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 F1 I0 R1
|
2892 |
75.3 |
5698161 |
66.1% |
3766484 |
59.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
834,800 |
G→A |
23.1% |
A1086A (GCG→GCA) |
narG → |
nitrate reductase 1, alpha subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 834,800 | 0 | G | A | 23.1%
| 93.9
/ 23.9
| 52 | A1086A (GCG→GCA) | narG | nitrate reductase 1, alpha subunit |
| Reads supporting (aligned to +/- strand): ref base G (27/13); new base A (4/8); total (31/21) |
| Fisher's exact test for biased strand distribution p-value = 4.76e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.31e-01 |
ATCGACACCCGTTCGGTGAAAGAAGTGATAGGCCAGAAATCCAACGGCAACCAGGAAAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCTGCTGATGCT > minE/834738‑834868
|
aTCGACACCCGTTCGGTGAAAGAAGTGATAGGCCAGAAATCCAACGGCAACCAGGAAAAAGCGCTCAACtt < 1:1290384/71‑1 (MQ=255)
tCGACACCCGTTCGGTGAAAGAAGTGATAGGCCAGAAATCCAACGGCAACCAGGAAAAAGCGCTCAACTTc > 1:3964320/1‑71 (MQ=255)
cacCCGTTCGGTGAAAGAAGTGATAGGCCAGAAATCCAACGGCAACCAGGAAAAAGCGCTCAACTTCCTGa > 1:2512077/1‑71 (MQ=255)
cGTTCGGTGAAAGAAGTGATAGGCCAGAAATCCAACGGCAACCAGGAAAAAGCGCTCAACTTCCTGAcgcc > 1:1942171/1‑71 (MQ=255)
ttCGGTGAAAGAAGTGATAGGCCAGAAATCCAACGGCAACCAGGAAAAAGCGCTCAACTTCCTGAcgccg > 1:1860830/1‑70 (MQ=255)
tCGGTGAAAGAAGTGATAGGCCAGAAATCCAACGGCAACCAGGAAAAAGCGCTCaa < 1:646229/56‑1 (MQ=255)
tCGGTGAAAGAAGTGATAGGCCAGAAATCCAACGGCAACCAGGAAAAAGCGCTCaa < 1:4653643/56‑1 (MQ=255)
tCGGTGAAAGAAGTGATAGGCCAGAAATCCAACGGCAACCAGGAAAAAGCGCTCaa < 1:4660310/56‑1 (MQ=255)
tGAAAGAAGTGATAGGCCAGAAATCCAACGGCAACCAGGAAAAAGCGCTCAACTTCCTGACGCCGCACCAg < 1:3783649/71‑1 (MQ=255)
aaggaagTGATAGGCCAGAAATCCAACGGCAACCAGGAAAAAGCGCTCAACTTCCTGACGCCGCACCAg > 1:2448961/4‑69 (MQ=255)
aaaGAAGTGATAGGCCAGAAATCCAACGGCAACCAGGAAAAAGCGCTCaa > 1:1140262/1‑50 (MQ=255)
aaaGAAGTGATAGGCCAGAAATCCAACGGCAACCAGGAAAAAGCGCTCAACTTCCTGACGCCGCACCAg > 1:4116286/1‑69 (MQ=255)
aaaGAAGTGATAGGCCAGAAATCCAACGGCAACCAGGAAAAAGCGCTCAACTTCCTGACGCCGCACCAg > 1:5163039/1‑69 (MQ=255)
aaaGAAGTGATAGGCCAGAAATCCAACGGCAACCAGGAAAAAGCGCTCAACTTCCTGACGCCGCACCAg > 1:2099681/1‑69 (MQ=255)
agaagTGATAGGCCAGAAATCCAACGGCAACCAGGAAAAAGCGCTCAACTTCCt > 1:5091367/1‑54 (MQ=255)
agaagTGATAGGCCAGAAATCCAACGGCAACCAGGAAAAAGCGCTCAACTTCCTGACGCCGCACCAGaa > 1:2419018/1‑69 (MQ=255)
agaagTGATAGGCCAGAAATCCAACGGCAACCAGGAAAAAGCGCTCAACTTCCTGACGCCGCACCAGa > 1:5003297/1‑68 (MQ=255)
aagTGATAGGCCAGAAATCCAACGGCAACCAGGAAAAAGCGCT‑AACTTCCTGACGCCGCACCAGAAGTggg > 1:4676859/1‑71 (MQ=255)
gTGATAGGCCAGAAATCCAACGGCAACCAGGAAAAAGCGCTCAACTTCCTGAcgccgc > 1:2202719/1‑58 (MQ=255)
gTGATAGGCCAGAAATCCAACGGCAACCAGGAAAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTgggg < 1:13723/71‑1 (MQ=255)
gTGATAGGCCAGAAATCCAACGGCAACCAGGAAAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTgggg < 1:1587241/71‑1 (MQ=255)
cAGAAATCCAACGGCAACCAGGAAAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTAtccactc > 1:2093182/1‑71 (MQ=255)
aTCCAACGGCAACCAGGAAAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCAcc > 1:4653409/1‑70 (MQ=255)
cAACGGCAACCAGGAAAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTa > 1:5375499/1‑69 (MQ=255)
aaCGGCTTCCCGGAAAAAGCACTTAACTTCCTGACGCCGCACCAGAAATggggca < 1:173406/55‑3 (MQ=255)
cGGCAACCAGGAAAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAg > 1:2368751/1‑69 (MQ=255)
cGGCAACCAGGAAAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGc > 1:4637303/1‑70 (MQ=255)
ggCAACCAGGAAAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGa > 1:2051331/1‑71 (MQ=255)
cAACCAGGAAAAAGCGCTCAACTTTCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACa < 1:3852092/71‑1 (MQ=255)
aaCCAGGAAAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACa < 1:2695136/70‑1 (MQ=255)
ccggAAAAAGCACTTAACTTCCTGACGCCGCACCAGAAATGGGGCATTCACTCAACCTACAGTGAAAAcc < 1:4368715/68‑1 (MQ=255)
cAGGAAAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACaa > 1:1402299/1‑68 (MQ=255)
cggAAAAAGCACTTAACTTCCTGACGCCGCACCAGAAATGGGGCATTCACTCAACCTACAGTGAAAAc < 1:189225/67‑1 (MQ=255)
cggAAAAAGCACTTAACTTCCTGACGCCGCACCAGAAATGGGGCATTCACTCAACCTACAGTGAAAAc < 1:3157486/67‑1 (MQ=255)
cggAAAAAGCACTTAACTTCCTGACGCCGCACCAGAAATGGGGCATTCACTCAACCTACAGTGAAAAc < 1:567457/67‑1 (MQ=255)
aGGAAAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACctg > 1:3144394/1‑71 (MQ=255)
gAAAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTAtcca > 1:2401833/1‑47 (MQ=255)
gAAAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACctgct < 1:916451/71‑1 (MQ=255)
gAAAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACctgct < 1:1125150/71‑1 (MQ=255)
gAAAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACctgct < 1:3603640/71‑1 (MQ=255)
gAAAAAGCACTTAACTTCCTGACGCCGCACCAGAAATGGGGCATTCACTCAACCTAGAGTGAAAACct > 1:2600314/1‑68 (MQ=255)
gAAAAAGCACTTAACTTCCTGACGCCGCACCAGAAATGGGGCATTCACTCAACCTACAgtg < 1:2542890/61‑3 (MQ=255)
aaaaGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCtgctga > 1:4887880/1‑71 (MQ=255)
aaaGCACTTAACTTCCTGACGCCGCACCAGAAATGGGGCAttcact > 1:2436063/1‑46 (MQ=21)
aaaGCACTTAACTTCCTGACGCCGCACCAGAAATGGGGCATTCACTCAACCTACAGTGAAAACCtgctaat > 1:4634689/1‑71 (MQ=255)
aaGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTAtc < 1:666464/41‑1 (MQ=255)
aaGCACTTAACTTCCTGACGCCGCACCAGAAATGGGGCATTCACTCAACCTACAGTGAAAACCtgctaatg < 1:3896675/71‑1 (MQ=255)
aaGCACTTAACTTCCTGACGCCGCACCAGAAATGGGGCATTCACTCAACCTACAGTGAAAACCtgctaatg < 1:5477393/71‑1 (MQ=255)
aGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTAtcca > 1:4597606/1‑42 (MQ=255)
aGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTAtcca > 1:1472731/1‑42 (MQ=255)
aGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTAtcca > 1:3706156/1‑42 (MQ=255)
aGCACTTAACTTCCTGACGCCGCACCAGAAATGGGGCATTCACTCAACCTACAGTGAAAACCtgctaatgc > 1:305566/1‑71 (MQ=255)
gcgcTCAACTTCCTGACGCCGCACCAGAAGTGGGGTAtccactccac > 1:1098225/1‑47 (MQ=255)
gcgcTCAACTTCCTGACGCCGCACCAGAAGTGGGGTAtccactccac > 1:839167/1‑47 (MQ=255)
gcgcTCAACTTCCTGACGCCGCACCAGAAGTGGGGTAtccactccac > 1:5217717/1‑47 (MQ=255)
gcgcTCAACTTCCTGACGCCGCACCAGAAGTGGGGTAtccactccac > 1:5211438/1‑47 (MQ=255)
gcgcTCAACTTCCTGACGCCGCACCAGAAGTGGGGTAtccactcca > 1:1030869/1‑46 (MQ=255)
gcgcTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCtgctgatgct < 1:4230928/71‑1 (MQ=255)
gcgcTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCtgctgatgct < 1:778149/71‑1 (MQ=255)
gcgcTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCtgctgatgct < 1:3647857/71‑1 (MQ=255)
cgcTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCtgctgatgct > 1:3873271/1‑70 (MQ=255)
|
ATCGACACCCGTTCGGTGAAAGAAGTGATAGGCCAGAAATCCAACGGCAACCAGGAAAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCTGCTGATGCT > minE/834738‑834868
|
| 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
