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 |
|
A23 F22 I0 R1
|
38 |
28.5 |
1079870 |
90.4% |
976202 |
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 | 96.1%
| 56.4
/ ‑4.2
| 26 | noncoding (35/75 nt) | glnX | tRNA‑Gln |
| Reads supporting (aligned to +/- strand): ref base C (1/0); new base T (15/10); total (16/10) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.47e-01 |
| 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. |
CGCATCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGA > NC_000913/696333‑696609
|
cGCATCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGACTGCCAGAATTAGGAt > 2:129029/1‑143 (MQ=255)
cATCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAGGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACGTCGGAAGGCCGGAATTAGAATcc > 1:152/1‑143 (MQ=255)
acgctgcaGGAAAAGACGTGTCAACCTCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGcc < 2:152/136‑1 (MQ=37)
gATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCtt > 2:529791/1‑143 (MQ=255)
acaaGCCGGGTCAACAGCGCTGTCGACATTGAATGAACGCAGAAGAGCAAAAAGCTCGCCGAAGCGAGCTCTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGACTTAGAATCCGGTGCCTTACCGCtta < 2:39939/141‑2 (MQ=25)
gtgtCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATAc > 2:226429/1‑143 (MQ=255)
tgtCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATAcc < 1:385811/143‑1 (MQ=255)
gtCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGACCCTCGGAATGCCGGAAGTAGAATCCGGTCCCTCACCGCTTGGCGCTAccc > 2:122815/1‑143 (MQ=37)
gtCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGAtgaac > 1:474037/1‑139 (MQ=255)
aTCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTg > 1:38225/1‑143 (MQ=255)
cagtgaatgaaCGCAGAAAGGCAAAAAGGTCGCCGAAGGGTGGTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGACCTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTAc < 2:355322/140‑1 (MQ=21)
ctgaatgaaCGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACaa < 1:317579/142‑1 (MQ=255)
gCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATaa > 1:141292/1‑143 (MQ=255)
gaaGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCGTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTg < 1:210814/142‑1 (MQ=255)
aaGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACAGGTTGCACTTACAATGTCCGCGTATTTACTATATTgt > 2:349180/1‑142 (MQ=18)
gCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGGACTTACAAGGTAAGCGTATTGAATAAATTGGCTgggg > 1:220467/1‑143 (MQ=255)
aaTGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTAGGTGGACTTGCATGGGACGCGTATTGACGAAATAGTCTGGAGTACGAGGATTCGaagcga > 2:1618/1‑139 (MQ=17)
gtgtgGCGGGGGCAGGAGGGTGCGAGCCTCGGAATGGCGGCATTAGAATCCGTGGCCCTACCGCTTGGCGGTACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCg < 2:501072/142‑1 (MQ=255)
aggtgGCGCGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCg < 2:340876/141‑1 (MQ=255)
gAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAg < 1:539626/143‑1 (MQ=255)
aGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATACATTGGCTGGGGGACGAGGATTCGACCCTCGGAATGCCGGAGTCAgc > 1:446145/1‑142 (MQ=37)
cGAACCGCGGAATGCCGGAATTAGTACGCGGCGCCTTACCGCTTGGCGGTACCCCAACTGGGTGCACGTACGAGGTAAGCGGCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCgg < 2:256426/143‑1 (MQ=25)
gAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGACGATACCCCAACTGGGTGCACTTGCAATGTAAGCGTATTGAATAAATTTGCAGGCGTACGAGGCTACGAACCGCGGAACGACCGAAACAGAATCAgga > 2:430820/1‑142 (MQ=18)
gAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGACTCAGAATCCGGTGGCTTaac > 1:118592/1‑141 (MQ=255)
tGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGGCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGGGCCTTACCGCt > 1:133425/1‑143 (MQ=255)
aaTTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGGATTGGATAGATTGGCTGAGGTAGGAGGAGTCGAACCTCGGAATGGCGGAAGCAGAATCCGGTGCCTTACCGTTGGGcag > 1:337444/1‑141 (MQ=37)
|
CGCATCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGA > NC_000913/696333‑696609
|
| 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
