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 |
|
A15 F116 I0 R1
|
44 |
26.4 |
562224 |
96.5% |
542546 |
140.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
CP000730 |
1,420,434 |
G→A |
100% |
A229T (GCG→ACG) |
USA300HOU_1318 → |
M3 family oligoendopeptidase F |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | CP000730 | 1,420,434 | 0 | G | A | 72.4%
| 23.2
/ 17.3
| 30 | A229T (GCG→ACG) | USA300HOU_1318 | M3 family oligoendopeptidase F |
| Reads supporting (aligned to +/- strand): ref base G (8/0); new base A (10/10); total (20/10) |
| Fisher's exact test for biased strand distribution p-value = 2.51e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.15e-02 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
TGAACATGATGGTACAACGTACCCTGTCGACTATGCTACGTTTGAAAATGATTATGAAGATAATAAAGATCCTGAGTTTAGACGTAAAAGTTTCAAATCGTTTAGCGATGGGATTCGAAAATATCAGCATACTACCGCGGCTACATATAATATGCAAGTACAACAAGAAAAAATTGAAGCTGATTTACGTGGATTTGAATCAGTCATCGATTATTTATTACATAGTCAAGAAGTAACGCGTGATATGTTTGACCGTCAAAT > CP000730/1420298‑1420558
|
tGAACATGATGGTACAACGTACCCTGTCGTCTATGCTACGTTTGAAAATGATTATGAAGATAATAAAGATCCTGAGTTTAGACGTAAAAGTTTCAAATCGTTTAGCGATGGGATTCGAAAATATCAGCATACTACCACGGc < 2:167630/141‑1 (MQ=255)
gAACATGATGGTACAACGTACCCTGTCGACTATGCTACGTTTGAAAATGATTATGAAGATAATAAAGATCCTGAGTTTAGACGTAAAAGTTTCAAATCGTTTAGCGATGGGATTCGAAAATATCAGCATACTACCACGGCt > 2:207982/1‑141 (MQ=255)
aCATGATGGTACAACGTACCCTGTCGACTATGCTACGTTTGAAAATGATTATGAAGATAATAAAGATCCTGAGTTTAGACGTAAAAGTTTCAAATCGTTTAGCGATGGGATTCGAAAATATCAGCATACTACCACGGCTAc > 1:223546/1‑141 (MQ=255)
cATGATGGTACAACGTATCCTGTCGACTATGCTACGTTTGAAAATGATTATGAAGATAATAAAGATCCTGAGTTTAGACGTAAAAGCTTCAAATCGTTTAGCGATGGGATTCGAAAATATCAGCATACTACCACGGCTACa < 2:123745/141‑1 (MQ=255)
gatgGTACAACGTACCCTGTCGACTATGCTACGTTTGAAAATGATTATGAAGATAATAAAGATCCTGAGTTTAGACGTAAAAGTTTCAAATCGTTTAGCGATGGGATTCGAAAATATCAGCATACTACTACGGCTACatga > 1:272833/1‑139 (MQ=255)
ggTACCACGTACCCTGTCGACTATGCTACGTTTGAAAATGATAAGGAAGATAATAAAGATACTAAGTTTAGACGTAAAAGTTTCAAATCGTTTAGCGATGGGATTCGAAAATATCAGCATACTACCCCGGCAACATctaaa > 2:4383/1‑140 (MQ=255)
aCGTACCCTGTCGACTATGCTACGTTTGAAAATGATTATGAAGATAATAAAGATCCTGAGTTTAGACGTAAAAGTTTCAAATCGTTTAGCGATGGGATTCGAAAATATCAGCATACTACCACGGCTACATATAATATGCaa > 1:236940/1‑141 (MQ=255)
aCCCTGTCGACTATGCTACGTTTGAAAATGATTATGAAGATAATAAAGATCCTGAGTTTAGACGTAAAAGTTTCAAATCGTTTAGCGATGGGATTCGAAAATATCAGCATACTACCACGGCTACATATAATATGCAAGTac > 1:43035/1‑141 (MQ=255)
caCTATGCTACGTTCGAAAATCAGTATTAAGATAATAAAAACCCTGAGTTTAGACGTAATAGTTTCAAATCGTTTAGCGATGGGATTCTAAAATATCAGCATACAACCACGGCTACATATAATATGCAAGTACAAAAAGat < 2:129598/140‑2 (MQ=255)
aCTATGCTACGTTTGAAAATGATTATGAAGATAATAAAGATCCTGAGTTTAGACGTAAAAGTTTCAAATCGTTTAGCGATGGGATTCGAAAATATCAGCATACTACCCGGGCTAGATAGAATAGGCAGGTACGGCaaaaaa > 2:264241/1‑141 (MQ=255)
aCTATGCTACGTTTGAAAATGATTATGAAGATAATAAAGATCCTGAGTTTAGACGTAAAAGTTTCAAATCGTTTAGCGATGGGATTCGAAAATATCAGCATACTACCACGGCTACATATAATATGTAAGTACAACAAGaaa < 1:207982/141‑1 (MQ=255)
aTGCTACGTTTGAAAATGATTATGAAGATAATAAAGATCCTGAGTTTAGACGTAAAAGTTTCAAATCGTTTAGCGATGGGATTCGAAAATATCAGCATACTACCACGGCTACATGTAATATGGAAGTACAACAAGaaaaaa > 1:142412/1‑141 (MQ=255)
tACGTTTGAAAATGATTATGAAGATAATAAAGATCCTGAGTTTAGACGTAAAAGTTTCAAATCGTTTAGCGATGGGATTCGAAAATATCAGCATACTACCACGGCTACATATAATATGCAAGTACAACAAGAAAAAATTGa < 2:236940/141‑1 (MQ=255)
tACGTTTGAAAATGATTATGAAGATAATAAAGATCCTGAGTTGGGACTTAAAAGTTTCAAATCGTTTAGCGATGGGATTCGAAAATATCAGCATACTACCGCGGCTACATATAATATGCAAGTACAACAAGAAAAAATTGa > 1:218516/1‑141 (MQ=255)
ttGAAAATGATTATGAAGATAATAAAGATCCTGAGTTTAGACGTAAAAGTTTCAAATCGTTTAGCGATGGGATTCGAAAATATCAGCATACTACCACGGCTACATATAATATGCAAGTACAACAAGAAAAAATTGAAGCTg > 2:226619/1‑141 (MQ=255)
aaTGATTATGAAGATAATAAAGATCCTGAGTTTAGACGTAAAAGTTTCAAATCGTTTAGCGATGGGATTCGAAAATATCAGCATACTACCGCGGCTACATATAATATGCAAGTAAAACAAGAAAAAATTGAAGCTGATTTa > 2:166907/1‑141 (MQ=255)
gAAGATAATAAAGATCCTGAGTTTAGACGTAAAAGTTTCAAATCGTTTAGCGATGGGATTCGAAAATATCAGCATACTACCGCGGCTACATATAATATGCAAGTACAACAAGAAAAAATTGAAGCTGATTTACGTGGAttt > 1:272020/1‑141 (MQ=255)
gATAATAAAGATCCTGAGTTTAGACGTAAAAGTTTCAAATCGTTTAGCGATGGGATTCGAAAATATCAGCATACTACCACGGCTACATATAATATGCAAGTACAACAAGAAAAAATTGAAGCTGATTTACGTGGATTTGaa < 2:7255/141‑1 (MQ=255)
gATCCTGAGTTTAGACGTAAAAGTTTCAAATCGTTTAGCGATGGGATTCGAAAATATCAGCATACTACCGCGGCTACATATAATATGCAAGTACAACAAGAAAAAATTGAAGCTGATTTACGTGGATATGAATCAGTCATc > 2:238889/1‑141 (MQ=255)
aCGTAAAAGTTTCAAATCGTTTAGCGATGGGATTCGAAAATATCGGCATACTACCAGGGCTACATATAATATGCAAGTACAACAAGAAAAAATTGAAGCTGATTTACGTGGATTTGAATCAGTCATCGAGTATTTATTACa > 2:11472/1‑141 (MQ=255)
aaaGTTTCAAATCTGTCAGCGATGGTATTCGAAAATATCAGCATACGACCACGGCTACATATAATATGCAAGTACAACAAGAAAAAATTGAAGCTGATTTACGTGGATTTGAATCAGTCAGCGATTATTTATTACATAGTc < 2:186543/141‑1 (MQ=255)
aaaTCGTTTAGCGATGGGATTCGAAAATATCAGCATACTACCACGGCTACATATAATATGCAAGTACAACAAGAAAAAATTGAAGCTGATTTAAGTGGATTTGAATCAGTCATCGATTATTTATTACATAGTCAAGAAGTa > 2:228228/1‑141 (MQ=255)
tCGTTTAGCGATGGGATTCGAAAATATCAGCATACTACCACGGCTACATATAATATGCAAGTACAACAAGAAAAAATTGAAGCTGATTTACGTGGATTTGAATCAGTCATCGATTATTTATTACATAGTCAAGAAGTAAcg > 1:200722/1‑141 (MQ=255)
gTTTAGCGATGGGATTCGAAAATATCAGCATACTACCACGGCTACATATAATATGCAAGTACAACAAGAAAAAATTGAAGCTGATTTACGTGGATTTGAATCAGTCATCGATTATTTATTACATAGTCAAGAAGTAAcgcg < 2:223546/141‑1 (MQ=255)
ttAGCGATGGGATTCGAAAATATCAGCATACTACCGCGGCTACATATAATATGCAAGTACAACAAGAAAAAATTGAAGCTGATTTACGTGGATTTGAATCAGTCATCGATTATTTATTACATAGTCAAGAAGTAACGCGTg > 1:2753/1‑141 (MQ=255)
gggATTCGAAAATATCAGCATACTACCGCGGCTACATATAATATGCAAGTACAACAAGAAAAAATTGAAGCTGATTTACGTGGATTTGAATCAGTCATCGATTATTTATTACATAGTCAAGAAGTAACGCGTGATATGttt > 2:83916/1‑141 (MQ=255)
ttCGAAAATATCAGCATACTACCGCGGCTACATATAATATGCAAGTACAACAAGAAAAAATTGAAGCTGATTTACGTGGATTTGAATCAGTCATCGATTATTTATTACATAGTCAAGAAGTAACGCGTGGTATGTTTGAcc > 1:102430/1‑141 (MQ=255)
tCGAAAATATCAGCATACTACCGCGGCTACATATAATATGCAAGTACAACAAGAAAAAATTGAAGCTGATTTACGTGGATTTGAATCAGTCATCGATTATTTATTACATAGTCAAGAAGTAACGCGTGATATGTTTGACCg > 1:207690/1‑141 (MQ=255)
tCGAAAATATCAGCATACTACCACGGCTACATATAATATGCAAGTACAACAAGAAAAAATTGAAGCTGATTTACGTGGATTTGAATCAGTCATCGATTATTTATTACATAGTCAAGAAGTAACGCGTGATATGTTTGACCg < 1:199629/141‑1 (MQ=255)
atatCAGCATACTACCACGGCTACATATAATATGCAAGTACAACAAGAAAAAATTGAAGCTGATTTACGTGGATTTGAATCAGTCATCGATTATTTATTACATAGTCAAGAAGTAACGCGTGATATGTTTGACCGTCAAAt < 2:160797/141‑1 (MQ=255)
|
TGAACATGATGGTACAACGTACCCTGTCGACTATGCTACGTTTGAAAATGATTATGAAGATAATAAAGATCCTGAGTTTAGACGTAAAAGTTTCAAATCGTTTAGCGATGGGATTCGAAAATATCAGCATACTACCGCGGCTACATATAATATGCAAGTACAACAAGAAAAAATTGAAGCTGATTTACGTGGATTTGAATCAGTCATCGATTATTTATTACATAGTCAAGAAGTAACGCGTGATATGTTTGACCGTCAAAT > CP000730/1420298‑1420558
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
