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 |
1,507,973 |
C→A |
100% |
A35S (GCG→TCG) |
yfbT ← |
predicted hydrolase or phosphatase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,507,973 | 0 | C | A | 81.8%
| 70.2
/ 12.5
| 44 | A35S (GCG→TCG) | yfbT | predicted hydrolase or phosphatase |
| Reads supporting (aligned to +/- strand): ref base C (3/5); new base A (36/0); total (39/5) |
| Fisher's exact test for biased strand distribution p-value = 5.16e-05 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.77e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
AAATGGCGCAGAGAGGTGATCGCCTGTTTACCGTGAATGAAAGCCAGCACCTCTTCCGGCGCTAACCCATGACGTCTGGCCCAGTTGCTCCACGCCCGTTCTACCGCAGGCAGGGAATCCACCA > minE/1507912‑1508035
|
aaaTGGCGCAGAGAGGTGATCGCCTGTTTACCGTGAATGAAAGCCAGCACCTCTTCCGGCGATAAccc > 1:2890528/1‑68 (MQ=255)
aaaTGGCGCAGAGAGGTGATCGCCTGTTTACCGTGAATGAAAGCCAGCACCTCTTCCGGCGATAAccc > 1:2677021/1‑68 (MQ=255)
aaaTGGCGCAGAGAGGTGATCGCCTGTTTACCGTGAATGAAAGCCAGCACCTCTTCCGGCGATAAccc > 1:738099/1‑68 (MQ=255)
aaaTGGCGCAGAGAGGTGATCGCCTGTTTACCGTGAATGAAAGCCAGCACCTCTTCCGGCGATAAccc > 1:1620062/1‑68 (MQ=255)
aaaTGGCGCAGAGAGGTGATCGCCTGTTTACCGTGAATGAAAGCCAGCACCTCTTCCGGCGATAAccc > 1:1739539/1‑68 (MQ=255)
aaaTGGCGCAGAGAGGTGATCGCCTGTTTACCGTGAATGAAAGCCAGCACCTCTTCCGGCGATAAccc > 1:383159/1‑68 (MQ=255)
aaaTGGCGCAGAGAGGTGATCGCCTGTTTACCGTGAATGAAAGCCAGCACCTCTTCCGGCGATAAccc > 1:650389/1‑68 (MQ=255)
aaaTGGCGCAGAGAGGTGATCGCCTGTTTACCGTGAATGAAAGCCAGCACCTCTTCCGGCGATAAccc > 1:2167354/1‑68 (MQ=255)
aaaTGGCGCAGAGAGGTGATCGCCTGTTTACCGTGAAAGAAAGCCAGCACCTCTTCCGGCGATAAccc > 1:3087283/1‑68 (MQ=255)
aTGGCGCAGAGAGGTGATCGCCTGTTTACCGTGAATGAAAGCCAGCACCTCTTCCGGCGCTAACCCAt < 1:2241640/68‑1 (MQ=255)
aTGGCGCAGAGAGGTGATCGCCTGTTTACCGTGAATGAAAGCCAGCACCTCTTCCGGCGCTAACCCAt < 1:295277/68‑1 (MQ=255)
aTGGCGCAGAGAGGTGATCGCCTGTTTACCGTGAATGAAAGCCAGCACCTCTTCCGGCGCTAACCCAt < 1:2027836/68‑1 (MQ=255)
aTGGCGCAGAGAGGTGATCGCCTGTTTACCGTGAATGAAAGCCAGCACCTCTTCCGGCGCTAACCCAt < 1:595952/68‑1 (MQ=255)
ggCGCAGAGAGGTGATCGCCTGTTTACCGTGAATGAAAGCCAGCACCTCTTCCGGCGCTAACCCATGAc < 1:432548/69‑1 (MQ=255)
aTCGCCTGTTTACCGTGAATGAAAGCCAGCACCTCTTCCGGCGATAACCCATGACGTCTgga > 1:2791641/1‑61 (MQ=255)
aTCGCCTGTTTACCGTGAATGAAAGCCAGCACCTCTTCCGGCGATAACCCATGACGTCTGGccc > 1:138801/1‑64 (MQ=255)
aTCGCCTGTTTACCGTGAATGAAAGCCAGCACCTCTTCCGGCGATAACCCATGACGTCTGGccc > 1:1795824/1‑64 (MQ=255)
aTCGCCTGTTTACCGTGAATGAAAGCCAGCACCTCTTCCGGCGATAACCCATGACGTCTGGccc > 1:2486400/1‑64 (MQ=255)
aTCGCCTGTTTACCGTGAATGAAAGCCAGCACCTCTTCCGGCGATAACCCATGACGTCTGGccc > 1:3394887/1‑64 (MQ=255)
ccGTGAATGAAAGCCAGCACCTCTTCCGGCGATAACCCATGACGta > 1:3268868/1‑45 (MQ=255)
ccGTGAATGAAAGCCAGCACCTCTTCCGGCGATAACCCATGACGt > 1:2112586/1‑45 (MQ=255)
ccGTGAATGAAAGCCAGCACCTCTTCCGGCGATAACCCATGACGTc > 1:3356464/1‑46 (MQ=255)
ccGTGAATGAAAGCCAGCACCTCTTCCGGCGATAACCCATGACGTc > 1:471646/1‑46 (MQ=255)
ccGTGAATGAAAGCCAGCACCTCTTCCGGCGATAACCCATGACGTc > 1:511207/1‑46 (MQ=255)
ccGTGAATGAAAGCCAGCACCTCTTCCGGCGATAACCCATGACGTc > 1:973487/1‑46 (MQ=255)
ccGTGAATGAAAGCCAGCACCTCTTCCGGCGATAACCCATGACGTc > 1:893016/1‑46 (MQ=255)
ccGTGAATGAAAGCCAGCACCTCTTCCGGCGATAACCCATGACGTc > 1:923362/1‑46 (MQ=255)
ccGTGAATGAAAGCCAGCACCTCTTCCGGCGATAACCCATGACGTc > 1:1005569/1‑46 (MQ=255)
ccGTGAATGAAAGCCAGCACCTCTTCCGGCGATAACCCATGACGTc > 1:3213791/1‑46 (MQ=255)
ccGTGAATGAAAGCCAGCACCTCTTCCGGCGATAACCCATGACGTc > 1:2721796/1‑46 (MQ=255)
ccGTGAATGAAAGCCAGCACCTCTTCCGGCGATAACCCATGACGTc > 1:2662571/1‑46 (MQ=255)
ccGTGAATGAAAGCCAGCACCTCTTCCGGCGATAACCCATGACGTc > 1:2502231/1‑46 (MQ=255)
ccGTGAATGAAAGCCAGCACCTCTTCCGGCGATAACCCATGACGTc > 1:2442918/1‑46 (MQ=255)
ccGTGAATGAAAGCCAGCACCTCTTCCGGCGATAACCCATGACGTc > 1:2428214/1‑46 (MQ=255)
ccGTGAATGAAAGCCAGCACCTCTTCCGGCGATAACCCATGACGTc > 1:2015341/1‑46 (MQ=255)
ccGTGAATGAAAGCCAGCACCTCTTCCGGCGATAACCCATGACGTc > 1:181631/1‑46 (MQ=255)
ccGTGAATGAAAGCCAGCACCTCTTCCGGCGATAACCCATGACGTc > 1:1508508/1‑46 (MQ=255)
ccGTGAATGAAAGCCAGCACCTCTTCCGGCGATAACCCATGACGTc > 1:1284976/1‑46 (MQ=255)
ccGTGAATGAAAGCCAGCACCTCTTCCGGCGATAACCCATGACGTc > 1:108782/1‑46 (MQ=255)
ccGTGAATGAAAGCCAGCACCTCTTCCGGCGATAACCCATGACGTc > 1:1059791/1‑46 (MQ=255)
acGTGAATGAAAGCCAGCACCTCTTCCGGCGATAACCCATGACGTc > 1:2470457/2‑46 (MQ=39)
tctTCCGGCGCTAACCCATGACTTCTGGCCCAGTTGCTCCACGCCCGTTCTACCGCAGGCAGGGAATcc > 1:3223882/1‑69 (MQ=255)
ccGGCGCTAACCCATGACGTCTGGCCCAGTTGCTCCACGCCCGTTCTACCGCAGGCAGGGAATccacca > 1:3263889/1‑69 (MQ=255)
ccGGCGCTAACCCATGACGTCTGGCCCAGTTGCTCCACGCCCGTTCTACCGCAGGCAGGGAATccacca > 1:2269370/1‑69 (MQ=255)
|
AAATGGCGCAGAGAGGTGATCGCCTGTTTACCGTGAATGAAAGCCAGCACCTCTTCCGGCGCTAACCCATGACGTCTGGCCCAGTTGCTCCACGCCCGTTCTACCGCAGGCAGGGAATCCACCA > minE/1507912‑1508035
|
| 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
