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 |
|
A1 F28 I2 R2
|
356 |
55.1 |
4139924 |
95.4% |
3949487 |
63.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,358,271 |
A→G |
K1262R (AAA→AGA) |
gltB → |
glutamate synthase, large subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,358,271 | 0 | A | G | 77.8%
| 71.6
/ 16.8
| 36 | K1262R (AAA→AGA) | gltB | glutamate synthase, large subunit |
| Reads supporting (aligned to +/- strand): ref base A (1/7); new base G (19/9); total (20/16) |
| Fisher's exact test for biased strand distribution p-value = 1.21e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.38e-01 |
TGATAACGGCCTGCTGAACGCGCAGTTGCTGCAACAGGCGAAACCGTTTGTCGATGAGCGCCAGAGCAAAACCTTCTGGTTCGATATTCGCAACACCGACCGTTCTGTCGGCGCGTCGCTTTCAGGCTATATCGCC > W3110S.gb/3358203‑3358338
|
tGATAACGGCCTGCTGAACGCGCAGTTGCTGCAACAGGCGAAACCGTTTGTCGATGAGCGCCAGAGCagaa > 1:710324/1‑71 (MQ=255)
tGATAACGGCCTGCTGAACGCGCAGTTGCTGCAACAGGCGAAACCGTTTGTCGATGAGCGCCAGAGCagaa > 1:2150003/1‑71 (MQ=255)
tAACGGCCTGCTGAACGCGCAGTTGCTGCAACAGGCGAAACCGTTTGTCGATGAGCGCCAGAGCAGAACCt > 1:624483/1‑71 (MQ=255)
tAACGGCCTGCTGAACGCGCAGTTGCTGCAACAGGCGAAACCGTTTGTCGATGAGCGCCAGAGCAGAACCt > 1:2119682/1‑71 (MQ=255)
tAACGGCCTGCTGAACGCGCAGTTGCTGCAACAGGCGAAACCGTTTGTCGATGAGCGCCAGAGCAGAACCt > 1:3447076/1‑71 (MQ=255)
ctgAACGCGCAGTTGCTGCAACAGGCGAAACCGTTTGTCGATGAGCGCCAGAGCAAAACCTTCTGGTTc < 1:2776675/69‑1 (MQ=255)
ctgAACGCGCAGTTGCTGCAACAGGCGAAACCGTTTGTCGATGAGCGCCAGAGCAAAACCTTCTGGTTc < 1:2606004/69‑1 (MQ=255)
ctgAACGCGCAGTTGCTGCAACAGGCGAAACCGTTTGTCGATGAGCGCCAGAGCAAAACCTTCTGGTTc < 1:1712940/69‑1 (MQ=255)
ctgAACGCGCAGTTGCTGCAACAGGCGAAACCGTTTGTCGATGAGCGCCAGAGCAAAACCTTCTGGTTc < 1:1863530/69‑1 (MQ=255)
ctgAACGCGCAGTTGCTGCAACAGGCGAAACCGTTTGTCGATGAGCGCCAGAGCAAAACCTTCTGGTTc < 1:552409/69‑1 (MQ=255)
ctgAACGCGCAGTTGCTGCAACAGGCGAAACCGTTTGTCGATGAGCGCCAGAGCAAAACCTTCTGGTTc < 1:3211574/69‑1 (MQ=255)
ctgAACGCGCAGTTGCTGCAACAGGCGAAACCGTTTGTCGATGAGCGCCAGAGCAAAACCTTCTGGTTc < 1:2390714/69‑1 (MQ=255)
ctgcAACAGGCGAAACCGTTTGTCGATGAGCGCCAGAGCagaa < 1:885570/43‑1 (MQ=255)
ctgcAACAGGCGAAACCGTTTGTCGATGAGCGCCAGAGCagaa < 1:3897707/43‑1 (MQ=255)
tgcAACAGGCGAAACCGTTTGTCGATGAGCGCCAGAGCAGAACCTTCTGGTTCGATATTCGCAACaccgac > 1:2427644/1‑71 (MQ=255)
tgcAACAGGCGAAACCGTTTGTCGATGAGCGCCAGAGCAGAACCTTCTGGTTCGATATTCGCAACaccgac > 1:3059178/1‑71 (MQ=255)
tgcAACAGGCGAAACCGTTTGTCGATGAGCGCCAGAGCAGAACCTTCTGGTTCGATATTCGCAACaccga > 1:3186002/1‑70 (MQ=255)
aCCGTTTGTCGATGAGCGCCAGAGCAGAACCTTCTGGTTCGATAtt < 1:871941/46‑1 (MQ=255)
gATGAGCGCCAGAGCAGAACCTTCTGGTTCGATATTCGc < 1:988202/39‑1 (MQ=255)
gATGAGCGCCAGAGCAGAACCTTCTGGTTCGATATTCGCAACACCGACCGTTCTGTCGGCGCGTCGCttt < 1:2847299/70‑1 (MQ=255)
gATGAGCGCCAGAGCAGAACCTTCTGGTTCGATATTCGCAACACCGACCGTTCTGTCGGCGCGTCGCttt < 1:2291749/70‑1 (MQ=255)
gATGAGCGCCAGAGCAGAACCTTCTGGTTCGATATTCGCAACACCGACCGTTCTGTCGGCGCGTCGCttt < 1:3944162/70‑1 (MQ=255)
tGAGCGCCAGAGCAGAACCTTCTGGTTCGATATTCGCAACACCGACCGTTCTGTCGGCGCGTCGCTTTCAg > 1:2450555/1‑71 (MQ=255)
tGAGCGCCAGAGCAGAACCTTCTGGTTCGATATTCGCAACACCGACCGTTCTGTCGGCGCGTCGCTTTCAg < 1:1120319/71‑1 (MQ=255)
tGAGCGCCAGAGCAGAACCTTCTGGTTCGATATTCGCAACACCGACCGTTCTGTCGGCGCGTCGCTTTCAg > 1:1565361/1‑71 (MQ=255)
tGAGCGCCAGAGCAGAACCTTCTGGTTCGATATTCGCAACACCGACCGTTCTGTCGGCGCGTCGCTTTCAg > 1:1940695/1‑71 (MQ=255)
tGAGCGCCAGAGCAGAACCTTCTGGTTCGATATTCGCAACACCGACCGTTCTGTCGGCGCGTCGCTTTCAg > 1:1945380/1‑71 (MQ=255)
tGAGCGCCAGAGCAGAACCTTCTGGTTCGATATTCGCAACACCGACCGTTCTGTCGGCGCGTCGCTTTCAg < 1:485348/71‑1 (MQ=255)
tGAGCGCCAGAGCAGAACCTTCTGGTTCGATATTCGCAACACCGACCGTTCTGTCGGCGCGTCGCTTTCAg > 1:4053817/1‑71 (MQ=255)
tGAGCGCCAGAGCAGAACCTTCTGGTTCGATATTCGCAACACCGACCGTTCTGTCGGCGCGTCGCTTTCAg > 1:3235526/1‑71 (MQ=255)
tGAGCGCCAGAGCAGAACCTTCTGGTTCGATATTCGCAACACCGACCGTTCTGTCGGCGCGTCGCTTTCAg > 1:2391801/1‑71 (MQ=255)
aGCGCCAGAGCAAAACCTTCTGGTTCGATATTCGCAACACCGACCGTTCTGTCGGCGCGTCGCTTTCAgg > 1:460759/1‑70 (MQ=255)
gagCAGAACCTTCTGGTTCGATATTCGCAACACCGACCGTTCTGTCGGCGCGTCGCttt < 1:1961567/59‑1 (MQ=255)
gagCAGAACCTTCTGGTTCGATATTCGCAACACCGACCGTTCTGTCGGCGCGTCGCttt < 1:3410498/59‑1 (MQ=255)
gCAGAACCTTCTGGTTCGATATTCGCAACACCGACCGTTCTGTCGGCGCGTCGCTTTCAGGCTATATCGcc > 1:3913189/1‑71 (MQ=255)
gCAGAACCTTCTGGTTCGATATTCGCAACACCGACCGTTCTGTCGGCGCGTCGCTTTCAGGCTATATCGcc > 1:3728614/1‑71 (MQ=255)
gCAGAACCTTCTGGTTCGATATTCGCAACACCGACCGTTCTGTCGGCGCGTCGCTTTCAGGCTATATCGcc > 1:3622434/1‑71 (MQ=255)
gCAGAACCTTCTGGTTCGATATTCGCAACACCGACCGTTCTGTCGGCGCGTCGCTTTCAGGCTATATCGcc > 1:972158/1‑71 (MQ=255)
gCAGAACCTTCTGGTTCGATATTCGCAACACCGACCGTTCTGTCGGCGCGTCGCTTTCAGGCTATATCGcc > 1:1114569/1‑71 (MQ=255)
gCAGAACCTACTGGTTCGATATTCGCAACACCGACCGt > 1:1255111/1‑38 (MQ=38)
|
TGATAACGGCCTGCTGAACGCGCAGTTGCTGCAACAGGCGAAACCGTTTGTCGATGAGCGCCAGAGCAAAACCTTCTGGTTCGATATTCGCAACACCGACCGTTCTGTCGGCGCGTCGCTTTCAGGCTATATCGCC > W3110S.gb/3358203‑3358338
|
| 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
