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 |
2,107,455 |
G→A |
60.0% |
P131P (CCG→CCA) |
agaS → |
tagatose‑6‑phosphate ketose/aldose isomerase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,107,455 | 0 | G | A | 60.0%
| 24.2
/ 44.3
| 65 | P131P (CCG→CCA) | agaS | tagatose‑6‑phosphate ketose/aldose isomerase |
| Reads supporting (aligned to +/- strand): ref base G (8/18); new base A (26/13); total (34/31) |
| Fisher's exact test for biased strand distribution p-value = 5.82e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TCGGTCGATCCGGCAACAGCCCGGAAAGCGTCGCAGCCGTGGAACTGGCAAATCAATTTGTACCGGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCAAAACGC > minE/2107391‑2107511
|
tCGGTCGATCCGGCAACAGCCCGGAAAGCGTCGCAGCCGTGGAACTGGCAAATCAATTTGTACCgg < 1:911557/66‑1 (MQ=255)
tCGGTCGATCCGGCAACAGCCCGGAAAGCGTCGCAGCCGTGGAACTGGCAAATCAATTTGTACCgg < 1:2159998/66‑1 (MQ=255)
tCGGTCGATCCGGCAACAGCCCGGAAAGCGTCGCAGCCGTGGAACTGGCAAATCAATTTGTACCGGAAt < 1:229310/69‑1 (MQ=255)
tCGGTCGATCCGGCAACAGCCCGGAAAGCGTCGCAGCCGTGGAACTGGCAAATCAATTTGTACCGGAAt < 1:3346630/69‑1 (MQ=255)
tCGGTCGATCCGGCAACAGCCCGGAAAGCGTCGCAGCCGTGGAACTGGCAAATCAATTTGTACCGGAAt < 1:1761602/69‑1 (MQ=255)
tCGATCCGGCAACAGCCCGGAAAGCGTCGCAGCCGTGGAACTGGCAAATCAATTTGTACCGGAATGCTa < 1:2173489/69‑1 (MQ=255)
tCGATCCGGCAACAGCCCGGAAAGCGTCGCAGCCGTGGAACTGGCAAATCAATTTGTACCGGAATGCTa < 1:3231003/69‑1 (MQ=255)
tCGATCCGGCAACAGCCCGGAAAGCGTCGCAGCCGTGGAACTGGCAAATCAATTTGTACCGGAATGCTa < 1:1816736/69‑1 (MQ=255)
tCGATCCGGCAACAGCCCGGAAAGCGTAGCAGCCGTGGAACTGGCAAATCAATTTGTACCGGAATGCTa < 1:1759658/69‑1 (MQ=255)
gATCCGGCAACAGCCCGGAAAGCGTCGCAGCCGTGGAACTGGCAAATCAATTTGTACCGGAATGCTATc < 1:1792545/69‑1 (MQ=255)
ccGGCAACAGCCCGGAAAGCGTCGCAGCCGTGGAACTGGCAAATCAATTTGTACCGGAATGCTATCAcc > 1:2679141/1‑69 (MQ=255)
ccGGCAACAGCCCGGAAAGCGTCGCAGCCGTGGAACTGGCAAATCAATTTGTACCGGAATGCTATCAc > 1:239098/1‑68 (MQ=255)
cGGCAACAGCCCGGAAAGCGTCGCAGCCGTGGAACTGGCAAATCAATTTGTACCGGAATGCTATCACCt < 1:2636686/69‑1 (MQ=255)
cGGCAACAGCCCGGAAAGCGTCGCAGCCGTGGAACTGGCAAATCAATTTGTACCGGAATGCTATCACCt < 1:2174893/69‑1 (MQ=255)
cGGCAACAGCCCGGAAAGCGTCGCAGCCGTGGAACTGGCAAATCAATTTGTACCGGAATGCTATCACCt < 1:411094/69‑1 (MQ=255)
cGGCAACAGCCCGGAAAGCGTCGCAGCCGTGGAACTGGCAAATCAATTTGTACCGGAATGCTATCACCt < 1:3207463/69‑1 (MQ=255)
cGGCAACAGCCCGGAAAGCGTCGCAGCCGTGGAACTGGCAAATCAATTTGTACCGGAATGCTATCACCt < 1:29549/69‑1 (MQ=255)
ggCAACAGCCCGGAAAGCGTCGCAGCCGTGGTACTGGCAAATCAATTTGTACCGGAATGCTATCACCt < 1:311109/68‑1 (MQ=255)
ggCAACAGCCCGGAAAGCGTCGCAGCCGTGGAACTGGCAAATCAATTTGTACCGGAATGCTATCACCt < 1:1564486/68‑1 (MQ=255)
aaCAGCCCGGAAAGAGTCGCAGCCGTGGAACTGGCAAATCAATTTGTACCGGAATGCTATCACCt < 1:2268387/65‑1 (MQ=255)
gCCCGGAAAGCTTCGCAGCCGTGGAACTGGCAAATCAATTTGTACCGGAATGCTATCACCt < 1:262935/61‑1 (MQ=255)
aaGCGTCGCCGCCGTGGAACTGGCAAATCAATTTGTACCAGAATGCTATCACCTGCCGCTCACCTGCa > 1:1796459/1‑68 (MQ=255)
aaGCGTCGCCGCCGTGGAACTGGCAAATCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCa > 1:3422795/1‑68 (MQ=255)
aaGCGTCGCCGCCGTGGAACTGGCAAATCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCa > 1:1602703/1‑68 (MQ=255)
aaGCGTCGCCGCCGTGGAACTGGCAAATCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCa > 1:605630/1‑68 (MQ=255)
aaGCGTCGCCGCCGTGGAACTGGCAAATCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCa > 1:2949524/1‑68 (MQ=255)
aaGCGTCGCCGCCGTGGAACTGGCAAATCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCa > 1:874257/1‑68 (MQ=255)
aaGCGTCGCCGCCGTGGAACTGGCAAATCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCa > 1:226864/1‑68 (MQ=255)
gTCGCAGCCGTGGAACTGGCAAATCAATTTGTACCgg < 1:662454/37‑1 (MQ=255)
gTGGAACTGGCAAATCAATTTGTACCGGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGct < 1:2033110/69‑1 (MQ=255)
cTGGCAAATCAATTTGTACCGGAATGCTATCACCTGCCGATCACCTGCAACGAAGc > 1:2742292/1‑56 (MQ=255)
cTGGCAAATCAATTTGTACCGGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCttt > 1:3428451/1‑67 (MQ=255)
cTGGCAAATCAATTTGTACCGGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTa > 1:1487877/1‑68 (MQ=255)
cTGGCAAATCAATTTGTACCGGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTa > 1:132125/1‑68 (MQ=255)
cTGGCAAATCAATTTGTACCGGAATGCTATCACCTGCCGATAACCTGCAACGAAGCGGgcgc > 1:2028306/1‑62 (MQ=255)
cTGGCAAATCAATTTGTACCGGAATGCTATCACCTGCAGATCACCTGCa > 1:2575276/1‑49 (MQ=255)
cAAATCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCaaa > 1:3172672/1‑69 (MQ=255)
cAAATCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCaaa > 1:3262959/1‑69 (MQ=255)
cAAATCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCaaa > 1:2966472/1‑69 (MQ=255)
cAAATCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCaaa > 1:3354292/1‑69 (MQ=255)
cAAATCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCaaa > 1:660423/1‑69 (MQ=255)
cAAATCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCaaa > 1:846028/1‑69 (MQ=255)
cAAATCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCaaa > 1:2367328/1‑69 (MQ=255)
cAAATCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCaaa > 1:1167694/1‑69 (MQ=255)
cAAATCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCaaa > 1:2480702/1‑69 (MQ=255)
cAAATCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCaaa > 1:1115298/1‑69 (MQ=255)
cAAATCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCaaa > 1:117185/1‑69 (MQ=255)
cAAATCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCaaa > 1:2337738/1‑69 (MQ=255)
cAAATCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCaaa > 1:1287177/1‑69 (MQ=255)
cAAATCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCaaa > 1:2013463/1‑69 (MQ=255)
cAAATCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCaaa > 1:1290077/1‑69 (MQ=255)
cAAATCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCaaa > 1:1507983/1‑69 (MQ=255)
cAAATCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCaaa > 1:1922177/1‑69 (MQ=255)
cAAATCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCaaa > 1:1873388/1‑69 (MQ=255)
cAAATCAATTTGTACCAGAATGCTATCACCTGCCGATAACCTGCAACGAAGCGGGCGCTCTTTACCaaa > 1:2898376/1‑69 (MQ=255)
tCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCAAAAcgc < 1:1139264/69‑1 (MQ=255)
tCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCAAAAcgc < 1:2866501/69‑1 (MQ=255)
tCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCAAAAcgc < 1:1566661/69‑1 (MQ=255)
tCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCAAAAcgc < 1:1858756/69‑1 (MQ=255)
tCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCAAAAcgc < 1:339487/69‑1 (MQ=255)
tCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCAAAAcgc < 1:1933376/69‑1 (MQ=255)
tCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCAAAAcgc < 1:3310461/69‑1 (MQ=255)
tCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCAAAAcgc < 1:1943459/69‑1 (MQ=255)
tCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCAAAAcgc < 1:2009368/69‑1 (MQ=255)
tCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCAAAAcgc < 1:2282396/69‑1 (MQ=255)
tCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCAAAAcgc < 1:2968772/69‑1 (MQ=255)
tCAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCAAAAcgc < 1:2929381/69‑1 (MQ=255)
cAATTTGTACCAGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCAAAAcgc < 1:2551729/68‑1 (MQ=255)
|
TCGGTCGATCCGGCAACAGCCCGGAAAGCGTCGCAGCCGTGGAACTGGCAAATCAATTTGTACCGGAATGCTATCACCTGCCGATCACCTGCAACGAAGCGGGCGCTCTTTACCAAAACGC > minE/2107391‑2107511
|
| 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
