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 F17 I0 R2
|
162 |
60.6 |
4616657 |
98.5% |
4547407 |
62.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,139,938 |
C→T |
6.0% |
R2H (CGT→CAT) |
hybD ← |
predicted maturation element for hydrogenase 2 |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,139,938 | 0 | C | T | 6.0%
| 217.8
/ 3.1
| 67 | R2H (CGT→CAT) | hybD | predicted maturation element for hydrogenase 2 |
| Reads supporting (aligned to +/- strand): ref base C (30/33); new base T (2/2); total (32/35) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.34e-01 |
CGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCGACCCCTAAGACTAAAATACGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGTCAGCATCCACTACGTGTACCGCACAGGCC > W3110S.gb/3139868‑3140005
|
cGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCGAACCCTAAGACTAAAATAc > 1:4500805/1‑71 (MQ=255)
cTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCGACCCCTAAGACTAAAATACg > 1:1182108/1‑70 (MQ=255)
ttCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCGACCCCTAAGACTAAAATACGCa > 1:3497081/1‑71 (MQ=255)
ttCGACAATACGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCGACCCCTAAGACTAAAATAcaca > 1:3477981/1‑71 (MQ=255)
tCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCGACCCCTAAGACTAAAATACGCAt > 1:3521472/1‑71 (MQ=255)
tCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCGACCCCTAAGACTAAAATACGCAt > 1:3103240/1‑71 (MQ=255)
aCAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCGACCCCTAAGACTAAAATACGCATTa > 1:336660/1‑70 (MQ=255)
aaTCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCGACCCCTAAGACTAAAATACGCATTa > 1:3222932/1‑68 (MQ=255)
cGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCGACCCCTAAGACTAAAATACGCATTACAGAAcc > 1:35230/1‑71 (MQ=255)
cacaCCGATGGCTTCATCGGTCAGCAAAATATTGCCGACCCCTAAGACTAAAATACGCATTACAGAACCtt < 1:1405399/71‑1 (MQ=255)
cacaCCGATGGCTTCATCGGTCAGCAAAATATTGCCGACCCCTAAGACTAAAATACGCATTACAGAACCtt < 1:1987794/71‑1 (MQ=255)
cacaCCGATGGCTTCATCGGTCAGCAAAATATTGCCGACCCCTAAGACTAAAATACGCATTACAGAACCtt < 1:256296/71‑1 (MQ=255)
cacCGATGGCTTCATCGGTCAGCAAAATATTGCCGACCCCTAAGACTAAAATACGCATTACAGAACCTTCa < 1:4605293/71‑1 (MQ=255)
acCGATGGCTTCATCGGTCAGCAAAATATTGCCGACCCCTAAGACTAAAATACGCATTACAGAACCTTCAc > 1:510229/1‑71 (MQ=255)
cGATGGCTTCATCGGTCAGCAAAATATTGCCGACCCCTAAGACTAAAATACGCATTAc < 1:3829441/58‑1 (MQ=255)
gATGGCTTCATCGGTCAGCAAAATATTGCCGACCCCTAAGACTAAAATACGCATTACAGAACCTTCACTGa < 1:305515/71‑1 (MQ=255)
gCTTCATCGGTCAGCAAAATATTGCCGACCCCTAAGACTAAAATACGCATTACAGAACCTTCACTGAAAcc < 1:1307490/71‑1 (MQ=255)
cTTCATAGGTCAGCAAAATATTGCCGACCCCTAAGACTAAAATACGCAATACAGAACCTTCACTGAAACCa < 1:1837988/71‑1 (MQ=255)
tCATCGGTCAGCAAAATATTGCCGACCCCTAAGACTAAAATACGCATTACAGAACCTTCACTGaaa > 1:4252680/1‑66 (MQ=255)
tCATCGGTCAGCAAAATATTGCCGACCCCTAAGACTAAAATACGCATTACAGAACCTTCACTGaa < 1:22920/65‑1 (MQ=255)
ggTCAGCAAAATATTGCCGACCCCTAAGACTAAAATACGCATTACAGAACCTTCACTGAAACCACTTCGtt < 1:1497788/71‑1 (MQ=255)
gTCAGCAAAATATTGCCGACCCCTAAGACTAAAATACGCATTACa < 1:3305350/45‑1 (MQ=255)
gTCAGCAAAATATTGCCGACCCCTAAGACTAAAATACGCATTACAGAACCTTCACTGAAACCACTTCGTTg < 1:4123052/71‑1 (MQ=255)
gTCAGCAAAATATTGCCGACCCCTAAGACTAAAATACGCATTACAGAACCTTCACTGAAACCACTTCGTTg > 1:1209240/1‑71 (MQ=255)
aGCAAAATATTGCCGACCCCTAAGACTAAAATATGCATTACAGAACCTTCACTGAAACCACTTCGTTGcc < 1:37091/70‑1 (MQ=255)
aGCAAAATATTGCCGACCCCTAAGACTAAAATACGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCg > 1:1980972/1‑71 (MQ=255)
aGCAAAATATTGCCGACCCCTAAGACTAAAATACGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCg > 1:1583229/1‑71 (MQ=255)
gCAAAATATTGCCGACCCCTAAGACTAAAATACGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGt < 1:3250100/71‑1 (MQ=255)
cAAAATATTGCCGACCCCTAAGACTAAAATACGCATTACAGAACCTTCa > 1:757462/1‑49 (MQ=255)
cAAAATATTGCCGACCCCTAAGACTAAAATACGCATTACAGAACCTTCACTGAAAc > 1:4601034/1‑56 (MQ=255)
cAAAATATTGCCGACCCCTAAGACTAAAATACGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGt > 1:1182979/1‑70 (MQ=255)
aaaTATTGCCGACCCCTAAGACTAAAATACGCATTACAGAAc > 1:4134248/1‑42 (MQ=255)
aaTATTGCCGACCCCTAAGACTAAAATACGCATTACAGa > 1:3438620/1‑39 (MQ=255)
aaTATTGCCGACCCCTAAGACTAAAATACGCATTACAGAACCTTCACTGAAAcc < 1:1720252/54‑1 (MQ=255)
atatTGCCGACCCCTAAGACTAAAATATGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGTCAGCa < 1:3812463/71‑1 (MQ=255)
ttGCCGACCCCTAAGACTAAAATACGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGTCAGCATc < 1:4459544/70‑1 (MQ=255)
ttGCCGACCCCTAAGACTAAAATACGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGTCAGCATc < 1:2355064/70‑1 (MQ=255)
ccGACCCCTAAGACTAAAATACGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGTCAGCATCCACt < 1:3911203/71‑1 (MQ=255)
cGACCCCTAAGACTAAAATACGCATTACAGAACCTTCACTGAAACCACTTCg < 1:470935/52‑1 (MQ=255)
cGACCCCTAAGACTAAAATACGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGTCAGCATc < 1:3659900/66‑1 (MQ=255)
gACCCCTAAGACTAAAATACGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGTCAGCATCCACTAc < 1:3190707/71‑1 (MQ=255)
aCCCCTAAGACTAAAATACGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGTc > 1:3186559/1‑58 (MQ=255)
cccTAAGACTAAAATACGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGTCAGCATc < 1:984808/62‑1 (MQ=255)
ccTAAGACTAAAATACGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGTCAGCATCCACTACgtgt < 1:2016765/71‑1 (MQ=255)
tAAGACTAAACTACGCATTACAGAACCTTCACTGAAACCACtt < 1:291498/43‑1 (MQ=255)
tAAGACTAAAATATGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGTCAGCATCCACTACGTGTAc > 1:3140553/1‑71 (MQ=255)
tAAGACTAAAATACGCATTACAGAACCTTCACTGaa > 1:1688664/1‑36 (MQ=255)
tAAGACTAAAATACGCATTACAGAACCTTCACTGaa > 1:4319623/1‑36 (MQ=255)
tAAGACTAAAATACGCATTACAGAACCTTCACTGa < 1:1357772/35‑1 (MQ=255)
tAAGACTAAAATACGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGTCAGCATCCACTACGTGTa > 1:4326464/1‑70 (MQ=255)
aaGACTAAAATACGCATTACAGAACCTTCACTGAAACCACTTCGt > 1:1650138/1‑45 (MQ=255)
aaGACTAAAATACGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGTCAGCATc < 1:3265330/58‑1 (MQ=255)
aaGACTAAAATACGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGTCAGCATCCACTACGTGTa > 1:3592014/1‑69 (MQ=255)
aaGACTAAAATACGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGTCAGCATCCACTACGTGTa > 1:2135157/1‑69 (MQ=255)
aGACTAAAATACGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGTCAGCATCCACTACGTGTa > 1:173141/1‑68 (MQ=255)
aGACTAAAATACGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGTCAGCATCCACTACGTGTACCg > 1:1536669/1‑71 (MQ=255)
aCTAAAATATGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGTCAGCATCCACTACGTGTACCGca > 1:3524301/1‑71 (MQ=255)
aCTAAAATACGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGTCAGCATCCACTACGTGTAcc > 1:2594205/1‑68 (MQ=255)
cTAAAATACGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGt > 1:455131/1‑47 (MQ=255)
cTAAAATACGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGTCAGCATCCACTACGTGTACCGcac < 1:1552751/71‑1 (MQ=255)
aaaaTACGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGTCAGCATCCACTa < 1:2178436/57‑1 (MQ=255)
aaaTACGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGTCAGCATCCACTACGTGTACCGCACAgg > 1:3312946/1‑71 (MQ=255)
aaaTACGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGTCAGCATCCACTACGTGTACCGCACAgg > 1:3357933/1‑71 (MQ=255)
aaTACGCATTACAGAACCTTCACTGAAACCACTTCg < 1:2622073/36‑1 (MQ=255)
aaTACGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGTCAGCATCCACTAc < 1:2683654/56‑1 (MQ=255)
aaTACGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGTCAGCATCCACTACGTGTACCGCACAGGc < 1:1827922/71‑1 (MQ=255)
aTACGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGTCa < 1:2087347/44‑1 (MQ=255)
aTACGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGTCAGCATc < 1:3723369/49‑1 (MQ=255)
aTACGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGTCAGCATCCACTACGTGTACCGCACAGGcc < 1:1637165/71‑1 (MQ=255)
cGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGTCAg < 1:1410821/42‑1 (MQ=255)
|
CGCTTCGACAATCCGCACACCGATGGCTTCATCGGTCAGCAAAATATTGCCGACCCCTAAGACTAAAATACGCATTACAGAACCTTCACTGAAACCACTTCGTTGCCGTCAGCATCCACTACGTGTACCGCACAGGCC > W3110S.gb/3139868‑3140005
|
| 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
