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 |
821,005 |
G→A |
39.5% |
P209P (CCG→CCA) |
kdsA → |
3‑deoxy‑D‑manno‑octulosonate 8‑phosphate synthase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 821,005 | 0 | G | A | 39.5%
| 24.1
/ 33.0
| 53 | P209P (CCG→CCA) | kdsA | 3‑deoxy‑D‑manno‑octulosonate 8‑phosphate synthase |
| Reads supporting (aligned to +/- strand): ref base G (2/30); new base A (18/3); total (20/33) |
| Fisher's exact test for biased strand distribution p-value = 3.29e-09 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.00e-01 |
TGGTAACTCGCCGGTGATTTTCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGC > minE/820951‑821067
|
tGGTAACTCGCCGGTGATTTTCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTc < 1:1285074/69‑1 (MQ=255)
tGGTAACTCGCCGGTGATTTTCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTc < 1:2285397/69‑1 (MQ=255)
tttCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCa < 1:2967138/69‑1 (MQ=255)
tttCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCa < 1:1772516/69‑1 (MQ=255)
tttCGACGTGACCCACGCACTGCAATCCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCa < 1:2231137/69‑1 (MQ=255)
ttCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCa < 1:1003026/68‑1 (MQ=255)
tGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTg < 1:3169277/69‑1 (MQ=255)
tGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGGCGTGCTCAGGTGGCTg < 1:1674045/69‑1 (MQ=255)
aCCCACGCACTGCAATGTCGCGATCCATTTGGCGCAGCTTcc > 1:1836794/1‑42 (MQ=37)
aCCCACGCACTGCAATGTCGCGATCCATTTGGCGCAGCTTcc > 1:2372961/1‑42 (MQ=37)
aCCCACGCACTGCAATGTCGCGATCCATTTGGCGCAGCTTcc > 1:2688820/1‑42 (MQ=37)
aCCCACGCACTGCAATGTCGCGATCCATTTGGCGCAGCTTcc > 1:2248500/1‑42 (MQ=37)
aCCCACGCACTGCAATGTCGCGATCCATTTGGCGCAGCTTcc > 1:2223960/1‑42 (MQ=37)
aCCCACGCACTGCAATGTCGCGATCCATTTGGCGCAGCTTcc > 1:2159067/1‑42 (MQ=37)
aCCCACGCACTGCAATGTCGCGATCCATTTGGCGCAGCTTcc > 1:3248353/1‑42 (MQ=37)
aCCCACGCACTGCAATGTCGCGATCCATTTGGCGCAGCTTcc > 1:1845407/1‑42 (MQ=37)
aCCCACGCACTGCAATGTCGCGATCCATTTGGCGCAGCTTcc > 1:3397273/1‑42 (MQ=37)
aCCCACGCACTGCAATGTCGCGATCCATTTGGCGCAGCTTcc > 1:1810549/1‑42 (MQ=37)
aCCCACGCACTGCAATGTCGCGATCCATTTGGCGCAGCTTcc > 1:1808122/1‑42 (MQ=37)
aCCCACGCACTGCAATGTCGCGATCCATTTGGCGCAGCTTcc > 1:539671/1‑42 (MQ=37)
aCCCACGCACTGCAATGTCGCGATCCATTTGGCGCAGCTTcc > 1:613002/1‑42 (MQ=37)
aCCCACGCACTGCAATGTCGCGATCCATTTGGCGCAGCTTcc > 1:1655583/1‑42 (MQ=37)
aCCCACGCACTGCAATGTCGCGATCCATTTGGCGCAGCTTcc > 1:1412011/1‑42 (MQ=37)
aCCCACGCACTGCAATGTCGCGATCCATTTGGCGCAGCTTcc > 1:743525/1‑42 (MQ=37)
aCCCACGCACTGCAATGTCGCGATCCATTTGGCGCAGCTTcc > 1:1559729/1‑42 (MQ=37)
aCCCACGCACTGCAATGTCGCGATCCATTTGGCGCAGCTTc > 1:3216017/1‑41 (MQ=37)
aCCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAg > 1:2334443/1‑69 (MQ=255)
aCCCACGCACTGCAATGCCGAGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAg > 1:108339/1‑69 (MQ=255)
cACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGGCGTGCTCAGGTGGCTg < 1:296607/64‑1 (MQ=255)
aTGTCGCGATCCATTTGGCGCAGCTTCCGGCGGTCGCCGTGCTCAGGTGGCTGAGCTGGCAAGAGcc < 1:2804642/67‑1 (MQ=255)
aTGTCGCGATCCATTTGGCGCAGCTTCCGGCGGTCGCCGTGCTCAGGTGGCTGAGCTGGCAAGAGcc < 1:1632833/67‑1 (MQ=255)
aTGTCGCGATCCATTTGGCGCAGCTTCCGGCGGTCGCCGTGCTCAGGTGGCTGAGCTGGCAAGAGcc < 1:1843741/67‑1 (MQ=255)
aTGCCGCGATCCGTTTGGCTCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCgg < 1:912482/69‑1 (MQ=255)
aTGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCgg < 1:2006786/69‑1 (MQ=255)
aTGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCgg < 1:1263678/69‑1 (MQ=255)
aTGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCgg < 1:1610949/69‑1 (MQ=255)
aTGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCgg < 1:1685421/69‑1 (MQ=255)
aTGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCgg < 1:611717/69‑1 (MQ=255)
aTGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCgg < 1:1752878/69‑1 (MQ=255)
aTGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCgg < 1:390994/69‑1 (MQ=255)
aTGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCgg < 1:1834614/69‑1 (MQ=255)
aTGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCgg < 1:2519931/69‑1 (MQ=255)
aTGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCgg < 1:2250642/69‑1 (MQ=255)
aTGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCgg < 1:2268090/69‑1 (MQ=255)
aTGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCgg < 1:2269991/69‑1 (MQ=255)
aTGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCgg < 1:2941368/69‑1 (MQ=255)
aTGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCgg < 1:2937427/69‑1 (MQ=255)
aTGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCgg < 1:2301656/69‑1 (MQ=255)
aTGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCgg < 1:2305849/69‑1 (MQ=255)
aTGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGGGGCTGAGCTGGCACGAGCCgg < 1:2945171/69‑1 (MQ=255)
tGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCgg < 1:781686/68‑1 (MQ=255)
cgATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGc < 1:1886486/69‑1 (MQ=255)
cgATCCGTTTGGCGCAGCTTCCGCTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGc < 1:264384/69‑1 (MQ=255)
|
TGGTAACTCGCCGGTGATTTTCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGC > minE/820951‑821067
|
| 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
