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 |
|
A4 F1 I2 R1
|
67 |
32.5 |
1435938 |
95.9% |
1377064 |
112.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,763,869 |
(T)7→8 |
coding (1285/1617 nt) |
yfjL ← |
CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,763,862 | 1 | . | T | 96.5%
| 93.0
/ ‑3.0
| 29 | coding (1292/1617 nt) | yfjL | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base T (14/14); total (14/15) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.19e-01 |
ATTAGAGTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGG‑A‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGC > NC_000913/2763735‑2763981
|
aTTAGAGTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGG‑A‑ttttttttgcg < 1:265092/139‑5 (MQ=255)
tAGAGTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGG‑ATTTTTTTTgcgcg < 1:608304/139‑1 (MQ=255)
agagTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGG‑ATTTTTTTTgcgcgc > 1:179829/1‑139 (MQ=255)
gCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGG‑ATTTTTTTTGCGCGCGGTATCGAt < 2:79054/139‑1 (MQ=255)
cGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGG‑ATTTTTTTTGCGCGCGGTATCGATGCAAt > 1:238333/1‑139 (MQ=255)
aaCGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGG‑ATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTcc < 1:392249/139‑1 (MQ=255)
aaCGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGG‑ATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTcc < 2:179829/139‑1 (MQ=255)
gAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGG‑ATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTa < 2:238333/139‑1 (MQ=255)
cGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGG‑ATTTTTTTTGCGCGCGGTATCGATGCAATCCGaa > 2:376641/1‑120 (MQ=255)
cGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGG‑ATTTTTTTTGCGCGCGGTATCGATGCAATCCGaa < 1:376641/120‑1 (MQ=255)
cATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGG‑ATTTTTTTTgcgcg > 1:153130/1‑91 (MQ=255)
cATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGG‑ATTTTTTTTgcgcg < 2:153130/91‑1 (MQ=255)
cATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGG‑ATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTAtct > 1:113041/1‑139 (MQ=255)
ccATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGG‑ATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCa < 2:113041/139‑1 (MQ=255)
ccATAAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGCT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCa < 2:639102/139‑1 (MQ=255)
tCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGG‑ATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAatat > 1:674584/1‑137 (MQ=255)
tCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGG‑ATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAatat < 2:674584/137‑1 (MQ=255)
tGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGG‑ATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCa > 2:215837/1‑139 (MQ=255)
aaGCAGGTAGTTATCGTCTTTAATGTCGAGG‑ATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGaa > 1:64551/1‑139 (MQ=255)
aGCAGGTAGTTATCGTCTTTAATGTCGAGG‑ATTTTTTTTGCGCGCGGTATCGATg < 1:42193/55‑1 (MQ=255)
aGCAGGTAGTTATCGTCTTTAATGTCGAGG‑ATTTTTTTTGCGCGCGGTATCGATg > 2:42193/1‑55 (MQ=255)
gCAGGTAGTTATCGTCTTTAATGTCGAGG‑ATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACaa < 2:278512/77‑1 (MQ=255)
gCAGGTAGTTATCGTCTTTAATGTCGAGG‑ATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACaa > 1:278512/1‑77 (MQ=255)
gTAGTTATCGTCTTTAATGTCGAGG‑ATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAAt > 2:217480/1‑139 (MQ=255)
tCTTTAATGTCGAGG‑ATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACgg > 1:530515/1‑92 (MQ=255)
tCTTTAATGTCGAGG‑ATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACgg < 2:530515/92‑1 (MQ=255)
cTTTAATGTCGAGG‑ATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGc < 2:343877/135‑1 (MQ=255)
cTTTAATGTCGAGG‑ATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGc > 1:343877/1‑135 (MQ=255)
cGAGG‑ATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGACAATGTTAATATCAGTCACCAACTCGCt > 1:89906/1‑110 (MQ=255)
cGAGG‑ATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGACAATGTTAATATCAGTCACCAACTCGCt < 2:89906/110‑1 (MQ=255)
|
ATTAGAGTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGG‑A‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGC > NC_000913/2763735‑2763981
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
