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 F17 I0 R2
|
276 |
45.3 |
3729697 |
93.0% |
3468618 |
60.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,894,340 |
C→T |
23.7% |
W32* (TGG→TGA) |
ygcQ ← |
predicted flavoprotein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,894,340 | 0 | C | T | 23.7%
| 70.5
/ 19.7
| 38 | W32* (TGG→TGA) | ygcQ | predicted flavoprotein |
| Reads supporting (aligned to +/- strand): ref base C (16/13); new base T (5/4); total (21/17) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.52e-01 |
CGCTGCCACTGTTCCACCAACGCATCCAGCACCTGTTCCGCCACTACAGGCTGAGGTTCAATCTGCCAGTGCGCCAGGGTACAACCGCTGAAATCCTGCGCCGCCAGCCAGCTTGCTATTGCGGCATTCT > W3110S.gb/2894275‑2894404
|
cGCTGCCACTGTTCCACCAACGCATCCAGCACCTGTTCCGCCACTACAGGCTGAGGTTCAATCTGcc > 1:833612/1‑67 (MQ=255)
cGCTGCCACTGTTCCACCAACGCATCCAGCACCTGTTCCGCCACTACAGGCTGAGGTTCAATCTGTCAg > 1:786683/1‑69 (MQ=255)
cGCTGCCACTGTTCCACCAACGCATCCAGCACCTGTTCCGCCACTACAGGCTGAGGTTCAATCTGCCa > 1:3541334/1‑68 (MQ=255)
cGCTGCCACTGTTCCACCAACGCATCCAGCACCTGTTCCGCCACTACAGGCTGAGGTTCAATCTGCCAg > 1:495065/1‑69 (MQ=255)
cGCTGCCACTGTTCCACCAACGCATCCAGCACCTGTTCCGCCACTAAAGGCTGAGGTTCAATCTGcc > 1:2818290/1‑67 (MQ=255)
cGCTGACACTGTTCCACCAACGCATCCAGCACCTGTTCCGCCACTACAGGCTGAGGTTCAATCTGcc > 1:323404/1‑67 (MQ=255)
gTTCCACCAACGCATCCAGCACCTGTTCCGCCACTACAGGCTGAGGTTCAATCTGCCAGTGCGCCAggg > 1:2363996/1‑69 (MQ=255)
gTTCCACCAACGCATCCAGCACCTGTTCCGCCACTACAGGCTGAGGTTCAATCTGCCAGTGCGCCAgg > 1:2537725/1‑68 (MQ=255)
ccaccaACGCATCCAGCACCTGTTCCGCCACTACAGGCTGAGGTTCAATCTGTCAGTGCGCCAGGGt < 1:1221939/67‑1 (MQ=255)
aaCGCATCCAGCACCTGTTCCGCCACTACAGGCTGAGGTTCAATCTGCCAGTGCGCCAGGGTACAACCg > 1:2228646/1‑69 (MQ=255)
gCATCCAGCACCTGTTCCGCCACTACAGGCTGAGGTTCAATCTGCCAGTGCGCCAGGGTACAACCGCTg < 1:2175230/69‑1 (MQ=255)
gCATCCAGCACCTGTTCCGCCACTACAGGCTGAGGTTCAATCTGCCAGTGCGCCAGGGTACAACCGCTg < 1:2414570/69‑1 (MQ=255)
cATCCAGCACCTGTTCCGCCACTACAGGCTGAGGTTCAATCTGCCAGTGCGCCAGGGTACAACCGCTGa > 1:158201/1‑69 (MQ=255)
cATCCAGCACCTGTTCCGCCACTACAGGCTGAGGTTCAATCTGCCAGTGCGCCAGGGTACAACCGCTGa > 1:2678739/1‑69 (MQ=255)
tCCAGCACCTGTTCCGCCACTACAGGCTGAGGTTCAATCTGCCAGTGCGCCAGGGTACAACCGCTGaaa < 1:555210/69‑1 (MQ=255)
cAGCACCTGTTCCGCCACTACAGGCTGAGGTTCAATCTGCCAGTGCGCCAGGGTACAACCGCTGAAATc > 1:1996435/1‑69 (MQ=255)
cAGCACCTGTTCCGCCACTACAGGCTGAGGTTCAATCTGCCAGTGCGCCAGGGTACAACCGCTGAAATc > 1:2849148/1‑69 (MQ=255)
aCCTGTTCCGCCACTACAGGCTGAGGTTCAATCTGCCAGTGCGCCAGGGTACAACCGCTGAAATCCTgc < 1:3389354/69‑1 (MQ=255)
ccTGTTCCGCCACTACAGGCTGAGGTTCAATCTGCCAGTGCGCCAGGGTACAACCGCTGAAATCCTgcg > 1:1829726/1‑69 (MQ=255)
ccTGTTCCGCCACTACAGGCTGAGGTTCAATCTGCCAGTGCGCCAGGGTACAACCGCTGAAATCCTgcg > 1:1972685/1‑69 (MQ=255)
ccGCCACTACAGGCTGAGGTTCAATCTGTCAGTGCGCCAGGGTACa > 1:1663705/1‑46 (MQ=255)
gCCACTACAGGCTGAGGTTCAATCTGTCAGTGCGCCAGGGTACAACCGCTGaa < 1:2632577/53‑1 (MQ=255)
aCAGGCTGAGGTTCAATCTGCCAGTGCGCCAGGGTACAACCGCTGa < 1:1273710/46‑1 (MQ=255)
aCAGGCTGAGGTTCAATCTGCCAGTGCGCCAGGGTACAACCGCTGa < 1:284882/46‑1 (MQ=255)
aCAGGCTGAGGTTCAATCTGCCAGTGCGCCAGGGTACAACCGCTGAAATc > 1:680478/1‑50 (MQ=255)
aCAGGCTGAGGTTCAATCTGCCAGTGCGCCAGGGTACAACCGCTGAAATc > 1:2421321/1‑50 (MQ=255)
cAGGCTGAGGTTCAATCTGCCAGTGCGCCAGGGTACAACCGCTGAAATCCTGCGCCGCCAGCCAGCtt > 1:45497/1‑68 (MQ=255)
ggCTGAGGTTCAATCTGCCAGTGCGCCAGGGTACAACCGCTGAAATCCTGCGCCGCCAGCCAGCTTGCt < 1:2483467/69‑1 (MQ=255)
ggCTGAGGTTCAATCTGCCAGTGCGCCAGGGTACAACCGCTGAAATCCTGCGCCGCCAGCCAGCTTGCt < 1:792313/69‑1 (MQ=255)
ggCTGAGGTTCAATCTGCCAGTGCGCCAGGGTACAACCGCTGAAATCCTGCGCCGCCAGCCAGCTTGCt < 1:2723479/69‑1 (MQ=255)
gCTGAGGTTCAATCTGTCAGTGCGCCAGGGTACAAc > 1:3326284/1‑36 (MQ=255)
tGAGGTTCAATCTGCCAGTGCGCCAGGGTACAACCGCTGAAATcc > 1:2407382/1‑45 (MQ=255)
aGGTTCAATCTGTCAGTGCGCCAGGGTACAACCGCTGAAATCCTGCGCCGCCAGCCAGCTTGCTATTGc > 1:1753460/1‑69 (MQ=255)
gTTCAATCTGCCAGTGCGCCAGGGTACAACCGCTGAAATCCTGCGCCGCCAGCCAGCTTGCTATTGCgg < 1:3453641/69‑1 (MQ=255)
ttCAATCTGTCAGTGCGCCAGGGTACAACCGCTGAAATCCTGCGCCGCCAGCCAGCTTGCTATTGCGGc > 1:2121328/1‑69 (MQ=255)
tCAATCTGTCAGTGCGCCAGGGTACAACCGCTGAAATCCTGCGCCGCCAGCCAGCTTGCTATTGCGGCa < 1:2163615/69‑1 (MQ=255)
aTCTGCCAGTGCGCCAGGGTACAACCGCTGAAATCCTGCGCCGCCAGCCAGCTTGCTATTGCGGCAtt < 1:1213186/68‑1 (MQ=255)
aTCTGCCAGTGCGCCAGGGTACAACCGCTGAAATCCTGCGCCGCCAGCCAGCTTGCTATTGCGGCAtt < 1:2021698/68‑1 (MQ=255)
tCTGCCAGTGCGCCAGGGTACAACCGCTGAAATCCTgcgc > 1:1879371/1‑40 (MQ=255)
tCTGCCAGTGCGCCAGGGTACAACCGCTGAAATCCTGCGCCGCCAGCCAGCTTGCTATTGCGGCATtc < 1:1900434/68‑1 (MQ=255)
cTGTCAGTGCGCCAGGGTACAACCGCTGAAATCCTGCGCCGCCAGCCAGCTTGCTATTGCGGCATtct < 1:78433/68‑1 (MQ=255)
|
CGCTGCCACTGTTCCACCAACGCATCCAGCACCTGTTCCGCCACTACAGGCTGAGGTTCAATCTGCCAGTGCGCCAGGGTACAACCGCTGAAATCCTGCGCCGCCAGCCAGCTTGCTATTGCGGCATTCT > W3110S.gb/2894275‑2894404
|
| 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
