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 |
705,295 |
A→G |
50.7% |
G32G (GGT→GGC) |
ymcB ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 705,295 | 0 | A | G | 50.7%
| 0.4
/ 92.0
| 67 | G32G (GGT→GGC) | ymcB | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (15/18); new base G (12/22); total (27/40) |
| Fisher's exact test for biased strand distribution p-value = 4.60e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GCGCAGTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCATTACGTAAAGTACGC > minE/705226‑705359
|
gcgcAGTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCAc < 1:1539634/71‑1 (MQ=255)
cgcAGTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGcc < 1:2356304/71‑1 (MQ=255)
gcAGTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCa < 1:2452920/71‑1 (MQ=255)
gCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCa > 1:2645671/1‑62 (MQ=255)
gCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCACCAgg > 1:2079479/1‑67 (MQ=255)
gCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCACCAGGCAg < 1:1332417/70‑1 (MQ=255)
ggTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGAt > 1:3389492/1‑70 (MQ=255)
ttGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATaaa > 1:1381312/1‑71 (MQ=255)
ttGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCACCAGGCAGATaaa < 1:3241335/71‑1 (MQ=255)
ttGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCACCAGGCAGATaaa > 1:3326829/1‑71 (MQ=255)
tgtgTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCACCa > 1:784414/1‑60 (MQ=255)
gtCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGt > 1:2473339/1‑71 (MQ=255)
tCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTc < 1:2416006/71‑1 (MQ=255)
aCCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCAc > 1:1559311/1‑71 (MQ=255)
ccAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATaaa > 1:1175016/1‑63 (MQ=255)
ccAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAg < 1:3388718/66‑1 (MQ=255)
ccAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAg < 1:3631957/66‑1 (MQ=255)
cAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCg > 1:1939040/1‑71 (MQ=255)
aaCTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGt > 1:3021618/1‑71 (MQ=255)
aaCTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGt > 1:2610967/1‑71 (MQ=255)
ggACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCt > 1:156855/1‑71 (MQ=255)
gACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATaa < 1:3180661/55‑1 (MQ=255)
gACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATaa < 1:3521487/55‑1 (MQ=255)
gACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTc < 1:1515770/61‑1 (MQ=255)
caacaTTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTgc > 1:886825/1‑71 (MQ=255)
caTTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATa < 1:2383298/53‑1 (MQ=255)
caTTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTgcgc > 1:1555160/1‑70 (MQ=255)
caTTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTg > 1:3359904/1‑67 (MQ=255)
caTTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCa < 1:431267/71‑1 (MQ=255)
aTTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATaaa < 1:618671/50‑1 (MQ=255)
aTTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCaa < 1:441345/71‑1 (MQ=255)
aTTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCaa < 1:499546/71‑1 (MQ=255)
ttttCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGt > 1:1515724/1‑53 (MQ=255)
tttCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATa > 1:703998/1‑50 (MQ=255)
ttCCACGGGGCCAACGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAg < 1:3645833/70‑1 (MQ=255)
ccACGGGGCCAACGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAgg < 1:2295147/69‑1 (MQ=255)
cACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGt < 1:1758485/54‑1 (MQ=255)
cACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCa < 1:3150948/70‑1 (MQ=255)
cACGGGGCCAACGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCAt > 1:1518357/1‑71 (MQ=255)
aCGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATg < 1:789255/71‑1 (MQ=255)
gCCAACGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGgtg < 1:3036538/71‑1 (MQ=255)
ccAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTcc < 1:3658690/50‑1 (MQ=255)
aaCGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGgtgt < 1:305730/69‑1 (MQ=255)
aaCGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCa < 1:54645/71‑1 (MQ=255)
cGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATg > 1:1121240/1‑61 (MQ=255)
cGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCAt > 1:2485860/1‑70 (MQ=255)
ggAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCATTa > 1:3507228/1‑71 (MQ=255)
aaaGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATggg < 1:742987/60‑1 (MQ=255)
aaaGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATggg < 1:1347144/60‑1 (MQ=255)
aGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCATTACGTa < 1:2410922/71‑1 (MQ=255)
aGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCATTACGTa < 1:3768739/71‑1 (MQ=255)
aGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCATTACGTa < 1:1096826/71‑1 (MQ=255)
aGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCATTACGTa < 1:2741461/71‑1 (MQ=255)
gtgtCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTgcgc < 1:3907594/46‑1 (MQ=255)
gtgtCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTgcgc < 1:1051350/46‑1 (MQ=255)
tgttgtTCGCCAGGCAGATAATTAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCATTAc < 1:1924616/62‑1 (MQ=255)
tgttgtTCACCAGGCAGATAAATAGTCACCGTTCCTTgcg > 1:1228834/1‑40 (MQ=255)
tgttgtTCACCAGGCAGATAAATAGTCACCGTTCCTTgcg > 1:3242917/1‑40 (MQ=255)
gttgttCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCa < 1:1985568/41‑1 (MQ=255)
gttgttCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCa < 1:2487142/41‑1 (MQ=255)
gttgttCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCa < 1:2187009/41‑1 (MQ=255)
ttgttCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCATTACGt > 1:3842433/1‑62 (MQ=255)
ttgttCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCATTACGt > 1:2596973/1‑62 (MQ=255)
ttgttCACCAGGCATATAAATAGTCACCGTTCCTTGCGCAAAGGCa < 1:873898/46‑1 (MQ=255)
ttgttCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCa < 1:1661703/46‑1 (MQ=255)
ttgttCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCa > 1:2232734/1‑46 (MQ=255)
ttgttCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCATTACGTAAAGTACGc < 1:332244/71‑1 (MQ=255)
ttCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCATTACGTAAAGTACg > 1:483210/1‑67 (MQ=255)
|
GCGCAGTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCATTACGTAAAGTACGC > minE/705226‑705359
|
| 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
