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 |
|
A5 F21 I0 R2
|
316 |
65.6 |
5147759 |
97.4% |
5013917 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,274,854 |
G→A |
29.1% |
T108M (ACG→ATG) |
ychN ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,274,854 | 0 | G | A | 29.1%
| 85.4
/ 39.9
| 55 | T108M (ACG→ATG) | ychN | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (20/19); new base A (9/7); total (29/26) |
| Fisher's exact test for biased strand distribution p-value = 7.75e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TTCCCGCATAGTGGGGCGTCAGACGCCCCCTCAAACATTAAAATGTGAGCACTTTATCGGCTGACAGCGTCCATTGCGCCAGTTCCACAAGAGTACCGATTTCCACCCCATCAATCAGAGGAAGTGTACT > W3110S.gb/1274786‑1274915
|
ttCCCGCATAGTGGGGCGTCAGCCGCCCCCTCAAACATTAAAATGTGAGCACTTTATCGGCTGACAGCGTc > 1:4120293/1‑71 (MQ=255)
ttCCCGCATAGTGGGGCGTCAGACGCCCCCTCAAACATTAAAATGTGAGCACTTTATCGGCTGACAGCGTc > 1:3950916/1‑71 (MQ=255)
ttCCCGCATAGTGGGGCGTCAGACGCCCCCTCAAACATTAAAATGTGAGCACTTTATCGGCTGACAGCGTc > 1:3056311/1‑71 (MQ=255)
cccGCATAGTGGGGCGTCAGACGCCCCCTCAAACATTAAAATGTGAGCACTTTATCGGCTGACAGCGTCCa > 1:4258232/1‑71 (MQ=255)
cccGCATAGTGGGGCGTCAGACGCCCCCTCAAACATTAAAATGTGAGCACTTTATCGGCTGACAGCATcc < 1:4398177/70‑1 (MQ=255)
tAGTGGGGCGTCAGACTCCCCCTCAAACATTAAAATGTGAGCACTTTATCGGCTGACAGCGTcc > 1:3513570/1‑64 (MQ=255)
tAGTGGGGCGTCAGACTCCCCCTCAAACATTAAAATGTGAGCACTTTATCGGCTGACAGCGTCCa > 1:1294253/1‑65 (MQ=255)
gggCGTCAGACGCCCCCTCAAACATTAAAATGTGAGCACTTTATCGGCTGACAGCGTCCATTGCGCCAGtt > 1:4767639/1‑71 (MQ=255)
aGACGCCCCCTCAAACATTAAAATGTGAGCACTTTATCGGCTGACAGCGTCCATTgc > 1:1206597/1‑57 (MQ=255)
cccTCAAACATTAAAATGTGAGCACTTTATCGGCTGACAGCGTcc < 1:4461428/45‑1 (MQ=255)
cccTCAAACATTAAAATGTGAGCACTTTATCGGCTGACAGCGTcc < 1:2191821/45‑1 (MQ=255)
cAAACATTAAAATGTGAGCACTTTATCGGCTGACAGCGTCCATTGCGCCAGTTCCACAAGAGTACCGAttt > 1:435499/1‑71 (MQ=255)
aaaCATTAAAATGTGAGCACTTTATCGGCTGACAGCGTCCATTGCGCCAGTTCCACAAGAGTACCGATTTc < 1:2593040/71‑1 (MQ=255)
aaaCATTAAAATGTGAGCACTTTATCGGCTGACAGCGTCCATTGCGCCAGTTCCACAAGAGTACCGATTTc < 1:2686817/71‑1 (MQ=255)
aaaCATTAAAATGTGAGCACTTTATCGGCTGACAGCGTCCATTGCGCCAGTTCCACAAGAGTACCGATTTc < 1:1941135/71‑1 (MQ=255)
aaaCATTAAAATGTGAGCACTTTATCGGCTGACAGCGTCCATTGCGCCAGTTCCACAAGAGTACCGATTTc < 1:3294131/71‑1 (MQ=255)
aaCATTAAAATGTGAGCACTTTATCGGCTGACAGCGTCCATTGCGCCAGTTCCACAAGAGTACCGATTTc < 1:2782814/70‑1 (MQ=255)
ttAAAATGTGAGCACTTTATCGGCTGACAGCGTCCATTgc < 1:434722/40‑1 (MQ=255)
ttAAAATGTGAGCACTTTATCGGCTGACAGCATCCATTGCGCCAGTTCca < 1:4899589/50‑1 (MQ=255)
tAAAATGTGAGCACTTTATCGGCTGACAGCGTCCATTGCGCCAGTTCCACAAGAGTACCGATTTCCAccc > 1:3912636/1‑70 (MQ=255)
aaaaTGTGAGCACTTTATCGGCTGACAGCGTCCATTGCGCCAGTTCCATAaga > 1:70815/1‑53 (MQ=255)
aaaaTGTGAGCACTTTATCGGCTGACAGCGTCCATTGCGCCAGTTCCACAaga > 1:4932695/1‑53 (MQ=255)
aaaaTGTGAGCACTTTATCGGCTGACAGCGTCCATTGCGCCAGTTCCACAAGAGTACCGATTTCCAcccc > 1:3298882/1‑70 (MQ=255)
aaaaTGTGAGCACTTTATCGGCTGACAGCGTCCATTGCGCCAGTTCCACAAGAGTACCGATTTCCAcccaa > 1:4061497/1‑69 (MQ=255)
aaaaTGTGAGCACTTTATCGGCTGACAGCATCCATTGCGCCAGTTCCACAAGAGTACCGa > 1:3609122/1‑60 (MQ=255)
aaaaTGTGAGCACTTTATCGGCTGACAGCATCCATTGCGCCAGTTCCACAAGAGTACCGa > 1:1169498/1‑60 (MQ=255)
aaaaTGTGAGCACTTTATCGGCTGACAGCATCCATTGCGCCAGTTCCACAAGAGTACCGa > 1:1492793/1‑60 (MQ=255)
aaaaTGTGAGCACTTTATCGGCTGACAGCATCCATTGCGCCAGTTCCACAAGAGTACCGATTTCCACCCCa > 1:322935/1‑71 (MQ=255)
aaaTGTGAGCACTTTATCGGCTGACAGCATCCATTGCGCCAGTTCCACAAGAGTACCGATTTCCACCCCat > 1:4070407/1‑71 (MQ=255)
aaaTGTGAGCACTTTATCGGCTGACAGCATCCATTGCGCCAGTTCCACAAGAGTACCGATTTCCAACCCa > 1:730911/1‑70 (MQ=255)
aaaTGTGAGAACTTTATCGGCTGACAGCATCCATTGCGCCAGTTCCACAAGAGTACCGATTTCCACCCCat > 1:3907756/1‑71 (MQ=255)
cACTTTATCGGCTGACAGCGTCCATTGCGCCAGTTCCACAAGAGTACCGATTTCCACCCCatcaat < 1:1773167/66‑1 (MQ=255)
cACTTTATCGGCTGACAGCGTCCATTGCGCCAGTTCCACAAGAGTACCGATTTCCACCCCatcaat < 1:2122691/66‑1 (MQ=255)
cACTTTATCGGCTGACAGCGTCCATTGCGCCAGTTCCACAAGAGTACCGATTTCCACCCCatcaat < 1:2399388/66‑1 (MQ=255)
aCTTTATCGGCTGACAGCGTCCATTGCGCCAGTTCCACAAGAGTACCGATTTCCACCCCATCAATCAGAgg < 1:1153263/71‑1 (MQ=255)
cTTTATCGGCTGACAGCGTCCATTGCGCCAGTTCCACAAGAGTACCGAt < 1:3431865/49‑1 (MQ=255)
cTTTATCGGCTGACAGCGTCCATTGCGCCAGTTCCACAAGAGTACCGATTTCCACCCCatcaatca > 1:2768454/1‑66 (MQ=255)
cTTTATCGGCTGACAGCGTCCATTGCGCCAGTTCCACAAGAGTACCGATTTCCACCCCatcaatca > 1:4392307/1‑66 (MQ=255)
tttATCGGCTGACAGCGTCCATTGCGCCAGTTCCACAAGAGTACCGAt < 1:3617477/48‑1 (MQ=255)
tATCGGCTGACAGCGTCCATTGCGCCAGTTCCACAagag < 1:2439749/39‑1 (MQ=255)
tATCGGCTGACAGCGTCCATTGCGCCAGTTCCACAagag < 1:3341269/39‑1 (MQ=255)
tATCGGCTGACAGCGTCCATTGCGCCAGTTCCACAAGAGTa > 1:1870373/1‑41 (MQ=255)
tATCGGCTGACAGCATCCATTGCGCCAGTTCCACAAGAGTACCGATTTCCAccc > 1:4227737/1‑54 (MQ=255)
tATCGGCTGACAGCATCCATTGCGCCAGTTCCACAAGAGTACCGATTTCCAccc > 1:4235861/1‑54 (MQ=255)
tCGGCTGACAGCGTCCATTGCGCCAGTTCCACAAGAGTACCGATTTCCACCCCATCAATCAGAGGAAg > 1:340008/1‑68 (MQ=255)
cGGCTGACAGCATCCATTGCGCCAGTTCCACAAGAGTACCGATTTCCACCCCATCAATCAGAGGAAgtg < 1:4089749/69‑1 (MQ=255)
gCTGACAGCGTCCATTGCGCCAGTTCCACAAGAGTACCGATTTCCACCCCATCAATCAGAGGAAGTGTACt < 1:4564310/71‑1 (MQ=255)
gACAGCGTCCATTGCGCCAGTTCCACAAGAGTAcc < 1:4797598/35‑1 (MQ=255)
gACAGCGTCCATTGCGCCAGTTCCACAAGAGTAcc < 1:3098801/35‑1 (MQ=255)
aCAGCATCCATTGCGCCAGTTCCACAAGAGTACCGATTTCCACCCCATCAATCAGAGGAAGTGTACt < 1:1798726/67‑1 (MQ=255)
aCAGCATCCATTGCGCCAGTTCCACAAGAGTACCGATTTCCACCCCATCAATCAGAGGAAGTGTACt < 1:1804564/67‑1 (MQ=255)
aCAGCATCCATTGCGCCAGTTCCACAAGAGTACCGATTTCCACCCCATCAATCAGAGGAAGTGTACt < 1:5124880/67‑1 (MQ=255)
aCAGCATCCATTGCGCCAGTTCCACAAGAGTACCGATTTCCACCCCATCAATCAGAGGAAGTGTACt < 1:556156/67‑1 (MQ=255)
cAGCGTCCATTGCGCCAGTTCCACAAGAGTACCGa > 1:809289/1‑35 (MQ=255)
cAGCGTCCATTGCGCCAGTTCCACAAGAGTACCGa > 1:815237/1‑35 (MQ=255)
|
TTCCCGCATAGTGGGGCGTCAGACGCCCCCTCAAACATTAAAATGTGAGCACTTTATCGGCTGACAGCGTCCATTGCGCCAGTTCCACAAGAGTACCGATTTCCACCCCATCAATCAGAGGAAGTGTACT > W3110S.gb/1274786‑1274915
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
