGTCTTTCAGGGCGTGCGCGTTCCGGTTGATTACATCCTCAACGGTTTCCAGc > 1:1773373/1‑69 (MQ=255)
ttACCCATTTTCGTCCCGTCTTTCAGGGCGTGCGCGTTCCGGTTGATTACATCCTCAACGGTTTCCAGc > 1:1784708/1‑69 (MQ=255)
ttACCCATTTTCGTCCCGTCTTTCAGGGCGTGCGCGTTCCGGTTGATTACATCCTCAACGGTTTCCAGc > 1:3130476/1‑69 (MQ=255)
ttACCCATTTTCGTCCCGTCTTTCAGGGCGTGCGCGTTCCGGTTGATTACATCCTCAACGGTTTCCAGc > 1:197805/1‑69 (MQ=255)
ttACCCATTTTCGTCCCGTCTTTCAGGGCGTGCGCGTTCCGGTTGATTACATCCTCAACGGTTTCCAGc > 1:1477595/1‑69 (MQ=255)
ttACCCATTTTCGTCCCGTCTTTCAGGGCGTGCGCGTTCCGGTTGATTACATCCTCAACGGTTTCCAGc > 1:2966784/1‑69 (MQ=255)
ccATTTCCGTCCCGTCTTCCAGGGGGTGCGCGTTCCGGTTGATTATATCCTCAACGGTTTCCAGCAAt < 1:3155063/68‑1 (MQ=255)
ccATTTCCGTCCCGTCTTCCAGGGCGTGCGCGTTCCGGTTGATTATATCCTCAACGGTTTCCAGCAAt < 1:431994/68‑1 (MQ=255)
ccATTTCCGTCCCGTCTTCCAGGGCGTGCGCGTTCCGGTTGATTATATCCTCAACGGTTTCCAGCAAt < 1:1657711/68‑1 (MQ=255)
ccATTTCCGTCCCGTCTTCCAGGGCGTGCGCGTTCCGGTTGATTATATCCTCAACGGTTTCCAGCAAt < 1:2151737/68‑1 (MQ=255)
ccATTTCCGTCCCGTCTTCCAGGGCGTGCGCGTTCCGGTTGATTATATCCTCAACGGTTTCCAGCAAt < 1:1294745/68‑1 (MQ=255)
ccATTTCCGTCCCGTCTTCCAGGGCGTGCGCGTTCCGGTTGATTATATCCTCAACGGTTTCCAGCAAt < 1:1295739/68‑1 (MQ=255)
ccATTTCCGTCCCGTCTTCCAGGGCGTGCGCGGTCCGGTTGATTATATCCTCAACGGTTTCCAGCAAt < 1:3260701/68‑1 (MQ=255)
tCCGTCCCGTCTTCCAGGGCGTGCGCGTTCCGGTTGATTATATCCTCAACGGTTTCCAGCAATtgctgc > 1:2643039/1‑69 (MQ=255)
tCCGTCCCGTCTTCCAGGGCGTGCGCGTTCCGGTTGATTATATCCTCAACGGTTTCCAGCAATtgctgc > 1:2711696/1‑69 (MQ=255)
tCCGTCCCGTCTTCCAGGGCGTGCGCGTTCCGGTTGATTATATCCTCAACGGTTTCCAGCAATtgctgc > 1:1229880/1‑69 (MQ=255)
tCCGTCCCGTCTTCCAGGGCGTGCGCGTTCCGGTTGATTATATCCTCAACGGTTTCCAGCAATtgctgc > 1:178044/1‑69 (MQ=255)
tCCGTCCCGTCTTCCAGGGCGTGCGCGTTCCGGTTGATTATATCCTCAACGGTTTCCAGCAATtgctgc > 1:3258793/1‑69 (MQ=255)
tCCGTCCCGTCTTCCAGGGCGTGCGCGTTCCGGTTGATTATATCCTCAACGGTTTCCAGCAATtgctgc > 1:1736385/1‑69 (MQ=255)
tCCGTCCCGTCTTCCAGGGCGTGCGCGTTCCGGTTGATTATATCCTCAACGGTTTCCAGCAATtgctg > 1:3022893/1‑68 (MQ=255)
tCCGTCCCGTCTTCCAGGGCGTGCGCGTTCCGGTTGATTATATCCTCAACGGTTTCCAGCAATtgctcc > 1:2624381/1‑67 (MQ=255)
|
TAAAACGCTGATCCCGCTCGACAGTTGGGTCACTGAAGGGATCGACTGGGTCGTTACCCATTTCCGTCCCGTCTTCCAGGGCGTGCGCGTTCCGGTTGATTATATCCTCAACGGTTTCCAGCAATTGCTGC > minE/1799348‑1799478
|
| 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
