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 |
1,971,412 |
T→C |
70.6% |
A498A (GCA→GCG) |
speA ← |
biosynthetic arginine decarboxylase, PLP‑binding |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,971,412 | 0 | T | C | 70.6%
| 59.8
/ 24.7
| 61 | A498A (GCA→GCG) | speA | biosynthetic arginine decarboxylase, PLP‑binding |
| Reads supporting (aligned to +/- strand): ref base T (13/5); new base C (27/16); total (40/21) |
| Fisher's exact test for biased strand distribution p-value = 5.64e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.10e-01 |
CGACGTTCCGGCACTTGATCCAGCCCTTCCAGCGGCAGAACCGGGAACAACTGGTCGATCCCCCATGCGTCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTCCGCCA > minE/1971347‑1971464
|
cgACGTTCCGGCACTTGATCCAGCCCTTCCAGCGGCAGAACCGGGAACAACTGGTCGATCCCCCATGCg < 1:2266865/69‑1 (MQ=255)
cgACGTTCCGGCACTTGATCCAGCCCTTCCAGCGGCAGAACCGGGAACAACTGGTCGATCCCCCATGCg < 1:3013807/69‑1 (MQ=255)
cgACGTTCCGGCACTTGATCCAGCCCTTCCAGCGGCAGAACCGGGAACAACTGGTCGATCCCCCATGCg < 1:3376070/69‑1 (MQ=255)
ccGGCACTTGATCCAGCCCTTCCAGCGGCAGAACCGGGAACAACTGGTCGATCCCCCATGCGTCCGGCa > 1:828735/1‑69 (MQ=255)
ccGGCACTTGATCCAGCCCTTCCAGCGGCAGAACCGGGAACAACTGGTCGATCCCCCATGCGTCCGGCa > 1:2697373/1‑69 (MQ=255)
ccGGCACTTGATCCAGCCCTTCCAGCGGCAGAACCGGGAACAACTGGTCGATCCCCCATGCGTCCGGCa > 1:2266270/1‑69 (MQ=255)
ccGGCACTTGATCCAGCCCTTCCAGCGGCAGAACCGGGAACAACTGGTCGATCCCCCATGCGTCCGGCa > 1:2856913/1‑69 (MQ=255)
ccGGCACTTGATCCAGCCCTTCCAGCGGCAGAACCGGGAACAACTGGTCGATCCCCCATGCGTCCGGCa > 1:1882600/1‑69 (MQ=255)
aCCGGGAACAACTGGTCGATCCCCCATGCGTCCGGCATCGTCTGGAACAGCGAGAAGTTGACGTACa > 1:1963343/1‑67 (MQ=255)
aCCGGGAACAACTGGTCGATCCCCCATGCGTCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACAtt > 1:2470712/1‑69 (MQ=255)
aCCGGGAACAACTGGTCGATCCCCCATGCGTCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACAtt > 1:1231988/1‑69 (MQ=255)
aCCGGGAACAACTGGTCGATCCCCCATGCGTCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACAtt > 1:3311384/1‑69 (MQ=255)
aCCGGGAACAACTGGTCGATCCCCCATGCGTCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACAt > 1:2405570/1‑68 (MQ=255)
gggAACAACTGGTCGATCCCCCATGCGTCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTg < 1:1515656/69‑1 (MQ=255)
gggAACAACTGGTCGATCCCCCATGCGTCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTg < 1:1542740/69‑1 (MQ=255)
acTGGTCGATCCCCCATGCGTCCGGCATCGCCTGGAACAGCGAGAAGTTGACGTACATTTTGTCCGc > 1:891378/1‑67 (MQ=255)
acTGGTCGATCCCCCATGCGTCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTCCGCCa > 1:702439/1‑69 (MQ=255)
acTGGTCGATCCCACATGCGTCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTCCGCCa > 1:2612549/1‑69 (MQ=255)
tggtggATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTc > 1:1712701/1‑62 (MQ=255)
tGGTCGATCCCCCACGCATCCGTCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTc > 1:1697590/1‑62 (MQ=255)
tGGTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGt > 1:1516608/1‑61 (MQ=255)
tGGTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTc > 1:3017142/1‑62 (MQ=255)
tGGTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTc > 1:2990494/1‑62 (MQ=255)
tGGTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTc > 1:3120919/1‑62 (MQ=255)
tGGTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTc > 1:2904992/1‑62 (MQ=255)
tGGTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTc > 1:2717943/1‑62 (MQ=255)
tGGTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTc > 1:361814/1‑62 (MQ=255)
tGGTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTc > 1:440515/1‑62 (MQ=255)
tGGTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTc > 1:2713576/1‑62 (MQ=255)
tGGTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTc > 1:267348/1‑62 (MQ=255)
tGGTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTc > 1:468621/1‑62 (MQ=255)
tGGTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTc > 1:885330/1‑62 (MQ=255)
tGGTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTc > 1:896602/1‑62 (MQ=255)
tGGTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTc > 1:2381396/1‑62 (MQ=255)
tGGTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTc > 1:1640097/1‑62 (MQ=255)
tGGTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTc > 1:1523980/1‑62 (MQ=255)
tGGTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTc > 1:1479302/1‑62 (MQ=255)
tGGTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTc > 1:1934168/1‑62 (MQ=255)
tGGTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTc > 1:1461241/1‑62 (MQ=255)
tGGTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTc > 1:1940206/1‑62 (MQ=255)
tGGTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTc > 1:128282/1‑62 (MQ=255)
tGGTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTc > 1:20276/1‑62 (MQ=255)
tGGTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTc > 1:1034882/1‑62 (MQ=255)
tGGTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTc > 1:2671614/1‑62 (MQ=255)
tGGTCCATCCCCCACGCATCCCGCATCCACTCGAACAGCGAGAAGTTGACGTACaat > 1:2841238/1‑55 (MQ=255)
gTCTATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTCCGc < 1:1619242/63‑1 (MQ=255)
gTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTCCGc < 1:1306123/63‑1 (MQ=255)
gTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTCCGc < 1:42378/63‑1 (MQ=255)
gTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTCCGc < 1:416832/63‑1 (MQ=255)
gTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTCCGc < 1:1536393/63‑1 (MQ=255)
gTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTCCGc < 1:1027727/63‑1 (MQ=255)
gTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTCCGc < 1:3220777/63‑1 (MQ=255)
gTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTCCGc < 1:1772704/63‑1 (MQ=255)
gTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTCCGc < 1:1775285/63‑1 (MQ=255)
gTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTCCGc < 1:1776092/63‑1 (MQ=255)
gTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTCCGc < 1:2899256/63‑1 (MQ=255)
gTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTCCGc < 1:2853059/63‑1 (MQ=255)
gTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTCCGc < 1:2812811/63‑1 (MQ=255)
gTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTCCGc < 1:227226/63‑1 (MQ=255)
gTCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTCCGc < 1:2278009/63‑1 (MQ=255)
tCGATCCCCCACGCATCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTCCGc < 1:1873075/62‑1 (MQ=255)
|
CGACGTTCCGGCACTTGATCCAGCCCTTCCAGCGGCAGAACCGGGAACAACTGGTCGATCCCCCATGCGTCCGGCATCGACTGGAACAGCGAGAAGTTGACGTACATTTTGTCCGCCA > minE/1971347‑1971464
|
| 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
