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 |
240,006 |
T→C |
100% |
L315L (CTA→CTG) |
araJ ← |
predicted transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 240,006 | 0 | T | C | 76.4%
| 23.0
/ 2.4
| 21 | L315L (CTA→CTG) | araJ | predicted transporter |
| Reads supporting (aligned to +/- strand): ref base T (5/0); new base C (14/2); total (19/2) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.88e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CGCTATTTGCCCACCTGCGGCACCTAATAACTCTCCGCCTTTGGCGTTTTGTAGTAACAATATTTGTAGCGGTGCTGAAAGGGCAAATAATCCCGCGCAACAAATAAAAGCAAAAATA > minE/239955‑240072
|
cGCTATTTGCCCACCTGCGGCACCTAATAACTCTCCGCCTTTGGCATTTTGCAGTAACAATATTTGCAg < 1:1659183/69‑1 (MQ=255)
cGCTATTTGCCCACCTGCGGCACCTAATAACTCTCCGCCTTTGGCATTTTGCAGTAACAATATTTGCAg < 1:2188125/69‑1 (MQ=255)
gCGGCACCTAATAACTCTCCGCCTTTGGCGTTTTGTAGTAACAATATTTGTAGCGGTGCTGAAAGGGCa > 1:3350643/1‑69 (MQ=255)
gCGGCACCTAATAACTCTCCGCCTTTGGCGTTTTGTAGTAACAATATTTGTAGCGGTGCTGAAAGGGCa > 1:2836595/1‑69 (MQ=255)
gCACCTAATAACTCTCCGCCTTTGGCGTTTTGTAGTAACAATATTTGTAGCGGTGCTGAAAGGGCAaat > 1:1824074/1‑69 (MQ=255)
cACCTAATAACTCTCCGCCTTTGGCATTTTGCAGTAACaa > 1:2596149/1‑40 (MQ=38)
cACCTAATAACTCTCCGCCTTTGGCATTTTGCAGTAACAATATTTGCGGTGGTGCTGAAAGGGCAaat > 1:2559719/1‑68 (MQ=255)
cACCTAATAACTCTCCGCCTTTGGCATTTTGCAGTAACAATATTTGCAGTGGTGCTGAAAGGGGAaata > 1:3210773/1‑69 (MQ=255)
cACCTAATAACTCTCCGCCTTTGGCATTTTGCAGTAACAATATTTGCAGTGGTGCTGAAAGGGCAaata > 1:2147928/1‑69 (MQ=255)
cACCTAATAACTCTCCGCCTTTGGCATTTTGCAGTAACAATATTTGCAGTGGTGCTGAAAGGGCAaata > 1:101816/1‑69 (MQ=255)
cACCTAATAACTCTCCGCCTTTGGCATTTTGCAGTAACAATATTTGCAGTGGTGCTGAAAGGGCAaata > 1:1725982/1‑69 (MQ=255)
cACCTAATAACTCTCCGCCTTTGGCATTTTGCAGTAACAATATTTGCAGTGGTGCTGAAAGGGCAaata > 1:834407/1‑69 (MQ=255)
cACCTAATAACTCTCCGCCTTTGGCATTTTGCAGTAACAATATTTGCAGTGGTGCTGAAAGGGCAaata > 1:1415425/1‑69 (MQ=255)
cACCTAATAACTCTCCGCCTTTGGCATTTTGCAGTAACAATATTTGCAGTGGTGCTGAAAGGGCAaata > 1:399514/1‑69 (MQ=255)
cACCTAATAACTCTCCGCCTTTGGCATTTTGCAGTAACAATATTTGCAGTGGTGCTGAAAGGGCAaata > 1:3044471/1‑69 (MQ=255)
cACCTAATAACTCTCCGCCTTTGGCATTTTGCAGTAACAATATTTGCAGTGGTGCTGAAAGGGCAaata > 1:3306532/1‑69 (MQ=255)
cACCTAATAACTCTCCGCCTTTGGCATTTTGCAGTAACAATATTTGCAGTGGTGCTGAAAGGGCAaata > 1:1386159/1‑69 (MQ=255)
cACCTAATAACTCTCCGCCTTTGGCATTTTGCAGTAACAATATTTGCAGTGGTGCTGAAAGGGCAaat > 1:895045/1‑68 (MQ=255)
cACCTAATAACTCTCCGCCTTTGGCATTTTGCAGTAACAATATTTGCAGTGGTGCTGAAAGGGCAaat > 1:2696679/1‑68 (MQ=255)
aaCTCTCCGCCTTTGGCGTTTTGTAGTAACAATATTTGTAGCGGTGCTGAAAGGGCAAATAATCCcgc > 1:2865873/1‑68 (MQ=255)
aaCTCTCCGCCTTTGGCGTTTTGTAGTAACAATATTTGTAGCGGTGCTGAAAGGGCAAATAATCCcgc > 1:827470/1‑68 (MQ=255)
gtagtaACAATATTTGTAGCGGTGCTGAAAGGGCAAATAATCCCGCGCAACAAATAAAAGCAAAAATa < 1:1886126/68‑1 (MQ=255)
|
CGCTATTTGCCCACCTGCGGCACCTAATAACTCTCCGCCTTTGGCGTTTTGTAGTAACAATATTTGTAGCGGTGCTGAAAGGGCAAATAATCCCGCGCAACAAATAAAAGCAAAAATA > minE/239955‑240072
|
| 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
