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 |
794,838 |
C→T |
40.4% |
E153K (GAA→AAA) |
ldcA ← |
L,D‑carboxypeptidase A |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 794,838 | 0 | C | T | 40.4%
| 15.8
/ 26.0
| 42 | E153K (GAA→AAA) | ldcA | L,D‑carboxypeptidase A |
| Reads supporting (aligned to +/- strand): ref base C (15/10); new base T (11/6); total (26/16) |
| 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 |
CACAACGTGCCTTCGGCCCGACATGTCGGGCCTTCCCCTTGCCATTCAATGGTGAAGGTTTCATTGCGTAACGCCAGCCAGAAATGGTGCTCGGTAAAGGCGTTCAGTTCATCCGCGCCAAAGTTTGC > minE/794777‑794904
|
cacaACGTGCCTTCGGCCCGACATGTCGGGCCTTCCCCTTGCCATTCAATGGTGAAGGTTTCATTGCGt < 1:2597/69‑1 (MQ=255)
cacaACGTGCCTTCGGCCCGACATGTCGGGCCTTCCCCTTGCCATTCAATGGTGAAGGTTTCATTGCGt < 1:1947233/69‑1 (MQ=255)
cacaACGGGCCTTCGGCCCGACATGTCGGGCCTTCCCCTTGCCATTCAATGGTGAAGGTTTCATTGCGt < 1:2740739/69‑1 (MQ=255)
acaACGTGCCTTCGGCCCGACATGTCGGGCCTTCCCCTTGCCATTCAATGGTGAAGGTTTc < 1:549428/61‑1 (MQ=255)
cccGACATGTCGGGCCTTCCCCTTGCCATTCAATGGTGAAGGTTTCATTGCGTAACGCCAGCCAGAAAt < 1:2911194/69‑1 (MQ=255)
cccGACATGTCGGGCCTTCCCCTTGCCATTCAATGGTGAAGGTTTCATTGCGTAACGCCAGCCAGAAAt < 1:174688/69‑1 (MQ=255)
ccGACATGTCGGGCCTTCCCCTTGCCATTCAATGGTGAAGGTTTCATTGCGTAACGCCAGCCAGAAAt < 1:1148402/68‑1 (MQ=255)
ccGACATGTCGGGCCTTCCCCTTGCCATTCAATGGTGAAGGTTTCATTGCGTAACGCCAGCCAGAAAt < 1:2501183/68‑1 (MQ=255)
ccGACATGTCGGGCCTTCCCCTTGCCACTCAATGGTGAAGGTTTCATTGCGTAACGCCAGCCAGAAAt < 1:348761/68‑1 (MQ=255)
aTGTCGGGCCTTCCCCTTGCCATTCAATGGTGAAGGTTTc < 1:1170029/40‑1 (MQ=255)
aTGTCGGGCCTTCCCCTTGCCATTCAATGGTGAAGGTTTc < 1:2408006/40‑1 (MQ=255)
aTGTCGGGCCTTCCCCTTGCCATTCAATGGTGAAGGTTTc < 1:3121166/40‑1 (MQ=255)
aTGTCGGGCCTTCCCCTTGCCATTCAATGGTGAAGGTTTc < 1:2192795/40‑1 (MQ=255)
aTGTCGGGCCTTCCCCTTGCCATTCAATGGTGAAGGTTTc < 1:2146179/40‑1 (MQ=255)
aTGTCGGGCCTTCCCCTTGCCATTCAATGGTGAAGGTTTc < 1:851390/40‑1 (MQ=255)
aTGTCGGGCCTTCCCCTTGCCATTCAATGGTGAAGGTTTc < 1:828487/40‑1 (MQ=255)
aTGTCGGGCCTTCCCCTTGCCATTCAATGGTGAAGGTTTc < 1:610298/40‑1 (MQ=255)
cGGGCCTTCCCCTTGCCATTCAATGGTGAACGTTTTAt > 1:270384/1‑38 (MQ=38)
cGGGCCTTCCCCTTGCCATTCAATGGTGAACGTTTTAt > 1:1931951/1‑38 (MQ=38)
cGGGCCTTCCCCTTGCCATTCAATGGTGAACGTTTTAt > 1:2886645/1‑38 (MQ=38)
cGGGCCTTCCCCTTGCCATTCAATGGTGAACGTTTTAt > 1:1265334/1‑38 (MQ=38)
cGGGCCTTCCCCTTGCCATTCAATGGTGAACGTTTTAt > 1:2461423/1‑38 (MQ=38)
cGGGCCTTCCCCTTGCCATTCAATGGTGAACGTTTTAt > 1:794289/1‑38 (MQ=38)
cGGGCCTTCCCCTTGCCATTCAATGGTGAACGTTTTAt > 1:1621516/1‑38 (MQ=38)
cGGGCCTTCCCCTTGCCATTCAATGGTGAACGTTTTAt > 1:1637834/1‑38 (MQ=38)
cGGGCCTTCCCCTTGCCATTCAATGGTGAACGTTTTAt > 1:1653493/1‑38 (MQ=38)
cGGGCCTTCCCCTTGCCATTCAATGGTGAACGTTTTAt > 1:3355773/1‑38 (MQ=38)
cGGGCCTTCCCCTTGCCATTCAATGGTGAACGTTTTAt > 1:595895/1‑38 (MQ=38)
cTTCCCCTTGCCATTCAATGGTGAAGGTTTCATTGCGTAACGCCTGCCAGAAATGGTGCTCGGTAAAgg > 1:3021604/1‑69 (MQ=255)
cTTCCCCTTGCCATTCAATGGTGAAGGTTTCATTGCGTAACGCCAGCCAGAAATGGTGCTCGGTAAAgg > 1:3261807/1‑69 (MQ=255)
cTTCCCCTTGCCATTCAATGGTGAAGGTTTCATTGCGTAACGCCAGCCAGAAATGGTGCTCGGTAAAgg > 1:25379/1‑69 (MQ=255)
cTTCCCCTTGCCATTCAATGGTGAAGGTTTCATTGCGTAACGCCAGCCAGAAATGGTGCTCGGTAAAgg > 1:1228236/1‑69 (MQ=255)
cTTCCCCTTGCCATTCAATGGTGAAGGTTTCATTGCGTAACGCCAGCCAGAAATGGTGCTCGGTAAAgg > 1:1695986/1‑69 (MQ=255)
cccTTGCCATTCAATGGTGAAGGTTTCATTGCGTAACGCCAGCCAGAAATGGTGCTCGGTAAAGGCg > 1:996682/1‑67 (MQ=255)
cccTTGCCATTCAATGGTGAAGGTTTCATTGCGTAACGCCAGCCAGAAATGGTGCTCGGTAAAGGCg > 1:1708763/1‑67 (MQ=255)
ccATTCAATGGTGAAGGTTTCATTGCGTAACGCAAGCCAGAAAt < 1:2989408/44‑1 (MQ=255)
aaGGTTTCATTGCGTAACGCCAGCCAGAAATGGTGCTCGGTAAAGGCGTTCAGTTCATCCGCGCCAAAg > 1:2669052/1‑69 (MQ=255)
aaGGTTTCATTGCGTAACGCCAGCCAGAAATGGTGCTCGGTAAAGGCGTTCAGTTCATCCGCGCCAAAg > 1:1600958/1‑69 (MQ=255)
aaGGTTTCATTGCGTAACGCCAGCCAGAAATGGTGCTCGGTAAAGGCGTTCAGTTCATCCGCGCCAAAg > 1:2887722/1‑69 (MQ=255)
ggTTTCATTGCGTAACGCCAGCCAGAAATGGTGCTCGGTAAAGGCGTTCAGTTCATCCGCGCCAAAGtt > 1:2024665/1‑69 (MQ=255)
ggTTTCATTGCGTAACGCCAGCCAGAAATGGTGCTCGGTAAAGGCGTTCAGTTCATCCGCGCCAAAGtt > 1:149175/1‑69 (MQ=255)
ggTTTCATTGCGTAACGCCAGCCAGAAATGGTGCTCGGTAAAGGCGTTCAGTTCATCCGCGCCAAAGtt > 1:925411/1‑69 (MQ=255)
ggTTTCATTGCGTAACGCCAGCCAGAAATGGTGCTCGGTAAAGGCGTTCAGTTCATCCGCGCCAAAGt > 1:144710/1‑68 (MQ=255)
cgTTTTATTGCGTAACGCCAGCCAGAAGTGGTGCTCGGTaa < 1:2969806/40‑1 (MQ=37)
cgTTTTATTGCGTAACGCCAGCCAGAAGTGGTGCTCGGTaa < 1:2249306/40‑1 (MQ=37)
cgTTTTATTGCGTAACGCCAGCCAGAAGTGGTGCTCGGTaa < 1:2249249/40‑1 (MQ=37)
cgTTTTATTGCGTAACGCCAGCCAGAAGTGGTGCTCGGTaa < 1:2057109/40‑1 (MQ=37)
cgTTTTATTGCGTAACGCCAGCCAGAAGTGGTGCTCGGTaa < 1:2358950/40‑1 (MQ=37)
cgTTTTATTGCGTAACGCCAGCCAGAAGTGGTGCTCGGTaa < 1:2808924/40‑1 (MQ=37)
ttCATTGCGTAACGCCAGCCAGAAATGGTGCTCGGTAAAGGCGTTCAGTTCATCCGCGCCAAAGTTTGc > 1:166624/1‑69 (MQ=255)
ttCATTGCGTAACGCCAGCCAGAAATGGTGCTCGGTAAAGGCGTTCAGTTCATCCGCGCCAAAGTTTGc < 1:2683285/69‑1 (MQ=255)
tacATTGCGTAACGCCAGCCAGAAATGGTGCTCGGTAAAGGCGTTCAGTTCATCCGCGCCAAAGTTTGc < 1:2605693/67‑1 (MQ=255)
|
CACAACGTGCCTTCGGCCCGACATGTCGGGCCTTCCCCTTGCCATTCAATGGTGAAGGTTTCATTGCGTAACGCCAGCCAGAAATGGTGCTCGGTAAAGGCGTTCAGTTCATCCGCGCCAAAGTTTGC > minE/794777‑794904
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
