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 |
|
A27 F124 I0 R1
|
44 |
29.6 |
1159012 |
90.6% |
1050064 |
142.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_000913 |
696,470 |
C→T |
100% |
noncoding (35/75 nt) |
glnX ← |
tRNA‑Gln |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 696,470 | 0 | C | T | 98.3%
| 55.8
/ ‑6.8
| 25 | noncoding (35/75 nt) | glnX | tRNA‑Gln |
| Reads supporting (aligned to +/- strand): ref base C (0/1); major base T (11/10); minor base G (0/2); total (11/14) |
| Fisher's exact test for biased strand distribution p-value = 4.78e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CGTCGCATCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGA > NC_000913/696330‑696609
|
cGTCGCATCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAg < 1:293519/143‑1 (MQ=255)
cGTCGCATCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAg < 1:293782/143‑1 (MQ=255)
gTCGCAGCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGCCATTGTTGTTGTTGTGTAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGa < 1:573413/143‑1 (MQ=25)
cGCATCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAAt > 2:128605/1‑143 (MQ=255)
gCATCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCTAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATc < 1:363380/143‑1 (MQ=255)
gACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTCGGATTGGCTGGCGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGc > 1:573540/1‑143 (MQ=37)
gACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCACGCCGAAGCGAGCTATTTTAATGTGGCTGGGGTACGAAGATTCGAACCACAGAATGCCGGAATTAGAAtacagaca > 2:38285/1‑136 (MQ=255)
gtCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCAGGTGCCTTACCGCTTGGCGATAccc > 1:84501/1‑143 (MQ=255)
aaCATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGGATCCGGTGCCTTACCGCTTGGCGAGACGCCaa > 1:308758/1‑143 (MQ=255)
ttCGACATTGAATGAGCGCAGAAAAGCAAAAAGCTCGCTGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGCATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCa < 2:258016/143‑1 (MQ=255)
tCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACCGGGTGCAc > 1:226009/1‑143 (MQ=255)
atgaaCGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTa > 1:327913/1‑143 (MQ=255)
tgaaCGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTaa < 1:67908/143‑1 (MQ=255)
gaaCGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTGTAATGTGGCTGGTGTACGAGGATTCGAACCTCGGAATGCAGGAATAAGAAGCCGGTGGCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAg < 1:24621/143‑1 (MQ=25)
aGAAACGCAAATGGCTCGCCGACGCGGGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCtt < 2:203854/143‑1 (MQ=21)
gCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGTGTGCACTTGCAAGGTACGCGTCTTGAAtga > 1:500952/1‑141 (MQ=255)
acTTTTTTACGGTGGCCGGGCTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTGCCGCTTGGCGATACCCCAACTCGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGAtt < 2:426425/142‑1 (MQ=25)
cTTTTGTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTc < 1:237022/143‑1 (MQ=255)
tttttAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTAGCTACATCGCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGa < 1:363586/143‑1 (MQ=25)
ggATTCGAACCTCGGAATGCCGGAATGAGAAGCCGGTGCCTTACCGCTTGGCGATACGCCAACTGGGTGCACGTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGaa < 2:264526/143‑1 (MQ=255)
cGGAAGGCCGGAATTAGAAGCCGGTGCCTTCCCGCTTGGCGATACCCCAACTGGGTGCACTTACACGGCAAGCCATTCATAGAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTa < 1:81641/143‑1 (MQ=21)
ggAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGCATGCCGGAATCCGAATCCGGTGCCTTag > 1:20693/1‑142 (MQ=255)
tGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGACTCAGAATCCGGTGCCTTCCCGCt > 1:504329/1‑143 (MQ=255)
ggAATGAGAATCCGGTGCATTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGc < 1:25824/143‑1 (MQ=255)
aaTTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTCCGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGGGCCTTACCGCTTGGCGa > 1:26278/1‑143 (MQ=255)
|
CGTCGCATCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGA > NC_000913/696330‑696609
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
