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 |
|
A4 F21 I0 R1
|
1009 |
73.8 |
4146436 |
87.4% |
3623985 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,582,992 |
T→C |
21.5% |
S81S (TCA→TCG) |
ligA ← |
DNA ligase, NAD(+)‑dependent |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,582,992 | 0 | T | C | 21.5%
| 145.9
/ 37.2
| 73 | S81S (TCA→TCG) | ligA | DNA ligase, NAD(+)‑dependent |
| Reads supporting (aligned to +/- strand): ref base T (31/26); new base C (6/9); total (38/35) |
| Fisher's exact test for biased strand distribution p-value = 3.91e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.33e-01 |
GTTTTTCAGACGGTCCTGCACACGTTTGTTGAAAGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGTGACAGCATTGGTACTTCATGGCGTATCTGGCTGAAAGCCGCCAGCGGCGCAGCGCCTACACGTTGAGTA > minE/1582923‑1583061
|
gttTTTCAGACGGTCCTGCACACGTTTGTTGAAAGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGt < 1:3947463/70‑1 (MQ=255)
gttTTTCAGACGGTCCTGCACACGTTTGTTGAAAGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGt > 1:2328043/1‑70 (MQ=255)
gttTTTCAGACGGTCCTGCACACGTTTGTTGAAAGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGt > 1:1584383/1‑70 (MQ=255)
tttCAGACGGTCCTGCACACGTTTGTTGAAAGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGTGa > 1:3763441/1‑69 (MQ=255)
tCAGACGGTCCTGCACACGTTTGTTGAAAGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGTGACAg < 1:1811291/70‑1 (MQ=255)
tCAGACGGTCCTGCACACGTTTGTTGAAAGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGTGACAg > 1:1239712/1‑70 (MQ=255)
aCGGTCCTGCACACGTTTGTTGAAAGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGTGACAg < 1:2553175/66‑1 (MQ=255)
aCGGTCCTGCACACGTTTGTTGAAAGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGTGACAg < 1:2548242/66‑1 (MQ=255)
aCGGTCCTGCACACGTTTGTTGAAAGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGTGACAg < 1:1635074/66‑1 (MQ=255)
aCGGTCCTGCACACGTTTGTTGAAAGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGCGACAGCATTg < 1:1690992/71‑1 (MQ=255)
cGGTCCTGCACACGTTTGTTGAAAGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGCGACAGCATTgg < 1:3074583/71‑1 (MQ=255)
cTGCACACGTTTGTTGAAAGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGTGACAGCATTGGTACt < 1:3072363/70‑1 (MQ=255)
cTGCACACGTTTGTTGAAAGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGCGACAGCATTGGTACtt > 1:2355017/1‑71 (MQ=255)
cTGCACACGTTTGTTGAAAGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGCGACAGCATTGGTACtt < 1:1750119/71‑1 (MQ=255)
gCACACGTTTGTTGAAAGCAAGAGAGCTTTCTTCATCAAAAACGTTATCCAGTGACAGCa > 1:3960222/1‑60 (MQ=255)
cacaCTTTTGTTGAAAGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGTGACAGCATTGGTACTTc < 1:2053133/69‑1 (MQ=255)
cacaCGTTTGTTGAAAGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGTGACAGCATTGGTACTTCAt < 1:4031940/71‑1 (MQ=255)
acacGTTTGTTGAAAGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGTGACAGCATTGGTACTTCATg < 1:3017930/71‑1 (MQ=255)
acacGTTTGTTGAAAGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGCGACAGc < 1:2591651/57‑1 (MQ=255)
acacGTTTGTTGAAAGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGCGACAGCATTGGTACTTCa > 1:1887926/1‑69 (MQ=255)
acacGTTTGTTGAAAGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGCGACAGCATTGGTACTTCa > 1:1739555/1‑69 (MQ=255)
acGTTTGTTGAAAGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGTGACAGCATTGGTACt > 1:2727565/1‑64 (MQ=255)
acGTTTGTTGAAAGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGTGACAGCATTGGTACt > 1:622224/1‑64 (MQ=255)
acGTTTGTTGAAAGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGTGACAGCATTGGTACt > 1:1719114/1‑64 (MQ=255)
acGTTTGTTGAAAGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGTGACAGCATTGGTACTTc < 1:3694488/66‑1 (MQ=255)
cGTTTGTTGAAAGCAAGTAAGCTTTCTTCATCAAAAACGTTATCCAGTGACAGc < 1:1050179/54‑1 (MQ=255)
cGTTTGTTGAAAGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGTGa > 1:149291/1‑50 (MQ=255)
tttGTTGAAAGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGTGACAGCATTGGTACTTCATGGCGTa > 1:36574/1‑71 (MQ=255)
tgttgAAAGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGTGACAGCATTGGTACTTCAt < 1:3194911/63‑1 (MQ=255)
tgttgAAAGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGTGACAGCATTGGTACTTCATGGCGTATc > 1:1412798/1‑71 (MQ=255)
gAAAGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGTGACAGCATTGGTa > 1:569332/1‑53 (MQ=255)
gAAAGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGTGACAGCATTGGTACTTCAt > 1:2548565/1‑59 (MQ=255)
aaaGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGt < 1:3660470/39‑1 (MQ=255)
aaaGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGt < 1:1999378/39‑1 (MQ=255)
gCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGTGACAGCATTGGTACTTCATGGCGTATCTGGCTGaa < 1:1987331/71‑1 (MQ=255)
cAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGTGACAGCATTGGTACTTCATGGCGTATCTGGCTGa > 1:1327764/1‑69 (MQ=255)
cAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGCGACAg < 1:3641862/40‑1 (MQ=255)
aaGAAAGCTTTCTTCATCAAAAACGTTATCCAGTGa > 1:1184483/1‑36 (MQ=255)
aGAAAGCTTTCTTCATCAAAAACGTTATCCAGTGACAGCATTGGTACtt < 1:3218686/49‑1 (MQ=255)
aaaGCTTTCTTCATCAAAAACGTTATCCAGTGACAg < 1:460765/36‑1 (MQ=255)
aaaGCTTTCTTCATCAAAAACGTTATCCAGTGACAGCATTGGTACTTCATGGCGTATCTGGCTGAAAgccg > 1:1724216/1‑71 (MQ=255)
aaaGCTTTCTTCATCAAAAACGTTATCCAGTGACAGCATTGGTACTTCATGGCGTATCTGGCTGAAAgccg > 1:3239544/1‑71 (MQ=255)
aaGGTTTCTTCATCAAAAACGTTATCCAGTGACAGCa > 1:115653/1‑37 (MQ=255)
aaGCTTTCTTCATCAAAAACGTTATCCAGTGACAGc > 1:1790300/1‑36 (MQ=255)
aaGCTTTCTTCATCAAAAACGTTATCCAGTGACAGCa > 1:2109459/1‑37 (MQ=255)
aaGCTTTCTTCATCAAAAACGTTATCCAGTGACAGCa > 1:2000678/1‑37 (MQ=255)
aaGCTTTCTTCATCAAAAACGTTATCCAGTGACAGCa > 1:3215833/1‑37 (MQ=255)
aaGCTTTCTTCATCAAAAACGTTATCCAGTGACAGCa > 1:1657716/1‑37 (MQ=255)
aaGCTTTCTTCATCAAAAACGTTATCCAGTGACAGCAt > 1:1084020/1‑38 (MQ=255)
aaGCTTTCTTCATCAAAAACGTTATCCAGCGACAGCATTGGTACTTCATGGCGTATCTGGCTGAAAgccgc > 1:1429169/1‑71 (MQ=255)
cTTTCTTCATCAAAAACGTTATCCAGTGACAGCATTGGTACTTCATGGCGTATCTGGCTGAAAGCCGCCAg > 1:3405330/1‑71 (MQ=255)
tttCTTCATCAAAAACGTTATCCAGTGACAGCATTGGTACTTCATGGCGTATCTGGCTGAAAgccg < 1:1245037/66‑1 (MQ=255)
tttCTTCATCAAAAACGTTATCCAGTGACAGCATTGGTACTTCATGGCGTATCTGGCTGAAAgccg < 1:480190/66‑1 (MQ=255)
tttCTTCATCAAAAACGTTATCCAGCGACAGCATTGGTACTTCa < 1:1141785/44‑1 (MQ=255)
tcttcATCAAAAACGTTATCCAGTGACAGCATTGGTACTTCATGGCGTATCTGGCTGAAAGCCGCCAgcgg > 1:4029119/1‑71 (MQ=255)
ttcATCAAAAACGTTATCCAGTGACAGCATTGGTAcatcat > 1:3507040/1‑41 (MQ=255)
ttcATCAAAAACGTTATCCAGTGACAGCATTGGTACTTCAt > 1:1735154/1‑41 (MQ=255)
catcaAAAACGTTATCCAGTGACAGCATTGGTACTTCATGGCGTATCTGGCTGAAAGCCGCCAGCGgcgc < 1:325278/70‑1 (MQ=255)
catcaAAAACGTTATCCAGCGACAGCATTGGTACTTCATGGCGTATCTg > 1:3650329/1‑49 (MQ=255)
catcaAAAACGTTATCCAGCGACAGCATTGGTACTTCATGGCGTATCTGGCTGAAAGCCGCCAGCGgcgc < 1:2230650/70‑1 (MQ=255)
tcaAAAACGTTATCCAGTGACAGCATTGGTACTTCATGGCGTATCTGGCTGaaa < 1:3685227/54‑1 (MQ=255)
aaaaaCGTTATCCAGTGACAGCATTGGTACTTCATGGCGTATCTGGCTGAAAgc > 1:3715757/1‑54 (MQ=255)
aaaaaCGTTATCCAGTGACAGCATTGGTACTTCATGGCGTATCTGGCTGAAAGCCGCCAGCGGCGCAgcgc > 1:2808137/1‑71 (MQ=255)
aaaaCGTTATCCAGTGACAGCATTGGTACTTCATGGCGTAt > 1:2375087/1‑41 (MQ=255)
aaaaCGTTATCCAGTGACAGCATTGGTACTTCATGGCGTATCTGGCTGAAAGCCGCCAGCGGCGCAGCGcc < 1:2030721/71‑1 (MQ=255)
aaaaCGTTATCCAGTGACAGCATTGGTACTTCATGGCGTATCTGGCTGAAAGCCGACAGCGGCGCa < 1:3984617/66‑1 (MQ=255)
aaCGTTATCCAGTGACAGCATTGGTACTTCATGGCGTATCTGGCTGAAAGCCGCCAGCGGCGCAGCGCCTa > 1:2943690/1‑71 (MQ=255)
aaCGTTATCCAGTGACAGCATTGGTACTTCATGGCGTATCTGGCTGAAAGCCGCCAGCGGCGCAGCGCCTa < 1:190410/71‑1 (MQ=255)
aaCGTTATCCAGCGACAGCATTGGTACTTCATGGCGTATCTGGCTGAAAgccgc < 1:1991947/54‑1 (MQ=255)
cGTTATCCAGCGACAGCATTGGTACTTCATGGCGTa < 1:3584580/36‑1 (MQ=255)
ttATCCAGGGACAGCATTGGTACTTCATGGCGTATc > 1:1722996/1‑36 (MQ=255)
ttATCCAGCGACAGCATTGGTACTTCATGGCGTATc > 1:206794/1‑36 (MQ=255)
aTCCAGTGACAGCATTGGTACTTCATGGCGTATCTGGCTGAAAGCCGCCAGCGGCGCAgc > 1:1587627/1‑60 (MQ=255)
tCCAGTGACAGCATTGGTACTTCATGGCGTATCTGGCTGAAAGCCGCCAGCGGCGCAGCGCCTACACGtt < 1:326530/70‑1 (MQ=255)
tCCAGTGACAGCATTGGTACTTCATGGCGTATCTGGCTGAAAGCCGCCAGCGGCGCAGCGCCTACACGtt < 1:1970032/70‑1 (MQ=255)
tCCAGTGACAGCATTGGTACTTCATGGCGTATCTGGCTGAAAGCCGCCAGCGGCGCAGCGCCTACACGTTg < 1:3766188/71‑1 (MQ=255)
cAGTGACAGCATTGGTACTTCATGGCGTATCTGGCTGAAAGCCGCCAGCGGCGCAGCGCCTACACGTTGa < 1:4133476/70‑1 (MQ=255)
gTGACAGCATTGGTACTTCATGGCGTATCTGGCTGAAAGCCGCCAGCGGCGCAGCGCCTACACGTTg < 1:888052/67‑1 (MQ=255)
tGACAGCATTGGTACTTCATGGCGTATCTGGCTGAAAGCCGCCAGCGGCGCa < 1:506267/52‑1 (MQ=255)
tGACAGCATTGGTACTTCATGGCGTATCTGGCTGAAAGCCGCCAGCGGCGCAGCGCCTACACGTTGAGTa < 1:282763/70‑1 (MQ=255)
|
GTTTTTCAGACGGTCCTGCACACGTTTGTTGAAAGCAAGAAAGCTTTCTTCATCAAAAACGTTATCCAGTGACAGCATTGGTACTTCATGGCGTATCTGGCTGAAAGCCGCCAGCGGCGCAGCGCCTACACGTTGAGTA > minE/1582923‑1583061
|
| 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
