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 |
|
A69 F1 I1 R1
|
20 |
59.3 |
3764421 |
95.9% |
3610079 |
75.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
2,562,715 |
G→A |
R317C (CGT→TGT) |
yfgA ← |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 2,562,715 | 0 | G | A | 98.5%
| 261.2
/ ‑3.7
| 66 | R317C (CGT→TGT) | yfgA | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (0/1); new base A (35/30); total (35/31) |
| Fisher's exact test for biased strand distribution p-value = 4.70e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.00e-01 |
CCCGTCTGTTACTGCGCCGGTGATTGTTCGGCATTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACGACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGCGGCTGGCGCACCAATTTTCAGTTTGTACG > REL606/2562642‑2562786
|
cccGTCTGTTACTGCGCCGGTGATTGTTCGGCATTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAaacaac < 1:1674980/76‑1 (MQ=255)
ccGTCTGTTACTGCGCCGGTGATTGTTCGGCATTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACt > 2:1839009/1‑76 (MQ=255)
ccGTCTGTTACTGCGCCGGTGATTGTTCGGCATTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACt > 1:999288/1‑76 (MQ=255)
cGTCTGTTACTGCGCCGGTGATTGTTCGGCATTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTc > 1:175098/1‑76 (MQ=255)
cTGTTACTGCGCCGGTGATTGTTCGGCATTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGa > 1:1250234/1‑76 (MQ=255)
tGTTACTGCGCCGGTGATTGTTCGGCATTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGAt < 2:1109553/76‑1 (MQ=255)
tGTTACTGCGCCGGTGATTGTTCGGCATTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGAt < 2:1453394/76‑1 (MQ=255)
gTTACTGCGCCGGTGATTGTTCGGCATTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGATc < 1:1144411/76‑1 (MQ=255)
ttACTGCGCCGGTGATTGTTCGGCATTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGATCg > 1:1097995/1‑76 (MQ=255)
tACTGCGCCGGTGATTGTTCGGCATTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGATCGa < 1:218119/76‑1 (MQ=255)
tACTGCGCCGGTGATTGTTCGGCATTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGATCGa > 1:294649/1‑76 (MQ=255)
tcTGCGCCGGTGATTGTTCGGCATTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGATCGAc < 1:1133725/75‑1 (MQ=255)
aCTGCGCCGGTGATTGTTCGGCATTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGATCGAc < 1:397865/76‑1 (MQ=255)
cTGCGCCGGTGATTGTTCGGCATTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGATCGACa < 1:1535318/76‑1 (MQ=255)
tGCGCCGGTGATTGTTCGGCATTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGATCGACAg < 2:1153868/76‑1 (MQ=255)
gcCGGTGATTGTTCGGCATTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGATCGACAGGtt < 1:1456334/76‑1 (MQ=255)
ccGGTGATTGTTCGGCATTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGATCGACAGGttt < 2:1243638/76‑1 (MQ=255)
ggTGATTGTTCGGCATTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTcc > 1:604339/1‑76 (MQ=255)
gTGATTGTTCGGCATTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAACCAACTCAGATCGACAGGTTTccc > 1:658720/1‑76 (MQ=255)
tGATTGTTCGGCATTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCt < 1:398716/76‑1 (MQ=255)
tGATTGTTCGGCATTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCt > 1:1401068/1‑76 (MQ=255)
tGATTGTTCGGCATTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCt < 1:1860194/76‑1 (MQ=255)
tGTTCGGCATTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGAt > 1:1020322/1‑76 (MQ=255)
gTTCGGCATTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATa > 1:1082080/1‑76 (MQ=255)
ttCGGCATTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATAc < 1:413509/76‑1 (MQ=255)
tCGGCATTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACGACTCAGATCGACAGGTTTCCCTTGATACt < 2:434346/76‑1 (MQ=255)
tCGGCATTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATACt < 1:585250/76‑1 (MQ=255)
cGGCATTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATACTg < 1:413942/76‑1 (MQ=255)
cGGCATTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATACTg > 1:577829/1‑76 (MQ=255)
gCATTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATACTGGa > 1:1329329/1‑76 (MQ=255)
aTTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATACTGCATc > 1:1751671/1‑76 (MQ=255)
ttGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATACTGGATCt < 2:300935/76‑1 (MQ=255)
gAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGt > 1:166207/1‑76 (MQ=255)
gAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGt < 2:1735292/76‑1 (MQ=255)
aGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTa > 1:1134521/1‑76 (MQ=255)
tCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGc > 1:413444/1‑76 (MQ=255)
tCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGc > 1:1343495/1‑76 (MQ=255)
tCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGc < 2:1202654/76‑1 (MQ=255)
tCAGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGc < 2:1163876/76‑1 (MQ=255)
aGACGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGCgg > 2:135938/1‑76 (MQ=255)
aCGCGCAACCTGGTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGCGGCt < 2:1329329/76‑1 (MQ=255)
cgcgCAACCTGGTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGCGGCTg < 1:324372/76‑1 (MQ=255)
cgcgCAACCTGGTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGCGGCTg < 1:1159301/76‑1 (MQ=255)
cgcAACCTGGTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGCGGCTGgc > 1:691938/1‑76 (MQ=255)
ccTGGTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGCGGCTGGCGCAcc > 1:1571705/1‑76 (MQ=255)
cTGGTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGCGGCTGGCGCACCa < 1:542855/76‑1 (MQ=255)
tGGTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGCGGCTGGCGCACCaa > 1:222556/1‑76 (MQ=255)
ggTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGCGGCTGGCGCACCAAt > 2:455254/1‑76 (MQ=255)
ggTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGCGGCTGGCGCACCAAt < 1:1539781/76‑1 (MQ=255)
ggTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGCGGCTGGCGCACCAAt > 1:1019535/1‑76 (MQ=255)
gTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGCGGCTGGCGCACCAAtt > 2:1183350/1‑76 (MQ=255)
gTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGCGGCTGGCGCACCAAtt > 1:1131887/1‑76 (MQ=255)
gTTAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGCGGCTGGCGCACCAAtt > 1:601048/1‑76 (MQ=255)
ttAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGCGGCTGGGGCACCAAttt > 2:980947/1‑76 (MQ=255)
ttAGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGCGGCTGGCGCACCAAttt > 1:1439218/1‑76 (MQ=255)
aGTTCTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGCGGCTGGCGCACCAATTTTc > 1:794142/1‑76 (MQ=255)
ttCTGATAAAACAACTCAGATCGACGGGTTTCCCTTGATACTGGATCTGTACTGCGGCTGGCGCACCAATTTTCAg < 1:1527194/76‑1 (MQ=255)
cTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGCGGCTGGCGCACCAATTTTTAGtt > 2:1200456/1‑76 (MQ=255)
cTGATAAAACAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGCGGCTGGCGCACCAATTTTCAGtt < 2:999288/76‑1 (MQ=255)
gagaaaaCAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGCGGCTGGCGCACCAATTTTCAGTTTg < 2:1543091/73‑1 (MQ=255)
gATAAAACAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGCGGCTGGCGCACCAATTTTCAGTTTg < 1:518713/76‑1 (MQ=255)
tAAAACAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGCGGCTGGCGCACCAATTTTCAGTTTGTa > 2:820228/1‑76 (MQ=255)
tAAAACAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGCGGCTGGCGCACCAATTTTCAGTTTGTa > 1:708706/1‑76 (MQ=255)
aaaaCAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGCGGCTGGCGCACCAATTTTCAGTTTGTAc < 2:1346612/76‑1 (MQ=255)
aaaaCAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGCGGCTGGCGCACCAATTTTCAGTTTGTAc < 2:601048/76‑1 (MQ=255)
aaaCAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGCGGCTGGCGCACCAATTTTTAGTTTGTACg > 2:771761/1‑76 (MQ=255)
aaaCAACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGCGGCTGGCGCACCAATTTTCAGTTTGTACg > 2:35528/1‑76 (MQ=255)
|
CCCGTCTGTTACTGCGCCGGTGATTGTTCGGCATTGAGGGTCAGACGCGCAACCTGGTTAGTTCTGATAAAACGACTCAGATCGACAGGTTTCCCTTGATACTGGATCTGTACTGCGGCTGGCGCACCAATTTTCAGTTTGTACG > REL606/2562642‑2562786
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
