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 I1 R1
|
748 |
32.0 |
1685426 |
92.6% |
1560704 |
103.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
3,240,984 |
(G)7→9 |
coding (1041/1245 nt) |
sstT → |
sodium:serine/threonine symporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,240,977 | 1 | . | G | 97.3%
| 129.1
/ ‑3.1
| 37 | coding (1034/1245 nt) | sstT | sodium:serine/threonine symporter |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base G (20/16); total (20/17) |
| Fisher's exact test for biased strand distribution p-value = 4.59e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01 |
| * | NC_000913 | 3,240,977 | 2 | . | G | 91.9%
| 118.9
/ 4.0
| 37 | coding (1034/1245 nt) | sstT | sodium:serine/threonine symporter |
| Reads supporting (aligned to +/- strand): ref base . (1/2); new base G (19/15); total (20/17) |
| Fisher's exact test for biased strand distribution p-value = 5.84e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.58e-01 |
TGGCGGGCGCAGCAATCACTATTACCGTGTTGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGC‑‑GTGGC‑‑GGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGCGTATTGCAGGACTCTTGCGAAA > NC_000913/3240842‑3241096
||
tGGCGGGCGCAGCAATCACTATTACCGTGTTGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGC‑‑GTGGC‑‑ggg > 1:840997/1‑139 (MQ=255)
cgggcgCAGCAATCACTATTACCGTGTTGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGC‑‑GTGGC‑‑gggggg > 2:737261/1‑139 (MQ=255)
gggcgCAGCAATCACTATTACCGTGTTGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGC‑‑GTGGC‑‑ggggggg > 2:307582/1‑139 (MQ=255)
tgtTGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGC‑‑GTGGCGGGGGGGGGTCTCTGCTGCTGATCCCACTg < 2:840997/139‑1 (MQ=255)
tgtTGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGC‑‑GTGGCGGGGGGGGGTCTCTGCTGCTGATCCCACTg > 2:817066/1‑139 (MQ=255)
tgtTGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGC‑‑GTGGCGGGGGGGGGTCTCTGCTGCTGATCCCACTg > 2:223924/1‑139 (MQ=255)
ttGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGC‑‑GTGGCGGGGGGGGGTCTCTGCTGCTGATCCCACTGGc > 1:811564/1‑139 (MQ=255)
ttGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGC‑‑GTGGCGGGGGGGGGTCTCTGCTGCTGATCCCACTGGc > 2:289113/1‑139 (MQ=255)
ttGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGC‑‑GTGGCGGGGGGGGGTCTCTGCTGCTGATCCCACTGGc > 1:646017/1‑139 (MQ=255)
ttGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGC‑‑GTGGCGGGGGGGGGTCTCTGCTGCTGATCCCACTGGc < 1:289113/139‑1 (MQ=255)
ttGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGC‑‑GTGGCGGGGGGGGGTCTCTGCTGCTGATCCCACTGGc < 1:307582/139‑1 (MQ=255)
ctggctgCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGC‑‑GTGGCGGGGGGGGGTCGCTGCTGCTGATCCCACTGGCCTGTaa > 2:818999/1‑139 (MQ=255)
gctgCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGC‑‑GTGGCGGGGGGGGGACTCTGCTGCTGATCCCACTGGCCTGTAatat > 1:459958/1‑139 (MQ=255)
gggTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGC‑‑GTGGCGGGGGGGGGTCTCTGCTGCTGa < 1:412683/103‑1 (MQ=255)
gggTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGC‑‑GTGGCGGGGGGGGGTCTCTGCTGCTGa > 2:412683/1‑103 (MQ=255)
ccGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGC‑‑GTGGCGGGGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGc < 2:811564/139‑1 (MQ=255)
tCGATCTGCCCACGGCGCTGCTGTTGGGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGC‑‑GTGGCGGGGGGGGGTCTCTGCTGCTGATCCCa > 2:666802/1‑97 (MQ=255)
tCGATCTGCCCACGGCGCTGCTGTTGGGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGC‑‑GTGGCGGGGGGGGGTCTCTGCTGCTGATCCCa < 1:666802/97‑1 (MQ=255)
tCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGC‑‑GTGGCGGGGGGGGGTCTCTGCTGCTGATCCCa > 1:427569/1‑97 (MQ=255)
tCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGC‑‑GTGGCGGGGGGGGGTCTCTGCTGCTGATCCCa < 2:427569/97‑1 (MQ=255)
tCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGC‑‑GTGGCGGGGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATg > 1:19586/1‑139 (MQ=255)
gATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGC‑‑GTGGCGGGGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTa > 1:382130/1‑117 (MQ=255)
gATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGC‑‑GTGGCGGGGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTa < 2:382130/117‑1 (MQ=255)
gctgctGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGC‑‑GTGGCGGGGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCg < 1:223924/139‑1 (MQ=255)
gAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGC‑‑GTGGCGGGGGGGGGTCTCTGCTGCTGa < 1:464262/67‑1 (MQ=255)
gAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGC‑‑GTGGCGGGGGGGGGTCTCTGCTGCTGa > 2:464262/1‑67 (MQ=255)
gAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGC‑‑GTGGCGGGGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTatca > 2:185609/1‑139 (MQ=255)
cGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGC‑‑GTGGCGGGGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCg > 1:447334/1‑139 (MQ=255)
cGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGC‑‑GTGGCGGGGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCg < 1:737261/139‑1 (MQ=255)
ggtggCTTCTCTGTGTGCCTGTGGCGCATCCGGC‑‑GTGGCGGGGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATTTGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGCg < 1:185609/139‑1 (MQ=255)
ttttgtttccttttgGCGCACCCGGCGGGGGGG‑‑GGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGCGTATTGCAg < 1:610285/126‑1 (MQ=255)
gtgtgCCTGTGGCGCATCCGGC‑‑GTGGCGGGGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGCg < 1:212056/127‑1 (MQ=255)
gtgtgCCTGTGGCGCATCCGGC‑‑GTGGCGGGGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGCg > 2:212056/1‑127 (MQ=255)
tgGCGCATCCGGC‑‑GTGGCGGGGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGCGTATTGCAGGACTCTTGCGaaa > 1:363032/1‑139 (MQ=255)
gcgcATCCGGC‑‑GTGGCGGGGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTAtt > 2:388059/1‑67 (MQ=255)
gcgcATCCGGC‑‑GTGGCGGGGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTAtt < 1:388059/67‑1 (MQ=255)
tCCGGC‑‑GTGGCGGGGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGa > 1:710600/1‑66 (MQ=255)
tCCGGC‑‑GTGGCGGGGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGa < 2:710600/66‑1 (MQ=255)
tCCGGC‑‑GTGGCG‑GGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCg > 1:657055/1‑56 (MQ=255)
tCCGGC‑‑GTGGCG‑GGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCg < 2:657055/56‑1 (MQ=255)
||
TGGCGGGCGCAGCAATCACTATTACCGTGTTGACGCTGGCTGCGGTTAATACGCTGGGTATTCCGGTCGATCTGCCCACGGCGCTGCTGTTGAGCGTGGTGGCTTCTCTGTGTGCCTGTGGCGCATCCGGC‑‑GTGGC‑‑GGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGCGTATTGCAGGACTCTTGCGAAA > NC_000913/3240842‑3241096
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
