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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,663,379 |
T→C |
48.3% |
G121G (GGT→GGC) |
rtcB → |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,663,379 | 0 | T | C | 48.3%
| ‑4.1
/ 51.7
| 58 | G121G (GGT→GGC) | rtcB | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (16/14); new base C (18/10); total (34/24) |
| Fisher's exact test for biased strand distribution p-value = 4.35e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.95e-01 |
GCGATTGAAACGGCCGTGCCGCACGGGCGTACCACTGGCCGTTGTAAACGTGATAAAGGTGCCTGGGAAAATCCACCTGTTAACGTCGATGCTAAATGGGCTGAGCTTGAAGCCGGTTATCAGTGGTT > minE/2663320‑2663447
|
gCGATTGAAACGGCCGTGCCGCACGGGCGTACCACTGGCCGTTGTAAACGTGATAAAGGTGCCTGGGaa < 1:521158/69‑1 (MQ=255)
cGTGCCGCACGGGCGTACCACTGGCCGTTGTAAACGTGATAAAGGTGCCTGGGAAAATCCACCTGTTaa < 1:1808062/69‑1 (MQ=255)
cGGGCGTACCACTGGCCGTTGTAAACGTGATAAAGGTGCCTGGGaa > 1:1643785/1‑46 (MQ=255)
cGGGCGTACCACTGGCCGTTGTAAACGTGATAAAGGTGCCTGGGAAAATCCACCTGTTAACGTCGATg > 1:647203/1‑68 (MQ=255)
tACCACTGGCCGTTGTAAACGTGATAAAGGTGCCTGGGAAAATCCACCTGTTAACGTCGATGCTAAATg < 1:2307762/69‑1 (MQ=255)
ggCCGTTGTAAACGTGATAAAGGTGCCTGGGAAAATCCACCTGTTAAc < 1:2326053/48‑1 (MQ=255)
ggCCGTTGTAAACGTGATAAAGGTGCCTGGGAAAATCCACCTGTTAAc < 1:3242240/48‑1 (MQ=255)
ggCCGTTGTAAACGTGATAAAGGTGCCTGGGAAAATCCACCTGTTAAc < 1:3129318/48‑1 (MQ=255)
tGTAAACGTGATAAAGGCGCATGGGAAAATCCGCCTGTTAACGTCGATGcga > 1:628142/1‑50 (MQ=255)
tGTAAACGTGATAAAGGCGCATGGGAAAATCCGCCTGTTAACGTCGATGcga > 1:2166315/1‑50 (MQ=255)
tGTAAACGTGATAAAGGCGCATGGGAAAATCCGCCTGTTAACGTCGATGcga > 1:2341915/1‑50 (MQ=255)
tGTAAACGTGATAAAGGCGCATGGGAAAATCCGCCTGTTAACGTCGATGcga > 1:2101999/1‑50 (MQ=255)
tGTAAACGTGATAAAGGCGCATGGGAAAATCCGCCTGTTAACGTCGATGcga > 1:205753/1‑50 (MQ=255)
tGTAAACGTGATAAAGGCGCATGGGAAAATCCGCCTGTTAACGTCGATGcga > 1:1031127/1‑50 (MQ=255)
tGTAAACGTGATAAAGGCGCATGGGAAAATCCGCCTGTTAACGTCGATGcga > 1:2521776/1‑50 (MQ=255)
tGTAAACGTGATAAAGGCGCATGGGAAAATCCGCCTGTTAACGTCGATGcga > 1:1975690/1‑50 (MQ=255)
tGTAAACGTGATAAAGGCGCATGGGAAAATCCGCCTGTTAACGTCGATGcga > 1:2567014/1‑50 (MQ=255)
tGTAAACGTGATAAAGGCGCATGGGAAAATCCGCCTGTTAACGTCGATGcga > 1:2965147/1‑50 (MQ=255)
tGTAAACGTGATAAAGGCGCATGGGAAAATCCGCCTGTTAACGTCGATGcga > 1:907828/1‑50 (MQ=255)
tGTAAACGTGATAAAGGCGCATGGGAAAATCCGCCTGTTAACGTCGATGcga > 1:693184/1‑50 (MQ=255)
tGTAAACGTGATAAAGGCGCATGGGAAAATCCGCCTGTTAACGTCGATGcga > 1:1474891/1‑50 (MQ=255)
tGTAAACGTGATAAAGGCGCATGGGAAAATCCGCCTGTTAACGTCGATGcga > 1:407693/1‑50 (MQ=255)
tGTAAACGTGATAAAGGCGCATGGGAAAATCCGCCTGTTAACGTCGATGcga > 1:471264/1‑50 (MQ=255)
tGTAAACGTGATAAAGGCGCATGGGAAAATCCGCCTGTTAACGTCGATGcga > 1:1234502/1‑50 (MQ=255)
tGTAAACGTGATAAAGGCGCATGGGAAAATCCGCCTGTTAACGTCGATGcga > 1:1329825/1‑50 (MQ=255)
tGTAAACGTGATAAAGGCGCATGGGAAAATCCGCCTGTTAACGTCGATGc > 1:2510630/1‑50 (MQ=255)
tGTAAACGTGATAAAGGCGCATGGGAAAATCCGCCTGTTAACGTCGATGCGAAATGGGCTGAGCTGGag < 1:234685/69‑2 (MQ=255)
tGTAAACGTGATAAAGGCGCATGGGAAAATCCGCCTGTTAACGTCGATGCGAAATGGGCTGAGCTGGag < 1:469046/69‑2 (MQ=255)
tGTAAACGTGATAAAGGCGCATGGGAAAATCCGCCTGTTAACGTCGATGCGAAATGGGCTGAGCTGGag < 1:1897040/69‑2 (MQ=255)
tGTAAACGTGATAAAGGCGCATGGGAAAATCCGCCTGTTAACGTCGATGCGAAATGGGCTGAGCTGGag < 1:1428075/69‑2 (MQ=255)
tGTAAACGTGATAAAGGCGCATGGGAAAATCCGCCTGTTAACGTCGATGCGAAATGGGCTGAGCTGGag < 1:366303/69‑2 (MQ=255)
tGTAAACGTGATAAAGGCGCATGGGAAAATCCGCCTGTTAACGTCGATGCGAAATGGGCTCAGCTGGag < 1:2112185/69‑2 (MQ=255)
gTAAACGTGATAAAGGCGCATGGGAAAATCCGCCTGTTAACGTCGATGCGAAATGGGCTGAGCTGGag < 1:2299436/68‑2 (MQ=255)
gTAAACGTGATAAAGGCGCATGGGAAAATCCGCCTGTTAACGTCGATGCGAAATGGGCTGAGCTGGag < 1:258261/68‑2 (MQ=255)
tAAACGTGATAAAGGCGCATGGGAAAATCCGCCTGTTAACGTCGATGCGAAATGGGCTGAGCTGGag < 1:1405006/67‑2 (MQ=255)
aCGTGATAAAGGCGCATGGGAAAATCCGCCTGTTAACGTCGATGCGAAATGGGCTGAGCTGGag < 1:437817/64‑2 (MQ=255)
aTAAAGGTGCCTGGGAAAATCCACCTGTTAACGTCGATGCTAAATGGGCTGAGCTTGAAGCCGGTTATc < 1:1047685/69‑1 (MQ=255)
aTAAAGGTGCCTGGGAAAATCCACCTGTTAACGTCGATGCTAAATGGGCTGAGCTTGAAGCCGGTTATc < 1:721529/69‑1 (MQ=255)
aTAAAGGTGCCTGGGAAAATCCACCTGTTAACGTCGATGCTAAATGGGCTGAGCTTGAAGCCGGTTATc < 1:122997/69‑1 (MQ=255)
aTAAAGGTGCCTGGGAAAATCCACCTGTTAACGTCGATGCTAAATGGGCTGAGCTTGAAGCCGGTTATc < 1:1302375/69‑1 (MQ=255)
aTAAAGGTGCCTGGGAAAATCCACCTGTTAACGTCGATGCTAAATGGGCTGAGCTTGAAGCCGGTTATc < 1:1864561/69‑1 (MQ=255)
aTAAAGGTGCCTGGGAAAATCCACCTGTTAACGTCGATGCTAAATGGGCTGAGCTTGAAGCCGGTTATc < 1:2413736/69‑1 (MQ=255)
aTAAAGGTGCCTGGGAAAATCCACCTGTTAACGTCGATGCTAAATGGGCTGAGCTTGAAGCCGGTTATc < 1:2548578/69‑1 (MQ=255)
aTAAAGGTGCCTGGGAAAATCCACCTGTTAACGTCGATGCTAAATGGGCTGAGCTTGAAGCCGGTTATc < 1:1952252/69‑1 (MQ=255)
aaGGTGCCTGGGAAAATCCACCTGTTAACGTCGATGCTAAATTGGCTGAGCTTGAAGCCGGTTATCAGt > 1:163944/1‑69 (MQ=255)
aaGGTGCCTGGGAAAATCCACCTGTTAACGTCGATGCTAAATGGGCTGAGCTTGAAGCCGGTTATCAg > 1:3061909/1‑68 (MQ=255)
aaGGTGCCTGGGAAAATCCACCTGTTAACGTCGATGCTAAATGGGCTGAGCTTGAAGCCGGTTATCAGt > 1:2856675/1‑69 (MQ=255)
aaGGTGCCTGGGAAAATCCACCTGTTAACGTCGATGCTAAATGGGCTGAGCTTGAAGCCGGTTATCAGt > 1:451811/1‑69 (MQ=255)
aaGGTGCCTGGGAAAATCCACCTGTTAACGTCGATGCTAAATGGGCTGAGCTTGAAGCCGGTTATCAGt > 1:1408305/1‑69 (MQ=255)
aaGGTGCCTGGGAAAATCCACCTGTTAACGTCGATGCTAAATGGGCTGAGCTTGAAGCCGGTTATCAGt > 1:3244650/1‑69 (MQ=255)
aaGGTGCCTGGGAAAATCCACCTGTTAACGTCGATGCTAAATGGGCTGAGCTTGAAGCCGGTTATCAGt > 1:585856/1‑69 (MQ=255)
aaGGTGCCTGGGAAAATCCACCTGTTAACGTCGATGCTAAATGGGCTGAGCTTGAAGCCGGTTATCAGt > 1:1398951/1‑69 (MQ=255)
aaGGTGCCTGGGAAAATCCACCTGTTAACGTCGATGCTAAATGGGCTGAGCTTGAAGCCGGTTATCAGt > 1:2534914/1‑69 (MQ=255)
aaGGTGCCTGGGAAAATCCACCTGTTAACGTCGATGCTAAATGGGCTGAGCTTGAAGCCGGTTATCAGt > 1:66497/1‑69 (MQ=255)
aaGGTGCCTGGGAAAATCCACCTGTTAACGTCGATGCTAAATGGGCTGAGCTTGAAGCCGGTTATCAGt > 1:2040559/1‑69 (MQ=255)
aaGGTGCCTGGGAAAATCCACCTGTTAACGTCGATGCTAAATGGGCTGAGCTTGAAGCCGGTTATCAGt > 1:2044473/1‑69 (MQ=255)
aaGGTGCCTGGGAAAATCCACCTGTTAACGTCGATGCTAAATGGGCTGAGCTTGAAGCCGGTTATCAGt > 1:824290/1‑69 (MQ=255)
aaGGTGCCTGGGAAAATCCACCTGTTAACGTCGATGCTAAATGGGCTGAGCTTGAAGCCGGTTATCAGt > 1:306580/1‑69 (MQ=255)
tGCCTGGGAAAATCCACCTGTTAACGTCGATGCTAAATGGGCTGAGCTTGAAGCCGGTTATCAGTGGtt < 1:3042300/69‑1 (MQ=255)
tGCCTGGGAAAATCCACCTGTTAACGTCGATGCTAAATGGGCTGAGCTTGAAGCCGGTTATCAGTGGtt < 1:45469/69‑1 (MQ=255)
|
GCGATTGAAACGGCCGTGCCGCACGGGCGTACCACTGGCCGTTGTAAACGTGATAAAGGTGCCTGGGAAAATCCACCTGTTAACGTCGATGCTAAATGGGCTGAGCTTGAAGCCGGTTATCAGTGGTT > minE/2663320‑2663447
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
