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 |
|
A5 F13 I0 R1
|
213 |
60.4 |
2554362 |
98.6% |
2518600 |
147.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
3,171,774 |
A→T |
17.5% |
I16F (ATT→TTT) |
PP_2784 → |
short‑chain dehydrogenase/reductase family oxidoreductase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 3,171,774 | 0 | A | T | 17.5%
| 51.4
/ 2.1
| 33 | I16F (ATT→TTT) | PP_2784 | short‑chain dehydrogenase/reductase family oxidoreductase |
| Reads supporting (aligned to +/- strand): ref base A (24/3); new base T (3/3); total (27/6) |
| Fisher's exact test for biased strand distribution p-value = 5.77e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GCCCGGCCTGAAGAAATTGCCGACGCGGTGCTGTATCTGGCCGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGCGGCCAATGGTATTGGCC‑GCGCCGTCGCGGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTGATCTTGCTTGATCGGGATCTGGCAACCTTGCAGGGGTGGGTCACCGAGGGCGAATTTGCCGCTCGTATCGAAACCCATCAAGCGAACATCGCC > NC_002947_CJ‑RC/3171628‑3171917
|
gCCCGGCCTGAAGAAATTGCCGACGCGGTGCTGTATCTGGCCGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGCGGCCAATGGTAtt < 6:130934/149‑1 (MQ=255)
cccGGCCTGAAGAAATTGCCGACGCGGTGCTGTATCTGGCCGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGCGGCCAATGGTATTg < 4:194897/149‑1 (MQ=255)
tGAAGAAATTGCCGACGCGGTGCTGTATCTGGCCGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGCGGCCAATGGTATTGGCC‑gcgc > 7:195700/1‑149 (MQ=255)
gaagaaATTGCCGACGCGGTGCTGTATCTGGCCGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGCGGCCAATGGTATTGGCC‑GCGcc > 5:146403/1‑149 (MQ=255)
aataaaTTGCCTACGCGGTGCTTTATCTGCCCGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGGCCGTCAACGGCGGTTTGAAAATGCCATGAGCCAGTTACGCACGTTTGTGATTACCGGCGCGGCAAATGGTTTTGGCC‑gcgc < 8:233041/144‑1 (MQ=255)
agaaATTGCCGACGCGGTGCTGTATCTGGCCGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTTAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGCGGCCAATGGTATTGGCC‑GCGCCg < 1:111766/148‑1 (MQ=255)
aaTTGCCGACGCGGTGCTGTATCTGGCCGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGACAGTTACGCACGATTGTGATTACCGGCGCGGCCAATGGTTTTGGCC‑GCGCCGgcgc > 4:273879/1‑149 (MQ=255)
gTATCTGGCCGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGCGGCCAATGGTATTGGCC‑GCGCCGTTGCGGAAAGTTTTGCAGcc > 8:154863/1‑147 (MQ=255)
gTATCTGGCCGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCCCGGCCAATGGTAATGGCC‑GCGCCGTCGCGGAAACTTTTTGAGcc > 6:171451/1‑147 (MQ=255)
tATCTGGCCGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGCGGCCAATGGTATTGGCC‑GCGCCGTCGCGGAAAGTTTTGCAGccccg > 8:211204/1‑147 (MQ=255)
tCTGGCCGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGCGGCCAATGGTATTGGCC‑GCGCCGTCGCGGAAAGTTTTGCAGCCCAGGc > 7:261467/1‑149 (MQ=255)
cGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGCGGCCCATGGTATTGGCC‑GCGCCGGGGCGGAAATTTTTTCAGCCCAGGCCGAggc > 1:311321/1‑147 (MQ=255)
cGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGCGGCCAATGGTATTGGCC‑GCGGCGTCGCGGAAAGTTTTTCAGCCCACGCCGAGcc > 5:132024/1‑148 (MQ=255)
ccTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGCGGCCAATTGTTTTGGCC‑GCGCCGTCGCGGTAAGTTTTTCAGCCCAGGCCCAGCACCTTTTggt > 1:53939/1‑147 (MQ=255)
ccTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGCGGCCAATGGTATTGGCC‑GCGCCGTCGCGGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTGAt > 6:217077/1‑149 (MQ=255)
cTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGCGGCCAATGGTATTGGCC‑GCGCCGTCGCGGAAAGTTTTGCAGCCCCGGCCGCGCACCGTTTGAta > 2:235300/1‑148 (MQ=255)
tACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGAGCGGCCCATGGTTTTTGCC‑GCGCCCTAGCGGGAAGATTTGCACCCCACCCCGCGCAACATTTGaaaat > 3:256166/1‑144 (MQ=255)
aTCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGCGGCCAATGGTATTGGCC‑GCGCCGTCGCGGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTGATcttgctt > 2:106641/1‑149 (MQ=255)
gCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGCGGCCAATGGTATTGGCC‑GCGCCGGCGCGGTAAGTTTTGCAGCCCAGGCCGAGCCCCGTTTGATGTTGGGTGATgggg > 4:173104/1‑149 (MQ=255)
cGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGCGGCCAATGGTATTGGCC‑GCGCCGTCGCGGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTGATATTGCTTGATAGGGa > 5:310606/1‑149 (MQ=255)
tCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGCGGCCAATGGTATTTGCC‑GCGCCGTCGCCGAAAATTTTTCAGCCCCAGCCCAGCACCATTTTATATTTCTTTATAGGGAtaaag > 4:261613/1‑145 (MQ=255)
cGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGCGGCCAATGGTATTGGCC‑GCGCCGGGGCGGTAAGTTTTTCAGCCCCGGCCGGGCACCGTTTGATGTTGCTTGATAGGGGTCTGGCAACCtt > 2:260540/1‑149 (MQ=255)
aaaTGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGCGGCCAATGGTATTGGCC‑GCGCCGTCGCGGGAAGTTTTGCAGCCCCGGGCGCGCCCCGTTTGGTCTTGGGTTATCGGGGTCTGGCAACCGTGCAGGGGTGGGTGACCg > 4:233188/1‑149 (MQ=255)
cATGAGCCAGTTACGCACGATTGTGATTACCGGCGCGGCCAATGGTATTGGCC‑GCGCCGTCGCGGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTGATCTTGCTTGATCGGGATCTGGCAACCTTGCAGGGGTGGGTCACCGAGGGc > 6:311547/1‑148 (MQ=255)
tGAGCCAGTTACGCACGATTGTGATTACCGGCGCGGCCAATGGTATTGGCC‑GCGCCGTCGCGGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTGATGTTGCTTGATCGGGATCTGGCAACCTTGCAGGGGTGGGTAACCGAGGGCGaa > 8:241732/1‑149 (MQ=255)
gCACGATTGTGATTACCTGCCCGGCCAATGGTATAGGCC‑CCGCCGTCGCCGAAAGTTTTGCAGCCCAGGCCCAGCACCTTTTGATCTTGCTTGAACGGGAACTGGCCACCTTGCAGCGGTGGGTCACCGAGGGCGAATTTGCCGCTCg > 6:144876/1‑148 (MQ=255)
ttGTGATTACCGGCGCCGCCAATGGTATTGGCC‑GCGCCGTCGCGGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTGATCTTTCTTGATCGGGATCTGGCAAACATGCAGGGGTGGGTCACCGAGGGCGAATTTGCCGCTCGTATCGa > 4:292085/1‑148 (MQ=255)
ttaTTCCCGGCG‑GGCCAATTGTTTTGGCCGGCGCCGTCGCGGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTGATCTTGCTTGATCGGGATCTGGCAACCTTGCAGGGGTGGGTCACCGAGGGCGAATTTGCCGCTCGTATCGAAAc < 6:132024/146‑1 (MQ=255)
aCCGGCGCGGCCAATGGTATTGGCC‑GCGCCGTCGCGGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTGATCTTGCGTGATCGGGGTCTGGCAACCTTGCAGGGGTGGGTCACCGAGGGCGAATTTGCCGCTCGTATCGAAACCCATc > 2:42980/1‑148 (MQ=255)
gcgGCCAATGGTATTGGCC‑GCGCCGTCGCGGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTGATCTTGCTTGATCGGGATCTGGCAACCTTGCAGGGGTGGGTCACCGAGGGCGAATTTGCCGCTCGTATCGAAACCCATCAAGCGaa > 2:276531/1‑149 (MQ=255)
gCCAATGGTATTGGCC‑GCGCCGTCGCGGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTGATCTTGCTTGATCGGGATCTGGCAACCTTGCAGGGGTGGGTCACCGAGGGCGAATTTGCCGCTCGTATCGAAACCCATCAAGCGAACAt > 5:7425/1‑149 (MQ=255)
aaTGGTTTTGGCCGGGGCCGTCGCGGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTGATCTTGCTTGATCGGGATCTGGCAACCTTGCAGGGGTGGGTCACCGAGGGTGAATTTGCCGCTCGTATCGAAACCCATCAAGCGAACATCg < 7:68453/149‑1 (MQ=255)
tGGTATTGGCC‑GCGCCGTCGCGGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTGATCTTGCTTGATCGGGATCTGGCAACCTTGCAGGGGTGGGTCACCGAGGGCGAATTTGCCGCTCGTATCGAAACCCATCAAGCGAACATCGcc > 6:207055/1‑148 (MQ=255)
|
GCCCGGCCTGAAGAAATTGCCGACGCGGTGCTGTATCTGGCCGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGCGGCCAATGGTATTGGCC‑GCGCCGTCGCGGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTGATCTTGCTTGATCGGGATCTGGCAACCTTGCAGGGGTGGGTCACCGAGGGCGAATTTGCCGCTCGTATCGAAACCCATCAAGCGAACATCGCC > NC_002947_CJ‑RC/3171628‑3171917
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
