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 |
1,941,264 |
T→C |
54.7% |
C228C (TGT→TGC) |
ygfZ → |
predicted folate‑dependent regulatory protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,941,264 | 0 | T | C | 54.7%
| 7.3
/ 40.9
| 53 | C228C (TGT→TGC) | ygfZ | predicted folate‑dependent regulatory protein |
| Reads supporting (aligned to +/- strand): ref base T (17/7); new base C (18/11); total (35/18) |
| Fisher's exact test for biased strand distribution p-value = 5.69e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.83e-01 |
AGCGGGCAGTTTATCCCACAGGCGACCAATCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGTTATACCGGACAAGAGATGGTGGCGCGAGCAAAATTCCGTGGTGCCAATAAACG > minE/1941196‑1941317
|
aGCGGGCAGTTTATCCCACAGGCGACCAATCTCCAGGCGCTGGGCTGTATCAGCTTTAAGAAAGGCTGt < 1:1731497/69‑1 (MQ=255)
aGCGGGCAGTTTATCCCACAGGCGACCAATCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGt < 1:3241144/69‑1 (MQ=255)
aGCGGGCAGTTTATCCCACAGGCGACCAATCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGt < 1:3186099/69‑1 (MQ=255)
aGCGGGCAGTTTATCCCACAGGCGACCAATCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGt < 1:2573987/69‑1 (MQ=255)
aGCGGGCAGTTTATCCCACAGGCGACCAATCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGt < 1:2528666/69‑1 (MQ=255)
aGCGGGCAGTTTATCCCACAGGCGACCAATCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGt < 1:1705205/69‑1 (MQ=255)
aGCGGGCAGTTTATCCCACAGGCGACCAATCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGt < 1:2455766/69‑1 (MQ=255)
aGCGGGCAGTTTATCCCACAGGCGACCAATCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGt < 1:2415906/69‑1 (MQ=255)
aGCGGGCAGTTTATCCCACAGGCGACCAATCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGt < 1:211389/69‑1 (MQ=255)
gCGGGCAGTTTATCCCACAGGCGACCAATCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGt < 1:3067506/68‑1 (MQ=255)
ttATCCCACAGGCGACCAATCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGTTATACCGGAc < 1:890764/69‑1 (MQ=255)
ttATCCCACAGGCGACCAATCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGTTATACCGGAc < 1:3395666/69‑1 (MQ=255)
tATCCCACAGGCGACCAATCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGTTATACCgg > 1:1202850/1‑66 (MQ=255)
tATCCCACAGGCGACCAATCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGTTATACCgg > 1:733169/1‑66 (MQ=255)
tATCCCACAGGCGACCAATCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGTTATACCgg > 1:480060/1‑66 (MQ=255)
tATCCCACAGGCGACCAATCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGTTATACCgg > 1:2106564/1‑66 (MQ=255)
tATCCCACAGGCGACCAATCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGTTATACCgg > 1:1521968/1‑66 (MQ=255)
ccACAGGCGACCAATCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGTTATACCGGTCAaga < 1:3110625/68‑1 (MQ=255)
ccACAGGCGACCAATCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGTTATACCGGACAaga < 1:2945847/68‑1 (MQ=255)
ccACAGGCAACCAATCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGTTATACCGGACAaga < 1:3158787/68‑1 (MQ=255)
acaGGCGACCAATCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGTTATACCGGACAAGAGAt < 1:555666/69‑1 (MQ=255)
acaGGCGACCAATCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGTTATACCGGACAAGAGAt < 1:3173143/69‑1 (MQ=255)
gACCAACCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGCTATACCGGACAaga > 1:1612778/1‑60 (MQ=255)
gACCAACCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGCTATACCGGACAaga > 1:2044616/1‑60 (MQ=255)
gACCAACCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGCTATACCGGACAaga > 1:298939/1‑60 (MQ=255)
gACCAACCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGCTATACCGGACAaga > 1:2914403/1‑60 (MQ=255)
gACCAACCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGCTATACCGGACAaga > 1:1290642/1‑60 (MQ=255)
gACCAACCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGCTATACCGGACAaga > 1:2599304/1‑60 (MQ=255)
gACCAACCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGCTATACCGGACAaga > 1:1637265/1‑60 (MQ=255)
gACCAACCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGCTATACCGGACAaga > 1:3176034/1‑60 (MQ=255)
gACCAACCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGCTATACCGGACAaga > 1:1848662/1‑60 (MQ=255)
gACCAACCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGCTATACCGGACAaga > 1:669650/1‑60 (MQ=255)
gACCAACCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGCTATACCGGACAaga > 1:323304/1‑60 (MQ=255)
gACCAACCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGCTATACCGGACAaga > 1:704687/1‑60 (MQ=255)
gACCAACCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGCTATACCGGACAaga > 1:417256/1‑60 (MQ=255)
gACCAACCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGCTATACCGGACAaga > 1:3262733/1‑60 (MQ=255)
gACCAACCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGCTATACCGGACAag > 1:1425842/1‑59 (MQ=255)
cAATCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGt < 1:1778892/43‑1 (MQ=255)
cAATCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGt < 1:453038/43‑1 (MQ=255)
aGCTTTAAGAAAGGCTGTTATACCGGACAAGAGATGGTGGCGCGAGCAGAATTCCGTGGTGCCAATaaa > 1:1139099/1‑69 (MQ=255)
aGCTTTAAGAAAGGCTGTTATACCGGACAAGAGATGGTGGCGCGAGCAAAATTCCGTGGTGCCAATaaa > 1:158441/1‑69 (MQ=255)
aGCTTTAAGAAAGGCTGTTATACCGGACAAGAGATGGTGGCGCGAGCAAAATTCCGTGGTGCCAATaaa > 1:3037744/1‑69 (MQ=255)
aGCTTTAAGAAAGGCTGTTATACCGGACAAGAGATGGTGGCGCGAGCAAAATTCCGTGGTGCCAATaaa > 1:504319/1‑69 (MQ=255)
aGCTTTAAGAAAGGCTGTTATACCGGACAAGAGATGGTGGCGCGAGCAAAATTCCGTGGTGCCAATaaa > 1:2577743/1‑69 (MQ=255)
aGCTTTAAGAAAGGCTGTTATACCGGACAAGAGATGGTGGCGCGAGCAAAATTCCGTGGTGCCAATaaa > 1:2512112/1‑69 (MQ=255)
aGCTTTAAGAAAGGCTGTTATACCGGACAAGAGATGGTGGCGCGAGCAAAATTCCGTGGTGCCAATaaa > 1:2473516/1‑69 (MQ=255)
aGCTTTAAGAAAGGCTGTTATACCGGACAAGAGATGGTGGCGCGAGCAAAATTCCGTGGTGCCAATaaa > 1:703797/1‑69 (MQ=255)
aGCTTTAAGAAAGGCTGTTATACCGGACAAGAGATGGTGGCGCGAGCAAAATTCCGTGGTGCCAATaaa > 1:707696/1‑69 (MQ=255)
aGCTTTAAGAAAGGCTGTTATACCGGACAAGAGATGGTGGCGCGAGCAAAATTCCGTGGTGCCAATaaa > 1:369656/1‑69 (MQ=255)
aGCTTTAAGAAAGGCTGTTATACCGGACAAGAGATGGTGGCGCGAGCAAAATTCCGTGGTGCCAATaaa > 1:3350238/1‑69 (MQ=255)
aGCTTTAAGAAAGGCTGTTATACCGGACAAGAGATGGTGGCGCGAGCAAAATTCCGTGGTGCCAATaaa > 1:3417425/1‑69 (MQ=255)
aGCTTTAAGAAAGGCTGCTATACCGGACAAGAGATGGTGGCGCGAGCAAAATTCCGTGGTGCcaacaa < 1:1253968/68‑1 (MQ=255)
aGCTTTAAGAAAGGCTGCTATACCGGACAAGAGATGGTGGCGCGAGCAAAATTCCGTGGTGCcaacaa < 1:3093395/68‑1 (MQ=255)
aGCTTTAAGAAAGGCTGCTATACCGGACAAGAGATGGTGGCGCGAGCAAAATTCCGTGGTGCcaacaa < 1:1430929/68‑1 (MQ=255)
aGCTTTAAGAAAGGCTGCTATACCGGACAAGAGATGGTGGCGCGAGCAAAATTCCGTGGTGCcaacaa < 1:2851339/68‑1 (MQ=255)
aGCTTTAAGAAAGGCTGCTATACCGGACAAGAGATGGTGGCGCGAGCAAAATTCCGTGGTGCcaacaa < 1:2807958/68‑1 (MQ=255)
aGCTTTAAGAAAGGCTGCTATACCGGACAAGAGATGGTGGCGCGAGCAAAATTCCGTGGTGCcaacaa < 1:2796636/68‑1 (MQ=255)
aGCTTTAAGAAAGGCTGCTATACCGGACAAGAGATGGTGGCGCGAGCAAAATTCCGTGGTGCcaacaa < 1:2324299/68‑1 (MQ=255)
aGCTTTAAGAAAGGCTGCTATACCGGACAAGAGATGGTGGCGCGAGCAAAATTCCGTGGTGCcaacaa < 1:2242180/68‑1 (MQ=255)
aGCTTTAAGAAAGGCTGCTATACCGGACAAGAGATGGTGGCGCGAGCAAAATTCCGTGGTGCcaacaa < 1:2240679/68‑1 (MQ=255)
aGCTTTAAGAAAGGCTGCTATACCGGACAAGAGATGGTGGAGCGAGCAAAATTCCGTGGTGCcaacaa < 1:1945229/68‑1 (MQ=255)
gCTTTAAGAAAGGCTGCTATACCGGACAAGAGATGGTGGCGCGAGCAAAATTCCGTGGTGCcaacaa < 1:2222959/67‑1 (MQ=255)
cTTTAAGAAAGGCTGCTATACCGGACAAGAGATGGTGGCGCGAGCAAAATTCCGTGGTGCCAACAAAc > 1:3312277/1‑68 (MQ=255)
cTTTAAGAAAGGCTGCTATACCGGACAAGAGATGGTGGCGCGAGCAAAATTCCGTGGTGCCAACAAACg > 1:2584374/1‑69 (MQ=255)
cTTTAAGAAAGGCTGCTATACCGGACAAGAGATGGTGGCGCGAGCAAAATTCCGTGGTGCCAACAAACg > 1:1867983/1‑69 (MQ=255)
|
AGCGGGCAGTTTATCCCACAGGCGACCAATCTCCAGGCGCTGGGCGGTATCAGCTTTAAGAAAGGCTGTTATACCGGACAAGAGATGGTGGCGCGAGCAAAATTCCGTGGTGCCAATAAACG > minE/1941196‑1941317
|
| 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
