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 |
2,101,487 |
A→G |
29.7% |
K373K (AAA→AAG) |
garD → |
(D)‑galactarate dehydrogenase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,101,487 | 0 | A | G | 29.7%
| 41.9
/ 19.0
| 47 | K373K (AAA→AAG) | garD | (D)‑galactarate dehydrogenase |
| Reads supporting (aligned to +/- strand): ref base A (10/23); new base G (4/10); total (14/33) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.30e-01 |
GTACGATAACTATCTCAATATGGGAAAAACCGACCGCAGCGCCAACCCTTCGCCGGGCAACAAGAAAGGCGGTCTGGCAAACGTGGTAGAGAAGGCACTCGGCTCCATTGCTAAATCGGGTAAAAGCGCAATT > minE/2101421‑2101553
|
gTACGATAACTATCTCAATATGGGAAAAACCGACCGCAGCGCCAACCCTTCGCCGGGCAACAAGAAAgg > 1:1462927/1‑69 (MQ=255)
gTACGATAACTATCTCAATATGGGAAAAACCGACCGCAGCGCCAACCCTTCGCCGGGCAACAAGAAAgg > 1:619871/1‑69 (MQ=255)
gTACGATAACTATCTCAATATGGGAAAAACCGACCGCAGCGCCAACCCTTCGCCGGGCAACAAGAAAgg > 1:3044804/1‑69 (MQ=255)
aCGATAACTATCTCAAAATGGGAAAAACCGACCGCAGCGCCAACCCTTCG‑CTGGCAACAAGAAAGGCg < 1:2435254/68‑1 (MQ=255)
tATCTCAATATGGGAAAAACCGACCGCAGCGCCAACCCTTCGCCGGGCAACAAGAAAGGCGGTCTGGCa < 1:2302856/69‑1 (MQ=255)
tATCTCAATATGGGAAAAACCGACCGCAGCGCCAACCCTTCGCCGGGCAACAAGAAAGGCGGTCTGGCa < 1:2113212/69‑1 (MQ=255)
tcAATATGGGAAAAACCGCCCGCAGCGCCAACCCTTCGCCGGGCAACAAGAAAGGCGGTCTGGCAAACg > 1:1472313/1‑69 (MQ=255)
tcAATATGGGAAAAACCGACCGCAGCGCCAACCCTTCGCCGGGCAACAAGAAAGGCgg > 1:20659/1‑58 (MQ=255)
tcAATATGGGAAAAACCGACCGCAGCGCCAACCCTTCGCCGGGCAACAAGAAAGGCgg > 1:2435712/1‑58 (MQ=255)
tcAATATGGGAAAAACCGACCGCAGCGCCAACCCTTCGCCGGGCAACAAGAAAGGCGGTCTGGCAAACg > 1:3062534/1‑69 (MQ=255)
tcAATATGGGAAAAACCGACCGCAGCGCCAACCCTTCGCCGGGCAACAAGAAAGGCGGTCTGGCAAACg > 1:1103659/1‑69 (MQ=255)
ggAAAAACCGACCGCAGCGCCAACCCTTCGCCGGGCAACAAGAAAGGCGGTCTGGCAAACGTGGTag > 1:3300202/1‑67 (MQ=255)
ggAAAAACCGACCGCAGCGCCAACCCTTCGCCGGGCAACAAGAAAGGCGGTCTGGCAAACGTGGTag > 1:738908/1‑67 (MQ=255)
caaaaCCGACCGCAGCGCCAACCCTTCGCGGGGCAACAAAAAGGGCGGCCTCGCCAACGTGGTAaaga < 1:1255650/67‑1 (MQ=255)
caaaaCCGACCGCAGCGCCAACCCTTCGCGGGGCAACAAAAAGGGCGGCCTCGCCAACGTGGTAaaga < 1:3150568/67‑1 (MQ=255)
caaaaCCGACCGCAGCGCCAACCCTTCGCGGGGCAACAAAAAGGGCGGCCTCGCCAACGTGGTAaaga < 1:2973933/67‑1 (MQ=255)
caaaaCCGACCGCAGCGCCAACCCTTCGCGGGGCAACAAAAAGGGCGGCCTCGCCAACGTGGTAaaga < 1:2698349/67‑1 (MQ=255)
caaaaCCGACCGCAGCGCCAACCCTTCGCGGGGCAACAAAAAGGGCGGCCTCGCCAACGTGGTAaaga < 1:2692130/67‑1 (MQ=255)
caaaaCCGACCGCAGCGCCAACCCTTCGCGGGGCAACAAAAAGGGCGGCCTCGCCAACGTGGTAaaga < 1:3359558/67‑1 (MQ=255)
caaaaCCGACCGCAGCGCCAACCCTTCGCGGGGCAACAAAAAGGGCGGCCTCGCCAACGTGGTAaaga < 1:625679/67‑1 (MQ=255)
caaaaCCGACCGCAGCGCCAACCCTTCGCGGGGCAACAAAAAGGGCGGCCTCGCCAACGTGGTAaaga < 1:1723724/67‑1 (MQ=255)
caaaaCCGACCGCAGCGCCAACCCTTCGCGGGGCAACAAAAAGGGCGGCCTCGCCAACGTGGTAaaga < 1:1284105/67‑1 (MQ=255)
aGCGCCAACCCTTCGCCGGGCAACAAGAAAGGCGGTCTGGCAAACGTGGTAGAGAAGGCACTCGGCTcc < 1:2978557/69‑1 (MQ=255)
gcCAACCCTTCGCGGGGCAACAAAAAGGGCGGCCTCGCCAACGTGGTAaaga < 1:1872603/52‑1 (MQ=255)
cccTTCGCCGGGCAACAAGAAAGGCGGTCTGGCAAACGTGGTAGAGAAGGCACTCGGCTCCATTGCTaa < 1:1791841/69‑1 (MQ=255)
cccTTCGCCGGGCAACAAGAAAGGCGGTCTGGCAAACGTGGTAGAGAAGGCACTCGGCTCCATTGCTaa < 1:1923480/69‑1 (MQ=255)
gcggggCAACAAAAAGGGCGGCCTCGCCAACGTGGTAAAGAAGGCACTCGGCTCCATTGCTAAATCgg > 1:3068996/4‑68 (MQ=255)
gcggggCAACAAAAAGGGCGGCCTCGCCAACGTGGTAAAGAAGGCACTCGGCTCCATTGCTAAATCgg > 1:2415932/4‑68 (MQ=255)
gcggggCAACAAAAAGGGCGGCCTCGCCAACGTGGTAAAGAAGGCACTCGGCTCCATTGCTAAATCgg > 1:246556/4‑68 (MQ=255)
gcggggCAAAAAAAAGGGCGGCCTCGCCAACGTGGTAAAGAAGGCACTCGGCTCCATTGCTAAATCgg > 1:2599369/4‑68 (MQ=255)
gggCAACAAGAAAGGCGGTCTGGCAAACGTGGTAGAGAAGGCa < 1:1661124/43‑1 (MQ=255)
gaacaaGAAAGGCGGTCTGGCAAATGTGGTGGAGAAGGCACTCGGCTCCAt < 1:193720/50‑1 (MQ=38)
gaacaaGAAAGGCGGTCTGGCAAATGTGGTGGAGAAGGCACTCGGCTCCAt < 1:2720146/50‑1 (MQ=38)
gaacaaGAAAGGCGGTCTGGCAAATGTGGTGGAGAAGGCACTCGGCTCCAt < 1:3374108/50‑1 (MQ=38)
gaacaaGAAAGGCGGTCTGGCAAATGTGGTGGAGAAGGCACTCGGCTCCAt < 1:2492262/50‑1 (MQ=38)
gaacaaGAAAGGCGGTCTGGCAAATGTGGTGGAGAAGGCACTCGGCTCCAt < 1:454303/50‑1 (MQ=38)
gaacaaGAAAGGCGGTCTGGCAAATGTGGTGGAGAAGGCACTCGGCTCCAt < 1:1978161/50‑1 (MQ=38)
gaacaaGAAAGGCGGTCTGGCAAATGTGGTGGAGAAGGCACTCGGCTCCAt < 1:1768426/50‑1 (MQ=38)
gaacaaGAAAGGCGGTCTGGCAAATGTGGTGGAGAAGGCACTCGGCTCCAt < 1:1556576/50‑1 (MQ=38)
gaacaaGAAAGGCGGTCTGGCAAATGTGGTGGAGAAGGCACTCGGCTCCAt < 1:3112989/50‑1 (MQ=38)
gaacaaGAAAGGCGGTCTGGCAAATGTGGTGGAGAAGGCACTCGGCTCCAt < 1:2170042/50‑1 (MQ=38)
aaGAAAGGCGGTCTGGCAAACGTGGTAGAGAAGGCACTCGGCTCCATTGCTAAATCGGGTAAAAGCGCa < 1:98983/69‑1 (MQ=255)
aaGAAAGGCGGTCTGGCAAACGTGGTAGAGAAGGCACTCGGCTCCATTGCTAAATCGGGTAAAAGCGCa < 1:1666318/69‑1 (MQ=255)
aaGAAAGGCGGTCTGGCAAACGTGGTAGAGAAGGCACTCGGCTCCATTGCTAAATCGGGTAAAAGCGCa < 1:286656/69‑1 (MQ=255)
aaGAAAGGCGGTCTGGCAAACGTGGTAGAGAAGGCACTCGGCTCCATTGCTAAATCGGGTAAAAGCGCa < 1:194294/69‑1 (MQ=255)
aaGAAAGGCGGTCTGGCAAACGTGGTAGAGAAGGCACTCGGCTCCATTGCTAAATCGGGTAAAAGCGCa < 1:2384718/69‑1 (MQ=255)
aaGAAAGGCGGTCTGGCAAACGTGGTAGAGAAGGCACTCGGCTCCATTGCTAAATCGGGTAAAAGCGCa < 1:2156827/69‑1 (MQ=255)
aaaGGCGGTCTGGCAAACGTGGTAGAGAAGGCACTCGGCTCCATTGCTAAATCGGGTaaa > 1:432610/1‑60 (MQ=255)
aaaGGCGGTCTGGCAAACGTGGTAGAGAAGGCACTCGGCTCCATTGCTAAATCGGGTaaa > 1:1293164/1‑60 (MQ=255)
aaaGGCGGTCTGGCAAACGTGGTAGAGAAGGCACTCGGCTCCATTGCTAAATCGGGTaaa > 1:2289005/1‑60 (MQ=255)
aaaGGCGGTCTGGCAAACGTGGTAGAGAAGGCACTCGGCTCCATTGCTAAATCGGGTAAAAGCGCAAtt < 1:3297728/69‑1 (MQ=255)
aaaGGCGGTCTGGCAAACGTGGTAGAGAAGGCACTCGGCTCCATTGCTAAATCGGGTAAAAGCGCAAtt < 1:522638/69‑1 (MQ=255)
|
GTACGATAACTATCTCAATATGGGAAAAACCGACCGCAGCGCCAACCCTTCGCCGGGCAACAAGAAAGGCGGTCTGGCAAACGTGGTAGAGAAGGCACTCGGCTCCATTGCTAAATCGGGTAAAAGCGCAATT > minE/2101421‑2101553
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
