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 |
|
A6 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,712,236 |
C→T |
24.0% |
A1066T (GCT→ACT) |
yphG ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,712,236 | 0 | C | T | 24.0%
| 90.3
/ 23.9
| 50 | A1066T (GCT→ACT) | yphG | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base C (21/17); new base T (6/6); total (27/23) |
| 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 |
AAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTT > minE/1712166‑1712305
|
aaaaTAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAgc < 1:3887322/71‑1 (MQ=255)
aTAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAgcgc > 1:3843902/1‑70 (MQ=255)
aaGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGTGCGAGCa < 1:1073108/71‑1 (MQ=255)
aGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAg > 1:3122773/1‑68 (MQ=255)
cATCACGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGTGCGAGCAGACt < 1:2805691/71‑1 (MQ=255)
cATCACGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACt < 1:2030014/71‑1 (MQ=255)
tCACGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGTGCGAGCAGAc < 1:16780/68‑1 (MQ=255)
aCGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCata > 1:322798/1‑71 (MQ=255)
aCGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCata > 1:2707181/1‑71 (MQ=255)
tgAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCata < 1:2688731/64‑1 (MQ=255)
ataatGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCa > 1:3141184/1‑53 (MQ=255)
ataatGCCGCTTTCGGACAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAAcc > 1:1881214/1‑71 (MQ=255)
atGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGTGCGAGCAGACTCATATTGCGCAACCTcc < 1:2058041/71‑1 (MQ=255)
atGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTcc > 1:2096059/1‑71 (MQ=255)
tGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTccc > 1:3614372/1‑71 (MQ=255)
ccGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTGATATTGCGCAACCTcccc > 1:3723093/1‑70 (MQ=255)
cGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCTCAACCTCCCCGa < 1:749680/71‑1 (MQ=255)
cGCTTTCGG‑CAAGCCGGATTAATCGCCGTCAATTCAGTGCGAGCAGACTCATATTGCGCAACCTCCCCGa < 1:1017114/70‑1 (MQ=255)
gCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAg > 1:502624/1‑71 (MQ=255)
cTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGTGCGAGCAGACTCATATTGCGCAACCTCCCCGAGt > 1:2093884/1‑71 (MQ=255)
tttCGGCCAAGCCGGATTAATCGCCGTCAATTCAGTGCGAGCAGACTCATATTGCGCa < 1:386189/58‑1 (MQ=255)
tCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTg > 1:1072036/1‑52 (MQ=255)
tCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTccc > 1:338083/1‑71 (MQ=255)
tCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTcc < 1:3634929/70‑1 (MQ=255)
cGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAg < 1:1617189/38‑1 (MQ=255)
cGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTccc < 1:2139563/70‑1 (MQ=255)
ggCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAAcc > 1:3892772/1‑57 (MQ=255)
gCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCcgcg < 1:2273409/71‑1 (MQ=255)
gCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCCCCCCGAGTCCcgcg < 1:1418593/71‑1 (MQ=255)
ccAAGCCGGATTAATCGCCGTCAATTCAGTGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCcgcg > 1:1887390/1‑70 (MQ=255)
cAAGCCGGATTAATCGCCGTCAATTCAGTGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGa > 1:760380/1‑71 (MQ=255)
cAAGCCGGATTAATCGCCGTCAATTCAGTGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGa > 1:1016383/1‑71 (MQ=255)
aaGCCGGATTAATCGCCGTCAATTCAGTGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGa > 1:820701/1‑70 (MQ=255)
aaGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATAtt > 1:2089673/1‑45 (MQ=255)
aaGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGAc > 1:2179658/1‑71 (MQ=255)
aaGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGAc > 1:1019680/1‑71 (MQ=255)
ccGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATAtt < 1:2077332/42‑1 (MQ=255)
ccGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTc > 1:3773033/1‑52 (MQ=255)
ccGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGcc < 1:1190907/71‑1 (MQ=255)
aTTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGc < 1:603116/70‑1 (MQ=255)
aTTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCa < 1:2809243/71‑1 (MQ=255)
ttAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCa > 1:1029465/1‑70 (MQ=255)
ttAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCAt < 1:2019366/71‑1 (MQ=255)
tAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATc > 1:2101800/1‑71 (MQ=255)
aTCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACCCCAGCATCg < 1:3158132/70‑1 (MQ=255)
gCCGTCAATTCAGTGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCg > 1:2799654/1‑67 (MQ=255)
cGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCACCATCGccacca < 1:503243/71‑1 (MQ=255)
gTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCAt < 1:2523190/71‑1 (MQ=255)
aaTTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCa < 1:350793/70‑1 (MQ=255)
ttCAGCGCGAGCAGACTCATATTGCGCAACCTCCCGGAGTCCcg > 1:624132/1‑44 (MQ=255)
ttCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCa > 1:1975865/1‑56 (MQ=255)
cAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCAt > 1:3361148/1‑71 (MQ=255)
gcgcGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCAttt > 1:3591900/1‑71 (MQ=255)
|
AAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTT > minE/1712166‑1712305
|
| 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
