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 |
|
A1 F8 I0 R2
|
422 |
46.8 |
3726540 |
94.7% |
3529033 |
61.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,910,539 |
C→A |
100% |
R590L (CGC→CTC) |
relA ← |
(p)ppGpp synthetase I/GTP pyrophosphokinase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,910,539 | 0 | C | A | 93.6%
| 118.5
/ 3.9
| 47 | R590L (CGC→CTC) | relA | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| Reads supporting (aligned to +/- strand): ref base C (3/0); new base A (20/24); total (23/24) |
| Fisher's exact test for biased strand distribution p-value = 1.09e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.74e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
GATGTGGTGCATCAGGTTGCCAACACCTTCGACTACCACGCGACCGTTATCTTTACTGCGGTTTTGCGGCGTGTAGCTTTTTTGCTGAAGTTGCTTCAGCGCGGCGGCGTCCTGCTCTTC > W3110S.gb/2910481‑2910600
|
gATGTGGTGCATCAGGTTGCCAACACCTTCGACTACCACGCGACCGTTATCTTTACTGAGGTTTTgcggcg < 1:599054/71‑1 (MQ=255)
gtgCATCAGGTTGCCAACACCTTCGACTACCACGCGACCGTTATCTTTACTGAGGTTTTg > 1:106490/1‑60 (MQ=255)
gtgCATCAGGTTGCCAACACCTTCGACTACCACGCGACCGTTATCTTTACTGAGGTTTTg > 1:1763460/1‑60 (MQ=255)
gtgCATCAGGTTGCCAACACCTTCGACTACCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGc > 1:3080793/1‑71 (MQ=255)
cATCAGGTTGCCAACACCTTCGACTACCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCtt < 1:2903693/70‑1 (MQ=255)
cATCAGGTTGCCAACACCTTCGACTACCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCtt < 1:1815373/70‑1 (MQ=255)
cATCAGGTTGCCAACACCTTCGACTACCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCtt < 1:3566331/70‑1 (MQ=255)
cATCAGGTAGCCAACACCTTCGACTACCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCtt < 1:236433/70‑1 (MQ=255)
aGGTTGCCAACACCTTCGACTACCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCtttttt > 1:1981890/1‑70 (MQ=255)
gCCAACACCTTCGACTACCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCTTTTTTGCTGa < 1:2928402/70‑1 (MQ=255)
gCCAACACCTTCGACTACCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCTTTTTTGCTGa < 1:370793/70‑1 (MQ=255)
gCCAACACCTTCGACTACCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCTTTTTTGCTGa < 1:649088/70‑1 (MQ=255)
gCCAACACCTTCGACTACCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCTTTTTTGCTGa < 1:2056868/70‑1 (MQ=255)
cacCTTCGACTACCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCTTTTTTGCTGAAGtt < 1:2192378/69‑1 (MQ=255)
cacCTTCGACTACCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCTTTTTTGCTGAAGtt < 1:1019518/69‑1 (MQ=255)
cacCTTCGACTACCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCTTTTTTGCTGAAGtt < 1:2161138/69‑1 (MQ=255)
cacCTTCGACTACCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCTTTTTTGCTGAAGtt < 1:1948668/69‑1 (MQ=255)
ttCGACTACCACGCGACCGTTATCTTTACTGCGGTTTTgcggc > 1:1147492/1‑43 (MQ=255)
ttCGACTACCACGCGACCGTTATCTTTACTGCGGTTTTGCGGCGTGTAGCttttt > 1:1088335/1‑55 (MQ=255)
ttCGACTACCACGCGACCGTTATCTTTACTGAGGttt > 1:1153927/1‑37 (MQ=255)
ttCGACTACCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCtttt > 1:2475490/1‑54 (MQ=255)
tCGACTACCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCTTTTTTGCTGAAGTTGCTTCAg > 1:194778/1‑71 (MQ=255)
tCGACTACCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCTTTTTTGCTGAAGTTGCTTCAg > 1:1901659/1‑71 (MQ=255)
cGACTACCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCTTTTTTGCTGAAGTTGCTTCAgc > 1:1158624/1‑71 (MQ=255)
gACTACCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCtt < 1:324462/49‑1 (MQ=255)
tACCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCTTTTTTGCTGAAGTTGCTTCAGCgcgg > 1:3064513/1‑71 (MQ=255)
aCCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCgtgt > 1:687327/1‑40 (MQ=255)
aCCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCttttt > 1:1915483/1‑48 (MQ=255)
aCCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCttttt > 1:495620/1‑48 (MQ=255)
aCCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCttttt > 1:1294257/1‑48 (MQ=255)
aCCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCttttt > 1:1651126/1‑48 (MQ=255)
aCCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCTTTTTTGCTGAAGTTGc > 1:1308632/1‑60 (MQ=255)
ccACGCGACCGTTATCTTTACTGAGGTTTTGCGGCgtg > 1:82774/1‑38 (MQ=255)
ccACGCGACCGTTATCTTTACTGAGGTTTTGCGGCgtg > 1:539053/1‑38 (MQ=255)
ccACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCTTTTTTGCTGAAGTTGCTTCAGCgcggcg > 1:234141/1‑71 (MQ=255)
ccACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCTTTTTTGCTGAAGTTGCTTAAGCgcggcg > 1:2796062/1‑71 (MQ=255)
cGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCTTTTTTGCTGAAGTTGCTTCAGCGCGGCGGCGTCCTGc < 1:2690655/71‑1 (MQ=255)
cGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCTTTTTTGCTGAAGTTGCTTCAGCGCGGCGGCGTCCTGc < 1:3280833/71‑1 (MQ=255)
cGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCTTTTTTGCTGAAGTTGCTTCAGCGCGGCGGCGTCCTGc < 1:354720/71‑1 (MQ=255)
cGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCTTTTTTGCTGAAGTTGCTTCAGCGCGGCGGCGTCCTGc < 1:1871580/71‑1 (MQ=255)
cGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCTTTTTTGCTGAAGTTGCTTCAGCGCGGCGGCGTCCTGc < 1:1900440/71‑1 (MQ=255)
aTCTTTACTGCGGTTTTGCGGCGTGTAGCTTTTTTGCTGAAGTTGCTTCAGCGCGGCGGCGTCCTGCTCtt > 1:1989024/1‑71 (MQ=255)
tCTTTACTGAGGTTTTGCGGCGTGTAGCTTTTTTGCTGa < 1:1229931/39‑1 (MQ=255)
tCTTTACTGAGGTTTTGCGGCGTGTAGCTTTTTTGCTGa < 1:2297484/39‑1 (MQ=255)
tCTTTACTGAGGTTTTGCGGCGTGTAGCTTTTTTGCTGa < 1:1854102/39‑1 (MQ=255)
tACTGAGGTTTTGCGGCGTGTAGCTTTTTTGCTGAAGTTGCTTCAGCGCGGCGGCGTCCTGCTCTTc < 1:737202/67‑1 (MQ=255)
tACTGAGGTTTTGCGGCGTGTAGCTTTTTTGCTGAAGTTGCTTCAGCGCGGCGGCGTCCTGCTCTTc < 1:2797933/67‑1 (MQ=255)
|
GATGTGGTGCATCAGGTTGCCAACACCTTCGACTACCACGCGACCGTTATCTTTACTGCGGTTTTGCGGCGTGTAGCTTTTTTGCTGAAGTTGCTTCAGCGCGGCGGCGTCCTGCTCTTC > W3110S.gb/2910481‑2910600
|
| 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
