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 |
|
A21 F117 I0 R1
|
36 |
24.6 |
540534 |
94.7% |
511885 |
140.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
CP000730 |
1,398,333 |
G→A |
100% |
Y101Y (TAC→TAT) |
msrA1 ← |
peptide‑methionine‑(S)‑S‑oxide reductase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | CP000730 | 1,398,333 | 0 | G | A | 94.0%
| 26.8
/ ‑5.9
| 11 | Y101Y (TAC→TAT) | msrA1 | peptide‑methionine‑(S)‑S‑oxide reductase |
| Reads supporting (aligned to +/- strand): ref base G (1/0); new base A (6/4); total (7/4) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| 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: Variant not supported by required number of reads on each strand. |
AAATCTTGGTGATAGTCTTCGGCTTTGTAAAATTGTGACGCTGGTAATATTTTTGTTGCAATTGCCTTATCAGCATTAATCGTATTTTTAAGCTGCTCGATATAAGTCTCAGCGAGTTCTTTTTGATGATCATTAGTGTAGAAAATAGCTGTTTGATATTGAGGACCACGGTCTTGATATTGACCACCTGTATCTAATGGGTCAATGACTGAGAAAAATATTTCTAATAACTTATTGTATGAGAATAATGCAACATCATATT > CP000730/1398196‑1398457
|
aaaTCTTGGTGATAGTCTTCGGCTTTGTAAAATTGTGACGCTGGTAATATTTTTGTTGCAATTGCCTTATCAGCATTAATCGTATTTTTAAGCTGCTCGATATAAGTCTCAGCGAGTTCTTTTTGATGATCATTAGTATAg > 1:147873/1‑141 (MQ=255)
gATAGTCTTCGGCTTTGTAAAATTGTGACGCTGGTAATATTTTTGTTGCAATTGCCTTATCAGCATTAATCGTATTTTTAAGCTGCTCGATATAAGTCTCAGCGAGTTCTTTTTGATGATCATTAGTATAGAAAATAGCTg > 1:186407/1‑141 (MQ=255)
cgTCCTCGGCTTTGTCAAATTGTGACGCTGGTAATATTTTTGTTGCAATTGCCTTCACAGCCTCCATCGTATTTTTAAGCTGCTCGATATACGTCTCAGCGAGGTCTTCTTTATGAGTACTAGTGTAGAAAGTAGGCGttt > 2:11881/2‑141 (MQ=255)
gCTTTGTAAAATTGTGACGCTGGTAATATTTTTGTTGCAATTGCCTTATCAGCATTAATCGTATTTTTAAGCTGCTCGATATAAGTCTCAGCGAGTTCTTTTTGATGATCATTAGTATAGAAAATAGCTGTTTGATATTGa < 1:99120/141‑1 (MQ=255)
tgttgCAATTGCCTTATCAGCATTAATCGTATTTTTAAGCTGCTCGATATAAGTCTCAGCGAGTTCTTTTTGATGATCATTAGTATAGAAGATAGCTGTTTGATATTGAGGACCACGGTCTTGATATTGACCACCTGTATc < 2:176375/141‑1 (MQ=255)
aaTCGTATTTTTAAGCTGCTCGATATAAGTCTCAGCGAGTTCTTTTTGATGATCATTAGTATAGAAAATAGCTGTTTGATATTGAGGACCACGGTCTTGATATTGACCACCTGTATCTAATGGGTCACTGACTGAGaaaaa > 1:262227/1‑141 (MQ=255)
aTTTTTAAGCTGGTCGATATACGTCTCAGCGAGTTCTTTTTGATGATCATTAGTATAGAAAATAGCTGTTTGATATTGAGGACCACGGTCTTGATATTGACCACCTGTATCTAATGGGTCAATGACTGAGAAAAATATTTc > 1:140742/1‑141 (MQ=255)
aGCGAGTTCTTTTTGATGATCATTAGTATAGAAAATAGCTGTTTGATATTGAGGACCACGGTCTTGATATTGACCACCTGTATCTAATGGGTCAATGACTGAGAAAAATATTTCTAATAACTTATTGTATGAGAATATTGc > 2:209011/1‑141 (MQ=255)
cGAGTTCTTTTTGATGATCATTAGTATAGAAAATAGCTGTTTGATATTGAGGACCACGGTCTTGATATTGACCACCTGTATCTAATGGGTCAATGACTGAGAAAAATATTTCTAATAACTTATTGTATGAGAATAATGCaa > 2:35964/1‑141 (MQ=255)
gTTCTTTTTGATGATCATTAGTATAGAAAATAGCTGTTTGATATTGAGGACCACGGTCTTGATATTGACCACCTGTATCTAATGGGTCAATGACTGAGAAAAATATTTCTAATAACTTATTGTATGAGAATAATGCAAcat < 1:258303/141‑1 (MQ=255)
tttGATGATCATTAGTATAGAAAATAGCTGTTTGATATTGAGGACCACGGTCTTGATATTGACCACCTGTATCTAATGGGTCAATGACTGAGAAAAATATTTCTAATAACTTATTGTATGAGAATAATGCAACATCATAtt < 1:121969/141‑1 (MQ=255)
|
AAATCTTGGTGATAGTCTTCGGCTTTGTAAAATTGTGACGCTGGTAATATTTTTGTTGCAATTGCCTTATCAGCATTAATCGTATTTTTAAGCTGCTCGATATAAGTCTCAGCGAGTTCTTTTTGATGATCATTAGTGTAGAAAATAGCTGTTTGATATTGAGGACCACGGTCTTGATATTGACCACCTGTATCTAATGGGTCAATGACTGAGAAAAATATTTCTAATAACTTATTGTATGAGAATAATGCAACATCATATT > CP000730/1398196‑1398457
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
