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 |
|
A54 F1 I1 R1
|
16 |
53.7 |
3449390 |
96.4% |
3325211 |
75.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
4,103,979 |
T→A |
intergenic (‑40/+116) |
cytR ← / ← priA |
DNA‑binding transcriptional dual regulator/primosome assembly protein PriA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 4,103,979 | 0 | T | A | 98.4%
| 239.7
/ ‑2.7
| 63 | intergenic (‑40/+116) | cytR/priA | DNA‑binding transcriptional dual regulator/primosome assembly protein PriA |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base A (31/31); total (31/32) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.23e-01 |
TCGCGGCAGTTTCCTGCTTCTTCGCTTTCACACTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCATGTTTACTTCACATCGGCAACATTTTTAGCAGATAGCGCGTGAAAACGGTTACAGAATTTTCATGAAAAGT > REL606/4103909‑4104049
|
tCGCGGCAGTTTCCTGCTTCTTCGCTTTCACACTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTa < 2:25339/76‑1 (MQ=255)
cgcgGCAGTTTCCTGCTTCTTCGCTTTCACACTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTAc < 1:661117/76‑1 (MQ=255)
cgGCAGTTTCCTGCTTCTTCGCTTTCACACTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACtt > 2:525417/1‑76 (MQ=255)
gCAGTTTCCTGCTTCTTCGCTTTCACACTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTca < 1:1233837/76‑1 (MQ=255)
gCAGTTTCCTGCTTCTTCGCTTTCACACTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTca > 2:826622/1‑76 (MQ=255)
gCAGTTTCCTGCTTCTTCGCTTTCACACTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTca < 1:820330/76‑1 (MQ=255)
cAGTTTCCTGCTTCTTCGCTTTCACACTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTcac > 1:685643/1‑76 (MQ=255)
cAGTTTCCTGCTTCTTCGCTTTCACACTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTcac > 1:773338/1‑76 (MQ=255)
aGTTTCCTGCTTCTTCGCTTTCACACTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTcaca > 2:630869/1‑76 (MQ=255)
gTTTCCTGCTTCTTCGCTTTCACACTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACAt < 2:267472/76‑1 (MQ=255)
ttCCTGCTTCTTCGCTTTCACACTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCg > 1:86867/1‑76 (MQ=255)
cgngCTTCTTCGCTTTCACACTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCTAGTTTAATTCACATCGGc > 2:1212404/4‑76 (MQ=255)
ccTGCTTCTTCGCTTTCACACTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGc > 2:1682586/1‑76 (MQ=255)
cangCTTCTTCGCTTTCACACTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGc > 2:1212391/4‑76 (MQ=255)
cTGCTTCTTCGCTTTCACACTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGCa > 2:1428730/1‑76 (MQ=255)
cttcttCGCTTTCACACTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGCAACa < 2:106631/76‑1 (MQ=255)
tcttcGCTGTCACACTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGCAACAtt < 2:938697/76‑1 (MQ=255)
cttcGCTTTCACACTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGCAACAttt > 1:957326/1‑76 (MQ=255)
cttcGCTTTCACACTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCAAGCTTACTTCACATCGGCAACAttt > 2:312664/1‑76 (MQ=255)
tcGCTTTCACACTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCATGTTTACTTCACATCGGCAACAttttt < 2:1640532/76‑1 (MQ=255)
tcGCTTTCACACTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGCAACAttttt > 1:1183022/1‑76 (MQ=255)
tcGCTTTCACACTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGCAACAttttt > 1:194183/1‑76 (MQ=255)
cGCTTTCACACTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTa < 1:1212270/76‑1 (MQ=255)
gCTTTCACACTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTAg < 2:52846/76‑1 (MQ=255)
gCTTTCACACTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTAg > 1:752490/1‑76 (MQ=255)
cTTTCACACTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTAGc < 1:312665/76‑1 (MQ=255)
ttCACACTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAg > 2:770635/1‑76 (MQ=255)
cacaCTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGAt < 1:206374/76‑1 (MQ=255)
cacaCTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGAt < 2:806073/76‑1 (MQ=255)
ccactcactCCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGAtn < 1:1576822/75‑2 (MQ=255)
acacTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATa < 2:1181436/76‑1 (MQ=255)
acacTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATa < 1:475264/76‑1 (MQ=255)
acacTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATa > 1:1630786/1‑76 (MQ=255)
acacTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATa > 1:29839/1‑76 (MQ=255)
actcactcCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATAgc > 2:1127757/1‑76 (MQ=255)
actcactcCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATAgc > 2:526768/1‑76 (MQ=255)
ctcactcCTCGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATAgcg < 1:226192/76‑1 (MQ=255)
ctcctcGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATAGCGCGTg < 2:1063819/76‑1 (MQ=255)
ctcGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATAGCGCGTGaaa < 1:606948/76‑1 (MQ=255)
tcGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATAGCGCGTGaaaa < 2:43254/76‑1 (MQ=255)
cGCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATAGCGCGTGAAAAc > 2:368897/1‑76 (MQ=255)
gCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATAGCGCGTGAAAACg < 2:1065169/76‑1 (MQ=255)
gCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATAGCGCGTGAAAACg < 1:1105362/76‑1 (MQ=255)
gCCTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATAGCGCGTGAAAACg < 1:261081/76‑1 (MQ=255)
cTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATAGCGCGTGAAAACGGt > 2:1102715/1‑76 (MQ=255)
cTGGCACGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATAGCGCGTGAAAACGGt > 1:81228/1‑76 (MQ=255)
aCGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATAGCGCGTGAAAACGGTTACAg > 1:900306/1‑76 (MQ=255)
aCGTCAGGCGTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATAGCGCGTGAAAACGGTTACAg < 2:339537/76‑1 (MQ=255)
cAGGCGTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATAGCGCGTGAAAACGGTTACAGAAtt > 2:820568/1‑76 (MQ=255)
aGGCGTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATAGCGCGTGAAAACGGTTACAGAAttt < 1:720283/76‑1 (MQ=255)
ggCGTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATAGCGCGTGAAAACGGTTACAGAAtttt < 1:349524/76‑1 (MQ=255)
cGTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATAGCGCGTGAAAACGGTTACAGAATTTTCa > 1:856014/1‑76 (MQ=255)
gTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATAGCGCGTGAAAACGGTTAc > 1:192669/1‑65 (MQ=255)
gTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATAGCGCGTGAAAACGGTTAc < 2:192669/65‑1 (MQ=255)
gTACTACATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATAGCGCGTGAAAACGGTTACAGAATTTTCAt > 2:31248/1‑76 (MQ=255)
tactacATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATAGCGCGTGAAAACGGTTACAGAATTTTCATg < 1:1026636/76‑1 (MQ=255)
tactacATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATAGCGCGTGAAAACGGTTACAGAATTTTCATg < 1:526769/76‑1 (MQ=255)
tactacATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATAGCGCGTGAAAACGGTTACAGAATTTTCATg > 1:390850/1‑76 (MQ=255)
tactacATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATAGCGCGTGAAAACGGTTACAGAATTTTCATg > 1:197398/1‑76 (MQ=255)
tactacATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATAGCGCGTGAAAACGGTTACAGAATTTTCATg > 1:848283/1‑76 (MQ=255)
actacATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATAGCGCGTGAAAACGGTTACAGAATTTTCATGa < 2:1497571/76‑1 (MQ=255)
tacATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATAGCGCGTGAAAACGGTTACAGAATTTTCATGaaa < 2:1347809/76‑1 (MQ=255)
cATCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATAGCGCGTGAAAACGGTTACAGAATTTTCATGAAAAg < 2:507387/76‑1 (MQ=255)
aTCCAAGTTTACTTCACATCGGCAACATTTTTAGCAGATAGCGCGTGAAAACGGTTACAGAATTTTCATGAAAAgt < 2:1259396/76‑1 (MQ=255)
|
TCGCGGCAGTTTCCTGCTTCTTCGCTTTCACACTCACTCCTCGCCTGGCACGTCAGGCGTACTACATCCATGTTTACTTCACATCGGCAACATTTTTAGCAGATAGCGCGTGAAAACGGTTACAGAATTTTCATGAAAAGT > REL606/4103909‑4104049
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
