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 |
2,183,120 |
C→T |
30.0% |
G1132G (GGC→GGT) |
gltB → |
glutamate synthase, large subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,183,120 | 0 | C | T | 30.0%
| 70.9
/ 31.9
| 73 | G1132G (GGC→GGT) | gltB | glutamate synthase, large subunit |
| Reads supporting (aligned to +/- strand): ref base C (24/27); new base T (10/12); total (34/39) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AAGGCGGCGATTCTCGGCGCAGAAAGCTTCGGCTTCGGCACTGGCCCGATGGTGGCGCTCGGCTGTAAATATCTACGTATTTGCCATCTGAACAACTGCGCAACGGGTGTAGCAACTCAGGATGACAAAC > minE/2183058‑2183187
|
aaGGCGGCGATTCTCGGCGCAGAAAGCTTCGGCTTCGGCACTGGCCCGATGGTGGCGCTCGGCTGTaaa < 1:3388961/69‑1 (MQ=255)
aaGGCGGCGATTCTCGGCGCAGAAAGCTTCGGCTTCGGCACTGGCCCGATGGTGGCGCTCGGCTGTaaa > 1:3252686/1‑69 (MQ=255)
aaGGCGGCGATTCTCGGCGCAGAAAGCTTCGGCTTCGGCACTGGCCCGATGGTGGCGCTCGGCTGTaaa < 1:1529656/69‑1 (MQ=255)
aaGGCGGCGATTCTCGGCGCAGAAAGCTTCGGCTTCGGCACTGGCCCGATGGTGGCGCTCGGCTGTaaa < 1:1107535/69‑1 (MQ=255)
aaGGCGGCGATTCTCGGCGCAGAAAGCTTCGGCTTCGGCACTGGCCCGATGGTGGCGCTCGGCTGTaaa < 1:2922741/69‑1 (MQ=255)
aaGGCGGCGATTCTCGGCGCAGAAAGCTTCGGCTTCGGCACTGGCCCGATGGTGGCGCTCGGCTGTaaa > 1:546540/1‑69 (MQ=255)
aaGGCGGCGATTCTCGGCGCAGAAAGCTTCGGCTTCGGCACTGGCCCGATGGTGGCGCTCGGCTGTaaa < 1:2606803/69‑1 (MQ=255)
aaGGCGGCGATTCTCGGCGCAGAAAGCTTCGGCTTCGGCACTGGCCCGATGGTGGCGCTCGGCTGTaaa < 1:672864/69‑1 (MQ=255)
aaGGCGGCGATTCTCGGCGCAGAAAGCTTCGGCTTCGGCACTGGCCCGATGGTGGCGCTCGGCTGTaa > 1:2867427/1‑68 (MQ=255)
cgcAGAAAGCTTCGGCTTCGGCACTGGCCCGATGGGGGCGCTCGGCTGTAAATATCTACGTATTTGcc < 1:3257194/68‑1 (MQ=255)
aGCTTCGGCTTCGGCACTGGCCCGATGGTGGCGCTCGGCTGTAAATATCTACGTAttt > 1:290469/1‑58 (MQ=255)
aGCTTCGGCTTCGGCACTGGCCCGATGGTGGCGCTCGGCTGTAAATATCTACGTATTTGCCATCTGaac > 1:2189568/1‑69 (MQ=255)
aGCTTCGGCTTCGGCACTGGCCCGATGGTGGCGCTCGGCTGTAAATATCTACGTATTTGCCATCTGaac > 1:816671/1‑69 (MQ=255)
aGCTTCGGCTTCGGCACTGGCCCGATGGTGGCGCTCGGCTGTAAATATCTACGTATTTGCCATCTGaac > 1:2143589/1‑69 (MQ=255)
aGCTTCGGCTTCGGCACTGGCCCGATGGTGGCGCTCGGCTGTAAATATCTACGTATTTGCCATCTGaac > 1:526153/1‑69 (MQ=255)
aGCTTCGGCTTCGGCACTGGCCCGATGGTGGCGCTCGGCTGTAAATATCTACGTATTTGCCATCTGaac > 1:1543498/1‑69 (MQ=255)
aGCTTCGGCTTCGGCACTGGCCCGATGGTGGCGCTCGGCTGTAAATATCTACGTATTTGCCATCTGaac < 1:1024019/69‑1 (MQ=255)
aGCTTCGGCTTCGGCACTGGCCCGATGGTGGCGCTCGGCTGTAAATATCTACGTATTTGCCATCTGaac > 1:1115124/1‑69 (MQ=255)
aGCTTCGGCTTCGGCACTGGCCCGATGGTGGCGCTCGGCTGTAAATATCTACGTATTTGCCATCTGaac > 1:1407097/1‑69 (MQ=255)
aGCTTCGGCTTCGGCACTGGCCCGATGGTGGCGCTCGGCTGTAAATATCTACGTATTTGCCATCTGaac > 1:1242417/1‑69 (MQ=255)
aGCTTCGGCTTCGGCACTGGCCCAATGGTCGCGCTCGGTTGTAAATATCtgc > 1:2206240/1‑50 (MQ=255)
aGCTTCGGCTTCGGCACTGGCCCAATGGTCGCGCTCGGTTGTAAATATCTGCGAATTTGCCACCTGaac > 1:2633564/1‑69 (MQ=255)
aGCTTCGGCTTCGGCACTGGCCCAATGGTCGCGCTCGGTTGTAAATATCTGCGAATTTGCCACCTGaac > 1:3378898/1‑69 (MQ=255)
aGCTTCGGCTTCGGCACTGGCCCAATGGTCGCGCTCGGTTGTAAATATCTGCGAATTTGCCACCTGaac > 1:2333293/1‑69 (MQ=255)
aGCTTCGGCTTCGGCACTGGCCCAATGGTCGCGCTCGGTTGTAAATATCTGCGAATTTGCCACCTGaac > 1:2220562/1‑69 (MQ=255)
aGCTTCGGCTTCGGCACTGGCCCAATGGTCGCGCTCGGTTGTAAATATCTGCGAATTTGCCACCTGaac > 1:2022886/1‑69 (MQ=255)
aGCTTCGGCTTCGGCACTGGCCCAATGGTCGCGCTCGGTTGTAAATATCTGCGAATTTGCCACCTGaac > 1:2164066/1‑69 (MQ=255)
aGCTTCGGCTTCGGCACTGGCCCAATGGTCGCGCTCGGTTGTAAATATCTGCGAATTTGCCACCTGaac > 1:1516898/1‑69 (MQ=255)
aGCTTCGGCTTCGGCACTGGCCCAATGGTCGCGCTCGGTTGTAAATATCTGCGAATTTGCCACCTGaac > 1:535709/1‑69 (MQ=255)
aGCTTCGGCTTCGGCACTGGCCCAATGGTCGCGCTCGGTTGTAAATATCTGCGAATTTGCCACCTGaac > 1:1632818/1‑69 (MQ=255)
cACTGGCCCGATGGTGGCGCTCGGCTGTAAATATCTACGTATTTGCCATCTGAACAACTGCGCAACggg < 1:193057/69‑1 (MQ=255)
aCTGGCCCGATGGTGGCGCTCGGCTGTAAATACCTACGTATTTGCCATCTGAACAACTGCGCAACggg < 1:2075011/68‑1 (MQ=255)
ggtggCGCTCGGCTGTAAATATCTACGTATTTGCCATCTGaac > 1:1634909/1‑43 (MQ=255)
ggtggCGCTCGGCTGTAAATATCTACGTATTTGCCATCTGaac > 1:1015473/1‑43 (MQ=255)
ggtggCGCTCGGCTGTAAATATCTACGTATTTGCCATCTGaac > 1:3173238/1‑43 (MQ=255)
ggtggCGCTCGGCTGTAAATATCTACGTATTTGCCATCTGaac > 1:1861980/1‑43 (MQ=255)
ggtggCGCTCGGCTGTAAATATCTACGTATTTGCCATCTGaac > 1:2203865/1‑43 (MQ=255)
ggtggCGCTCGGCTGTAAATATCTACGTATTTGCCATCTGaac > 1:2114402/1‑43 (MQ=255)
gtggCGCTCGGCTGTAAATATCTACGTATTTGCCATCTGAACAACTGCGCAACGGGTGTAGCAACTCAg < 1:3413043/69‑1 (MQ=255)
gtggCGCTCGGCTGTAAATATCTACGTATTTGCCATCTGAACAACTGCGCAACGGGTGTAGCAACTCAg < 1:3164691/69‑1 (MQ=255)
gtggCGCTCGGCTGTAAATATCTACGTATTTGCCATCTGAACAACTGCGCAACGGGTGTAGCAACTCAg < 1:1002187/69‑1 (MQ=255)
gtggCGCTCGGCTGTAAATATCTACGTATTTGCCATCTGAACAACTGCGCAACGGGTGTAGCAACTCAg < 1:588468/69‑1 (MQ=255)
gtggCGCTCGGCTGTAAATATCTACGTATTTGCCATCTGAACAACTGCGCAACGGGTGTAGCAACTCAg < 1:939263/69‑1 (MQ=255)
gtggCGCTCGGCTGTAAATATCTACGTATTTGCCATCTGAACAACTGCGCAACGGGTGTAGCAACTCAg < 1:2534805/69‑1 (MQ=255)
gtggCGCTCGGCTGTAAATATCTACGTATTTGCCATCTGAACAACTGCGCAACGGGTGTAGCAACTCAg < 1:1300017/69‑1 (MQ=255)
gtggCGCTCGGCTGTAAATATCTACGTATTTGCCATCTGAACAACTGCGCAACGGGTGTAGCAACTCAg < 1:2492895/69‑1 (MQ=255)
gtggCGCTCGGCTGTAAATATCTACGTATTTGCCATCTGAACAACTGCGCAACGGGTGTAGCAACTCAg < 1:1341210/69‑1 (MQ=255)
gtggCGCTCGGCTGTAAATATCTACGTATTTGCCATCTGAACAACTGCGCAACGGGTGTAGCAACTCAg < 1:2467274/69‑1 (MQ=255)
gtggCGCTCGGCTGTAAATATCTACGTATTTGCCATCTGAACAACTGCGCAACGGGTGTAGCAACTCAg < 1:2437629/69‑1 (MQ=255)
gtggCGCTCGGCTGTAAATATCTACGTATTTGCCATCTGAACAACTGCGCAACGGGTGTAGCAACTCAg < 1:1001932/69‑1 (MQ=255)
gtcgcgcTCGGTTGTAAATATCTGCGAATTTGCCACCTGAACAACTGCGCCACGGGTTTAGCAACTCAg < 1:32498/66‑1 (MQ=255)
gtcgcgcTCGGTTGTAAATATCTGCGAATTTGCCACCTGAACAACTGCGCCACGGGTGTAGCAACTCAg < 1:3375473/66‑1 (MQ=255)
gtcgcgcTCGGTTGTAAATATCTGCGAATTTGCCACCTGAACAACTGCGCCACGGGTGTAGCAACTCAg < 1:776663/66‑1 (MQ=255)
gtcgcgcTCGGTTGTAAATATCTGCGAATTTGCCACCTGAACAACTGCGCCACGGGTGTAGCAACTCAg < 1:772632/66‑1 (MQ=255)
gtcgcgcTCGGTTGTAAATATCTGCGAATTTGCCACCTGAACAACTGCGCCACGGGTGTAGCAACTCAg < 1:1291897/66‑1 (MQ=255)
gtcgcgcTCGGTTGTAAATATCTGCGAATTTGCCACCTGAACAACTGCGCCACGGGTGTAGCAACTCAg < 1:1527513/66‑1 (MQ=255)
gtcgcgcTCGGTTGTAAATATCTGCGAATTTGCCACCTGAACAACTGCGCCACGGGTGTAGCAACTCAg < 1:1636271/66‑1 (MQ=255)
gtcgcgcTCGGTTGTAAATATCTGCGAATTTGCCACCTGAACAACTGCGCCACGGGTGTAGCAACTCAg < 1:2184738/66‑1 (MQ=255)
gtcgcgcTCGGTTGTAAATATCTGCGAATTTGCCACCTGAACAACTGCGCCACGGGTGTAGCAACTCAg < 1:236592/66‑1 (MQ=255)
gtcgcgcTCGGTTGTAAATATCTGCGAATTTGCCACCTGAACAACTGCGCCACGGGTGTAGCAACTCAg < 1:3349278/66‑1 (MQ=255)
gtcgcgcTCGGTTGTAAATATCTGCGAATTTGCCACCTGAACAACTGCGCCACGGGTGTAGCAACTCAg < 1:322535/66‑1 (MQ=255)
gtcgcgcTCGGTTGTAAATATCTGCGAATTTGCCACCTGAACAACTGCGCCACGGGTGTAGCAACTCAg < 1:3203909/66‑1 (MQ=255)
gcgcTCGGCTGTAAATATCTACGTATTTGCCATCTGAACAACTGCGCAACGTGTGTAGCAACt < 1:417895/63‑1 (MQ=255)
gcgcTCGGCTGTAAATATCTACGTATTTGCCATCTGAACAACTGCGCAACGGGTGTAGCAACt < 1:2487055/63‑1 (MQ=255)
gcgcTCGGCTGTAAATATCTACGTATTTGCCATCTGAACAACTGCGCAACGGGTGTAGCAACt < 1:3063492/63‑1 (MQ=255)
gcgcTCGGCTGTAAATATCTACGTATTTGCCATCTGAACAACTGCGCAACGGGTGTAGCAACt < 1:2495295/63‑1 (MQ=255)
gcgcTCGGCTGTAAATATCTACGTATTTGCCATCTGAACAACTGCGCAACGGGTGTAGCAACt < 1:2919517/63‑1 (MQ=255)
cGGCTGTAAATATCTACGTATTTGCCATCTGAACAACTGCGCAACGGGTGTAGc > 1:3033403/1‑54 (MQ=255)
cGGCTGTAAATATCTACGTATTTGCCATCTGAACAACTGCGCAACGGGTGTAGCAACTCAGGATGACaa > 1:2194342/1‑69 (MQ=255)
cGGCTGTAAATATCTACGTATTTGCCATCTGAACAACTGCGCAACGGGTGTAGCAACTCAGGATGACaa > 1:1265113/1‑69 (MQ=255)
cGGCTGTAAATATCTACGTATTTGCCATCTGAACAACTGCGCAACGGGTGTAGCAACTCAGGATGACaa > 1:797120/1‑69 (MQ=255)
cGGCTGTAAATATCTACGTATTTGCCATCTGAACAACTGCGCAACGGGTGTAGCAACTCAGGATGACaa > 1:793284/1‑69 (MQ=255)
cGGCTGTAAATATCTACGTATTTGCCATCTGAACAACTGCGCAACGGGTGTAGCAACTCAGGATGACaa > 1:541354/1‑69 (MQ=255)
cTGTAAATATCTACGTATTTGCCATCTGAACAACTGCGCAACGGGTGTAGCAACTCAGGATGACAAAc < 1:2800633/68‑1 (MQ=255)
cTGTAAATATCTACGTATTTGCCATCTGAACAACTGCGCAACGGGTGTAGCAACTCAGGATGACAAAc < 1:975548/68‑1 (MQ=255)
|
AAGGCGGCGATTCTCGGCGCAGAAAGCTTCGGCTTCGGCACTGGCCCGATGGTGGCGCTCGGCTGTAAATATCTACGTATTTGCCATCTGAACAACTGCGCAACGGGTGTAGCAACTCAGGATGACAAAC > minE/2183058‑2183187
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
