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 |
|
A1 F71 I0 R1
|
28 |
19.0 |
797258 |
91.3% |
727896 |
142.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_000913 |
463,457 |
G→A |
45.0% |
G515S (GGT→AGT) |
ppiD → |
periplasmic folding chaperone |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 463,457 | 0 | G | A | 45.0%
| ‑0.9
/ 18.9
| 20 | G515S (GGT→AGT) | ppiD | periplasmic folding chaperone |
| Reads supporting (aligned to +/- strand): ref base G (7/4); new base A (4/5); total (11/9) |
| Fisher's exact test for biased strand distribution p-value = 6.53e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.37e-01 |
AGCGAGCACAAACCGGAAGCGGTGAAACCGTTGGCAGATGTTCAGGAACAAGTTAAGGCATTGGTTCAGCACAACAAAGCTGAACAACAGGCGAAAGTGGATGCTGAGAAACTGCTGGTTGATTTGAAAGCCGGCAAAGGTGCGGAAGCTATGCAGGCTGCCGGTCTGAAATTTGGCGAGCCGAAAACCTTAAGCCGTTCCGGTCGTGACCCGATTAGCCAGGCGGCGTTTGCACTGCCACTGCCAGCGAAAGACAAACCGAGCTACGGTATGGCGAC > NC_000913/463319‑463596
|
aGCGAGCACAAACCGGAAGCGGTGCAACAATTGGCAGATGTTCAGGAACCCGTTTTTTTATATTTTCACCACCTCTATTGTGAACAACAGGCGAGAGTGGATGCTGAGAAACTGCGGGGTGATTTGAAAGCCGGCACAGGTGc > 2:281882/1‑143 (MQ=255)
aaaCCGGAAGCGGTGAAACCGTTGGCAGATGTTCAGGAACAAGTTAAGGCATTGGTTCAGCACAACAAAGCTGAACAACAGGCGAAAGTGGATGCTGAGAAACGGCGGGTTGATTGGAAAGCCGGCAAAGGTGCCGCAGccag > 1:51240/1‑140 (MQ=255)
ggcaGCGGTGAACCCGTTGGAAGATGTTCAGGAAGAAGTTAAGGCATTGGTTCAGCACAACAAAGCTGAACAACAGGCGAAAGTGGATGCTGAGAAACTGCTGGTTGATTTGAAAGCCGGCAAAAGTGCGGAAGCTATGCAgg < 2:336090/140‑1 (MQ=255)
ggAAGCGGTGAAACCGTTGGCAGATGTTCAGGAACAAGTTAAGGCATTGGTTCAGCACAACAAAGCTGAACAACAGGCGAAAGTGGATGCTGAGAAACTGCTGGTTGATTTGAAAGCCGGCACAGGTGCGGAAGCTATGCAgg > 2:317492/1‑143 (MQ=255)
ggAAGCGGTGAAACCGTAGGCAGATGTTCAGGAACAAGTTAAGGCATTGGTTCAGCACAACAAAGCTGAACAACAGGCGAAAGTGGATGCTGAGAAACTGCTGGTTGATTTGAAAGCCGGCAAAAGTGCGGAAGCTATGCAgg < 1:266933/143‑1 (MQ=255)
tGAACCCCTTGGCAGACGTTCACGAACAAGTTAACGCATTGGTTCAGCACAACAAAGCTGAACAACAGGCGAAAGTGGATGCTGAGAAACTGCTGGTTGATTTGAAAGCCGGCAAAAGTGCGGAAGCTATGCAGGCTGCCGGt < 1:344161/143‑1 (MQ=255)
gAAACCGTTGGCAGATGTTCAGGAACAAGTTAAGGCATTGGTTCAGCACAACAAAGCTGAACAACAGGCGAAAGTGGATGCTGAGAAACTGCTGGTTGATTTGAAAGCCGGCAAAGGTGCGGAAGCTATGCAGGCTGCCGGTc < 2:130172/143‑1 (MQ=255)
aGGAACAAGTTAAGTCATTGGTTCAGCACAACAAAGCTGAACAACAGGCGAAAGTGGATGCTGAGAAACTGCTGGTTGATTTGAAAGCCGGCAAAGGTGCGGAAGCTATGCAGGCTGCCGGTCTGAAATTTGGCGAGCCGaaa < 1:262115/143‑1 (MQ=255)
aaGGCATTGGTTCAGCACAACAAAGCTGAACAACAGGCGAAAGTGGATGCTGAGAAACTGCTGGTTGATTTGAAAGCCGGCAAAAGTGCGGAAGCTATGCAGGCTGCCGGTCTGAAATTTGGCGAGCCGAAAACCCTAAGCCg > 2:393920/1‑143 (MQ=255)
gCATTGGTTCAGCACAACAAAGCGGAACAACAGGCGAAAGTGGATGCGGAGAAACTGCTGGTTGATTTGAAAGCCGGCAAAGGTGCGGAAGCTATGCAGGCTGCCGGTCTGAAATTTGGCGAGCCGAAAACCTTAAGCCGTTc < 1:226514/143‑1 (MQ=255)
ttCAGCACAACAAAGCTGAACAACAGGCGAAAGTGGATGCTGAGAAACTGCTGGTTGATTTGAAAGCCGGCAAAGGTGCGGAAGCTATGCAGGCTGCCGGTCTGAAATTTGGCGAGCCGAAAACCTTAAGCCGTTCCGGTCGt > 2:835/1‑143 (MQ=255)
gCGAAAGTGGATGCTGAGAAACTGCTGGTTGATTTGAAAGCCGGCAAAGGTGCGGAAGCTATGCAGGCTGCCGGTCTGAAATTTGGCGAGCCGAAAACCTTAAGCCGGTCCGGTCGTGACCCGATTAGCCAGgcggcgggtcc > 2:60102/1‑138 (MQ=255)
tGAGAAACTGCTGGTTGATTTGAAAGCCGGCAAAAGTGCGGAAGCTATGCAGGCTGCCGGTCTGAAATTTGGCGAGCCGAAAACCTTAAGCCGTTCCGGTCGTGACCCGATTAGCCAGGCGGCGTTTGCACTGCCACTGCCAg > 1:298512/1‑143 (MQ=255)
gagaAACTGCTGGTTGATTTGAAAGCCGGCAAAAGGGCGGAAGCTATGCAGGCTGCCGGTCTGAAATTTGGCGAGCCGAAAACCTTAAGCCGTTCCGGTCGTGACCCGATTAGCCAGGCGGCGTTTGCACTGCCACTGCCAGc < 1:219674/143‑1 (MQ=255)
aaaCTGCTGGTTGATTTGAAAGCCGCCAAAAGTGCGGAAGCTATGCAGGCTGCCGGTCTGAAATTTGGCGAGCCGAAAACCTTAAGCCGTTCCGGTCGTGACCCGATTAGCCAGGCGGCGTTTGCACTGCCACTGCCAGCGaa < 2:317013/143‑1 (MQ=255)
tgGTTGATTTGAAAGCCGGCAAAAGTGCGGAAGCTATGCAGGCTGCCGGTCTGAAATTTGGCGAGCCGAAAACCTTAAGCCGTTCCGGTCGTGACCCGATTAGCCAGGCGGCGTTTGCACTGCCACTGCCCGCGAAAGACaaa > 2:102942/1‑143 (MQ=255)
aTTTGAAAGCCGGCAAAAGTGCGGAAGCTATGCAGGCTGCCGGTCTGAAATTTGGCGAGCCGAAAACCTTAAGCCGTTCCGGTCGTGACCCGATTAGCCAGGCGGCGTTTGCACTGCCACTGCCAGCGAAAGGCAAACCGAGc > 2:242551/1‑143 (MQ=255)
ccGGCAAAGGTGCGGAAGCTATGCAGGCTGCCGGTCTGAAATTTGGCGAGCCGACAACCTCAAGCCGTTCCGGTCGTGACCCGATTAGCCAGGCGGCGTTTGCACGGCCACTGCCAGCGAAAGACCAACCGAGCTACggcagc > 1:149499/1‑139 (MQ=255)
ccGGCAAAGGTGCGGAAGCTATGCAGGCTGCCGGTCTGAAATTTGGCGAGCCGAAAACCTTAAGCCGTTCCGGTCGTGACCCGATTAGCCAGGCGGCGTTTGCACTGCCACTGCCAGCGAAAGACAAACCGAGCTCCAGTATg > 1:165852/1‑143 (MQ=255)
aaaGGTGCGGAAGCTATGCAGGCTGCCGGTCTGAAATTTGGCGAGCCGAAAACCTTAAGCCGTTCCGGTCGTGACCCGATTAGCCAGGCGGCGTTTGCACTGCCACTGCCAGCGAAAGACAAACCGAGCTACGGTATGGCGAc < 1:317492/143‑1 (MQ=255)
|
AGCGAGCACAAACCGGAAGCGGTGAAACCGTTGGCAGATGTTCAGGAACAAGTTAAGGCATTGGTTCAGCACAACAAAGCTGAACAACAGGCGAAAGTGGATGCTGAGAAACTGCTGGTTGATTTGAAAGCCGGCAAAGGTGCGGAAGCTATGCAGGCTGCCGGTCTGAAATTTGGCGAGCCGAAAACCTTAAGCCGTTCCGGTCGTGACCCGATTAGCCAGGCGGCGTTTGCACTGCCACTGCCAGCGAAAGACAAACCGAGCTACGGTATGGCGAC > NC_000913/463319‑463596
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
