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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,776,358 |
G→T |
33.3% |
L16L (CTG→CTT) |
yfiB → |
predicted outer membrane lipoprotein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,776,358 | 0 | G | T | 33.3%
| 30.3
/ 16.6
| 30 | L16L (CTG→CTT) | yfiB | predicted outer membrane lipoprotein |
| Reads supporting (aligned to +/- strand): ref base G (10/10); new base T (5/5); total (15/15) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AGATAACAAGGATATATCGATATGATAAAGCACCTGGTAGCACCCCTGGTTTTCACCTCACTAATACTGACTGGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTGAGCAAGTCGCCGCTATGCAATCTTATGGATT > minE/1776290‑1776426
|
agaTAACAAGGATATATCGATATGATAAAGCACCTGGTAGCACCCCTGGTTTTCACCTCACTAATactg < 1:2838722/69‑1 (MQ=255)
agaTAACAAGGATATATCGATATGATAAAGCACCTGGTAGCACCCCTGGTTTTCACCTCACTAATactg < 1:1738447/69‑1 (MQ=255)
atatCGATATGATAAAGCACCTGGTAGCACCCCTGGTTTTCACCTCACTAATACTGACTGGCTGCCAGt < 1:1105060/69‑1 (MQ=255)
atatCGATATGATAAAGCACCTGGTAGCACCCCTGGTTTTCACCTCACTAATACTGACTGGCTGCCAGt < 1:2587874/69‑1 (MQ=255)
atatCGATATGATAAAGCACCTGGTAGCACCCCTGGTTTTCACCTCACTAATACTGACTGGCTGCCAGt < 1:2782386/69‑1 (MQ=255)
tCGATATGATAAAGCACCTGGTAGCACCCCTGGTTTTCACCTCACTAATACTGACTGGCTGCCAGTccc > 1:850751/1‑69 (MQ=255)
tCGATATGATAAAGCACCTGGTAGCACCCCTGGTTTTCACCTCACTAATACTGACTGGCTGCCAGTccc > 1:2648371/1‑69 (MQ=255)
tCGATATGATAAAGCACCTGGTAGCACCCCTGGTTTTCACCTCACTAATACTGACTGGCTGCCAGTccc > 1:564183/1‑69 (MQ=255)
aaGCACCTGGTAGCACCCCTGGTTTTCACCTCACTAATACTGACTGGCTGCCAGTCCCCTCAGGGAAAg < 1:2415376/69‑1 (MQ=255)
aaGCACCTGCTAGCACCCCTGATTTTCACCTCGCTAATACTTACTGGCTGCCAGTCCCCTCAGGGAAAg > 1:1345237/1‑69 (MQ=255)
aaGCACCTGCTAGCACCCCTGATTTTCACCTCGCTAATACTTACTGGCTGCCAGTCCCCTCAGGGAAAg > 1:727844/1‑69 (MQ=255)
aaGCACCTGCTAGCACCCCTGATTTTCACCTCGCTAATACTTACTGGCTGCCAGTCCCCTCAGGGAAAg > 1:1339137/1‑69 (MQ=255)
gCACCTGGTAGCACCCCTGGTTTTCACCTCACTAATACTGACTGGCTGCCAGTCCCCTCAGGGAAAGtt < 1:2310587/69‑1 (MQ=255)
gCACCTGGTAGCACCCCTGGTTTTCACCTCACTAATACTGACTGGCTGCCAGTCCCCTCAGGGAAAGtt < 1:1797482/69‑1 (MQ=255)
gCACCTGGTAGCACCCCTGGTTTTCACCTCACTAATACTGACTGGCTGCCAGTCCCCTCAGGGAAAGtt < 1:1825689/69‑1 (MQ=255)
agaaCCCCTGGTTTTCACCTCACTAATACTGACTGGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTg > 1:625271/4‑68 (MQ=255)
aGCACCCCTGGTTTTCACCTCACTAATACTGACTGGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTg > 1:2783184/1‑68 (MQ=255)
gTTTTCACCTCACTAATACTGACTGGCTGCCAGTCCCCTCAGGGAAAGTTTAGTCCTGAGCAAGTcgcc > 1:3210366/1‑69 (MQ=255)
gTTTTCACCTCACTAATACTGACTGGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTGAGCAAGTcgcc > 1:2754357/1‑69 (MQ=255)
gTTTTCACCTCACTAATACTGACTGGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTGAGCAAGTcgcc > 1:3176491/1‑69 (MQ=255)
gTTTTCACCTCACTAATACTGACTGGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTGAGCAAGTcgc > 1:2811819/1‑68 (MQ=255)
tttCACCTCACTAATACTGACTGGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTGAGCAAGTcgccgc < 1:2594862/69‑1 (MQ=255)
tttCACCTCACTAATACTGACTGGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTGAGCAAGTcgccgc < 1:537631/69‑1 (MQ=255)
ttCACCTCACTAATACTGACTGGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTGAGCAAGTCGCCGCt > 1:172842/1‑69 (MQ=255)
tAATACTTACTGGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTGAGCAAGTCGCCGCTATGCAATc < 1:1065184/67‑1 (MQ=255)
tAATACTTACTGGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTGAGCAAGTCGCCGCTATGCAATc < 1:2961487/67‑1 (MQ=255)
tAATACTTACTGGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTGAGCAAGTCGCCGCTATGCAATc < 1:338385/67‑1 (MQ=255)
tAATACTTACTGGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTGAGCAAGTCGCCGCTATGCAATc < 1:37543/67‑1 (MQ=255)
tAATACTTACTGGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTGAGCAAGTCGCCGCTATGCAATc < 1:1753512/67‑1 (MQ=255)
tAATACTTACTGGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTGAGCAAGTCGCCGCTATGCAATCtt > 1:1815851/1‑69 (MQ=255)
tAATACTTACTGGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTGAGCAAGTCGCCGCTATGCAATCtt > 1:1445275/1‑69 (MQ=255)
tAATACTGACTGGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTGAGCAAGTCGCCGCTATGCAATCt < 1:389276/68‑1 (MQ=255)
actgactgGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTGAGCAAGTCGCCGCTATGCAATCTTATgg > 1:2308842/1‑69 (MQ=255)
actgactgGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTGAGCAAGTCGCCGCTATGCAATCTTATgg > 1:2181859/1‑69 (MQ=255)
actgactgGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTGAGCAAGTCGCCGCTATGCAATCTTATgg > 1:2466723/1‑69 (MQ=255)
actgactgGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTGAGCAAGTCGCCGCTATGCAATCTTATgg > 1:1366404/1‑69 (MQ=255)
ctgactgGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTGAGCAAGTCGCCGCTATGCAATCTTATGGa > 1:713675/1‑69 (MQ=255)
gactgGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTGAGCAAGTCGCCGCTATGCAATCTTATGGAtt > 1:1032050/1‑69 (MQ=255)
gactgGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTGAGCAAGTCGCCGCTATGCAATCTTATGGAtt < 1:1180057/69‑1 (MQ=255)
gactgGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTGAGCAAGTCGCCGCTATGCAATCTTATGGAtt > 1:67127/1‑69 (MQ=255)
gactgGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTGAGCAAGTCGCCGCTATGCAATCTTATGGAtt > 1:1304560/1‑69 (MQ=255)
gactgGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTGAGCAAGTCGCCGCTATGCAATCTTATGGAtt < 1:1392763/69‑1 (MQ=255)
gactgGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTGAGCAAGTCGCCGCTATGCAATCTTATGGAtt < 1:3037979/69‑1 (MQ=255)
gactgGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTGAGCAAGTCGCCGCTATGCAATCTTATGGAtt > 1:1907288/1‑69 (MQ=255)
gactgGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTGAGCAAGTCGCCGCTATGCAATCTTATGGAtt < 1:2953903/69‑1 (MQ=255)
gactgGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTGAGCAAGTCGCCGCTATGCAATCTTATGGAtt < 1:1914560/69‑1 (MQ=255)
gactgGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTGAGCAAGTCGCCGCTATGCAATCTTATGGAtt < 1:2070853/69‑1 (MQ=255)
gactgGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTGAGCAAGTCGCCGCTATGCAATCTTATGGAt > 1:1570487/1‑68 (MQ=255)
|
AGATAACAAGGATATATCGATATGATAAAGCACCTGGTAGCACCCCTGGTTTTCACCTCACTAATACTGACTGGCTGCCAGTCCCCTCAGGGAAAGTTTACTCCTGAGCAAGTCGCCGCTATGCAATCTTATGGATT > minE/1776290‑1776426
|
| 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
