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 |
|
A8 F73 I1 R1
|
23 |
85.6 |
2911730 |
99.3% |
2891347 |
139.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
4,209,679 |
C→A |
noncoding (1533/1542 nt) |
rrsE → |
16S ribosomal RNA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 4,209,679 | 0 | C | A | 97.1%
| 68.9
/ ‑2.7
| 34 | noncoding (1533/1542 nt) | rrsE | 16S ribosomal RNA |
| Reads supporting (aligned to +/- strand): ref base C (1/0); new base A (19/14); total (20/14) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.00e-01 |
TTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑CACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCAC > NC_000913/4209596‑4209812
|
ttCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGa < 2:238646/140‑1 (MQ=11)
ttCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGa < 1:726975/140‑1 (MQ=11)
cGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGaaa > 1:810782/1‑140 (MQ=17)
gggAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAg > 1:38164/1‑140 (MQ=17)
ggCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGaaa > 1:674135/1‑140 (MQ=17)
aCCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAgg > 1:312326/1‑140 (MQ=17)
cTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTc < 2:1284379/140‑1 (MQ=18)
cATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAGGCAAGGCGTCTTGCGAAGCa < 1:726739/140‑1 (MQ=16)
tGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGa < 1:248658/140‑1 (MQ=18)
gggTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATa > 2:717079/1‑140 (MQ=17)
gggTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATa > 2:347648/1‑140 (MQ=17)
gggTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATa > 2:178949/1‑140 (MQ=17)
ggTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAGAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATAc > 1:1179557/1‑140 (MQ=17)
gTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTc > 1:1229359/1‑140 (MQ=17)
aGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTag < 2:38164/140‑1 (MQ=17)
aGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTag < 1:590165/140‑1 (MQ=17)
aGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTag < 1:717079/140‑1 (MQ=17)
aGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTag < 2:312326/140‑1 (MQ=17)
gTAACCGTAGGGGAACCTGCGGTTGTAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTagag < 2:525775/140‑1 (MQ=17)
gTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGCAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTagag > 2:1028850/1‑140 (MQ=17)
gTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTagag > 2:1188504/1‑140 (MQ=17)
gTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTagag < 1:347648/140‑1 (MQ=17)
ccGTAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGccc < 2:409689/140‑1 (MQ=17)
gTAGGGGAACCTGCGGTTGGATAACCTCCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGcc > 1:797440/1‑140 (MQ=11)
tAGGGGAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAgg > 2:1373267/1‑140 (MQ=17)
ggggAACCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGac > 2:540790/1‑140 (MQ=17)
aaCCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCg < 2:968404/140‑1 (MQ=17)
aCCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGc > 1:795881/1‑140 (MQ=17)
aCCTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGc > 2:479266/1‑140 (MQ=17)
ccTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGcc > 1:226873/1‑140 (MQ=17)
ccTGCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGcc > 1:118999/1‑140 (MQ=17)
gCGGTTGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCtt > 1:793672/1‑140 (MQ=17)
ttGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCAc < 2:1179557/140‑1 (MQ=17)
ttGGAT‑‑‑AACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCAc > 1:1008191/1‑140 (MQ=17)
|
TTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGAT‑‑‑CACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGAAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCAC > NC_000913/4209596‑4209812
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
