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 |
|
A6 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
833,912 |
G→C |
28.9% |
A790A (GCG→GCC) |
narG → |
nitrate reductase 1, alpha subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 833,912 | 0 | G | C | 28.9%
| 83.4
/ 41.5
| 59 | A790A (GCG→GCC) | narG | nitrate reductase 1, alpha subunit |
| Reads supporting (aligned to +/- strand): ref base G (20/21); new base C (10/7); total (31/28) |
| Fisher's exact test for biased strand distribution p-value = 5.70e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.66e-01 |
TCTGGTGGTTACGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGTTTATTCACCCGCTGTCTGCGGCG > minE/833843‑833981
|
tCTGGTGGTTACGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGa > 1:1051907/1‑71 (MQ=255)
cTGGTGGTTACGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGAc > 1:1257131/1‑71 (MQ=255)
gtggtTACGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCt < 1:3694872/70‑1 (MQ=255)
gtggtTACGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTg > 1:1699652/1‑71 (MQ=255)
tggtTACGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTgg < 1:2478699/71‑1 (MQ=255)
ggtTACGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTgg > 1:2571116/1‑70 (MQ=255)
ggtTACGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTgg > 1:2964215/1‑70 (MQ=255)
gtTACGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGt < 1:1800876/70‑1 (MQ=255)
aCGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTg > 1:2002814/1‑65 (MQ=255)
aCGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTg > 1:1969392/1‑65 (MQ=255)
cGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGaa < 1:1824569/71‑1 (MQ=255)
gCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGaaa < 1:1861217/71‑1 (MQ=255)
gCTCGACTTCCGCATGTCCAGTACCTGCCTGTTCTCCGATATCGTTCTGCCCACCGCCACCTGGTACGaaa < 1:2948002/71‑1 (MQ=255)
tcgACTTCCGCATGTCCAGTACCTGCCTGTTCTCCGATATCGTTCTGCCCACCGCCACCTGGTACGaaa > 1:3614129/3‑69 (MQ=255)
tcgACTTCCGCATGTCCAGTACCTGCCTGTTCTCCGATATCGTTCTGCCCACCGCCACCTGGTACGaa > 1:1667589/3‑68 (MQ=255)
tGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGAc > 1:1817918/1‑58 (MQ=255)
cgACTTCCGCATGTCCAGTACCTGCCTGTTCTCCGATATCGTTCTGCCCACCGACACCTGGTACGaaa > 1:2271443/2‑68 (MQ=255)
gACTTCCGTCTGTCGAGCACGTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGaaaaat < 1:1768595/70‑2 (MQ=255)
gACTTCCGCATGTCCAGTACCTGCCTGTTCTCCGATATCGTTCTGCCCACCGCCACCTGGTACGAAAAAga > 1:1895780/1‑71 (MQ=255)
ttCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCt < 1:2947024/55‑1 (MQ=255)
ttCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCt < 1:1625578/55‑1 (MQ=255)
tGTCCAGTACCTGCCTGTTCTCCGATATCGTTCTGCCCACCGCCACCTGGTACGaaa < 1:2073247/57‑1 (MQ=255)
tCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGaa < 1:3617365/68‑1 (MQ=255)
tCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATAc > 1:1785461/1‑71 (MQ=255)
gAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACtt > 1:1507433/1‑71 (MQ=255)
tGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATg < 1:2630184/57‑1 (MQ=255)
gTCTCTATTCCGACATCATTTTGCCGACGGCGAcc < 1:1438584/35‑1 (MQ=255)
actctATTCCGACATCATTTTGCCGACGGCTACCTg > 1:3879545/2‑36 (MQ=38)
ctctATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCa > 1:1652325/1‑71 (MQ=255)
ttctCCGATATCGTTCTGCCCACCGCCACCTGGTACGAAAAAGACGATATGAACACCTCGGATATGCAt < 1:2153056/66‑1 (MQ=255)
ttCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGaa < 1:601654/51‑1 (MQ=255)
ttCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCg < 1:2145552/70‑1 (MQ=255)
tCCGACATCATTTTGCCGACGGCGACCTGGTACGaaaaa > 1:1879485/1‑39 (MQ=255)
tCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGtt > 1:729285/1‑71 (MQ=255)
ccGACATCATTTTGCCGACGGCGACCTGGTACGaa > 1:1191007/1‑35 (MQ=255)
ccGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATc > 1:406587/1‑66 (MQ=255)
cGATATCGTTCTGCCCACCGCCACCTGGTACGAAAAAGACGATATGAACACCTCGGa > 1:2581712/1‑57 (MQ=255)
cGATATCGTTCTGCCCACCGCCACCTGGTACGAAAAAGACGATATGAACACCTCGGATATGCATCCGTTTa < 1:1145252/71‑1 (MQ=255)
cGATATCGTTCTGCCCACCGCCACCT‑GTACGAAAAAGACGATATGAACACCTCGGATATGc > 1:684424/1‑61 (MQ=255)
gACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGt < 1:2051805/67‑1 (MQ=255)
gACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGt < 1:3459817/67‑1 (MQ=255)
atatcgtTCTGCCCACCGCCACCTGGTACGAAAAAGACGATATGAACACCTCGGATATGCAt > 1:3230386/3‑62 (MQ=255)
tatcgtTCTGCCCACCGCCACCTGGTACGAAAAAGACGATATGAACACCTCGGATATGCATCCGTTTATTc < 1:2742127/70‑1 (MQ=255)
tatcgtTCTGCCCACCGCCACCTGGTACGAAAAAGACGATATGAACACCTCGGATATGCATCCGTTTATTc < 1:3029061/70‑1 (MQ=255)
tatcgtTCTGCCCACCGCCACCTGGTACGAAAAAGACGATATGAACACCTCGGATATGCATCCGTTTATTc < 1:2565881/70‑1 (MQ=255)
catcatTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGTTTATTc < 1:169395/71‑1 (MQ=255)
catcatTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGTTTATTc < 1:720934/71‑1 (MQ=255)
atcgtTCTGCCCACCGCCACCTGGTACGAAAAAGACGATATGaa > 1:2478943/1‑44 (MQ=16)
atcgtTCTGCCCACCGCCACCTGGTACGAAAAAGACGATATGaa > 1:2818811/1‑44 (MQ=16)
atcatTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGTTTATTCa < 1:171742/71‑1 (MQ=255)
catTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGc > 1:2837136/1‑56 (MQ=255)
catTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGTTTATTCAc > 1:1547707/1‑70 (MQ=255)
ttttGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGTTTAtt < 1:3586881/65‑1 (MQ=255)
tctGCCCACCGCCACCTGGTACGAAAAAGACGATATGAACACCTCGGat > 1:2069477/3‑49 (MQ=255)
cGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGa < 1:300223/43‑1 (MQ=255)
aCGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGatat > 1:2091941/1‑44 (MQ=255)
aCGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGata > 1:1347391/1‑43 (MQ=255)
aCGGCGACCTGGTACGAAAAAGACGACATGAATACTTAGGATATGCATCCGTTTATTCACCCGCTGTCTgc > 1:184044/1‑71 (MQ=255)
cGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGTTTATTCACCCGCTGTCTgcggcg < 1:1316571/71‑1 (MQ=255)
|
TCTGGTGGTTACGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGTTTATTCACCCGCTGTCTGCGGCG > minE/833843‑833981
|
| 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
