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 |
2,290,611 |
G→A |
54.4% |
L441L (CTG→CTA) |
ppc → |
phosphoenolpyruvate carboxylase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,290,611 | 0 | G | A | 54.4%
| 3.4
/ 42.6
| 54 | L441L (CTG→CTA) | ppc | phosphoenolpyruvate carboxylase |
| Reads supporting (aligned to +/- strand): ref base G (6/18); new base A (21/8); total (28/26) |
| Fisher's exact test for biased strand distribution p-value = 8.73e-04 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.69e-01 |
AAACAGGCGTTCCTGATCCGCGAACTGAACTCCAAACGTCCGCTTCTGCCGCGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTCGATACCTGCCAGGTG > minE/2290564‑2290668
|
aaaCAGGCGTTCCTGATCCGCGAACTGAACTCCAAACGTCCGCTTCTGCCGCGCAACTGGCAACCAAgc > 1:202168/1‑69 (MQ=255)
aaaCAGGCGTTCCTGATCCGCGAACTGAACTCCAAACGTCCGCTTCTGCCGCGCAACTGGCAACCAAgc > 1:1415531/1‑69 (MQ=255)
aCAGGCGTTCCTGATCCGCGAACTGAACTCCAAACGTCCGCTTCTGCCGCGCAACTGGCAACCAAgcg > 1:2392992/1‑68 (MQ=255)
aCAGGCGTTCCTGATCCGCGAACTGAACTCCAAACGTCCGCTTCTGCCGCGCAACTGGCAACCAAgcg > 1:1543282/1‑68 (MQ=255)
cAGGCGTTCCTGATCCGCGAACTGAACTCCAAACGTCCGCTTCTACCACGCAACTGGCAACGAAGCGcc < 1:3103149/69‑1 (MQ=255)
cAGGCGTTCCTGATCCGCGAACTGAACTCCAAACGTCCGCTTCTACCACGCAACTGGCAACCAAGCGcc < 1:1218655/69‑1 (MQ=255)
cAGGCGTTCCTGATCCGCGAACTGAACTCCAAACGTCCGCTTCTACCACGCAACTGGCAACCAAGCGcc < 1:1890102/69‑1 (MQ=255)
cAGGCGTTCCTGATCCGCGAACTGAACTCCAAACGTCCGCTTCTACCACGCAACTGGCAACCAAGCGcc < 1:1706367/69‑1 (MQ=255)
cAGGCGTTCCTGATCCGCGAACTGAACTCCAAACGTCCGCTTCTACCACGCAACTGGCAACCAAGCGcc < 1:3308789/69‑1 (MQ=255)
cAGGCGTTCCTGATCCGCGAACTGAACTCCAAACGTCCGCTTCTACCACGCAACTGGCAACCAAGCGcc < 1:526992/69‑1 (MQ=255)
cAGGCGTTCCTGATCCGCGAACTGAACTCCAAACGTCCGCTTCTACCACGCAACTGGCAACCAAGCGcc < 1:737453/69‑1 (MQ=255)
cAGGCGTTCCTGATCCGCGAACTGAACTCCAAACGTCCGCTTCTACCACGCAACTGGCAACCAAGCGcc < 1:997602/69‑1 (MQ=255)
ccTGATCCGCGAACTGAACTCCAAACGTCCGCTTCTGCCGCGCAACTGGCAACCAAGCGCCGAAAcgc > 1:152723/1‑68 (MQ=255)
ccTGATCCGCGAACTGAACTCCAAACGTCCGCTTCTGCCGCGCAACTGGCAACCAAGCGCCGAAAcgc > 1:579750/1‑68 (MQ=255)
gaactgaactCCAAACGTCCGCTTCTGCCGCGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTc < 1:3298691/69‑1 (MQ=255)
gaactgaactCCAAACGTCCGCTTCTGCCGCGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTc < 1:598417/69‑1 (MQ=255)
gaactgaactCCAAACGTCCGCTTCTGCCGCGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTc < 1:2984537/69‑1 (MQ=255)
gaactgaactCCAAACGTCCGCTTCTGCCGCGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTc < 1:1232411/69‑1 (MQ=255)
gaactgaactCCAAACGTCCGCTTCTGCCGCGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTc < 1:2962175/69‑1 (MQ=255)
gaactgaactCCAAACGTCCGCTTCTGCCGCGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTc < 1:2875254/69‑1 (MQ=255)
gaactgaactCCAAACGTCCGCTTCTGCCGCGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTc < 1:2711120/69‑1 (MQ=255)
gaactgaactCCAAACGTCCGCTTCTGCCGCGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTc < 1:2413532/69‑1 (MQ=255)
gaactgaactCCAAACGTCCGCTTCTGCCGCGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTc < 1:2603784/69‑1 (MQ=255)
ctgaactCCAAACGTCCGCTTCTGCCGCGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTCGAt < 1:215277/69‑1 (MQ=255)
ctgaactCCAAACGTCCGCTTCTGCCGCGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTCGAt < 1:3328730/69‑1 (MQ=255)
ctCCAAACGTCCGCTTCTACCACGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTCGATACCt > 1:151401/1‑68 (MQ=255)
ctCCAAACGTCCGCTTCTACCACGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTCGATACCt > 1:1358087/1‑68 (MQ=255)
ctCCAAACGTCCGCTTCTACCACGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTCGATACCt > 1:947325/1‑68 (MQ=255)
ctCCAAACGTCCGCTTCTACCACGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTCGATACCt > 1:883312/1‑68 (MQ=255)
ctCCAAACGTCCGCTTCTACCACGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTCGATACCt > 1:864300/1‑68 (MQ=255)
ctCCAAACGTCCGCTTCTACCACGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTCGATACCt > 1:862442/1‑68 (MQ=255)
ctCCAAACGTCCGCTTCTACCACGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTCGATACCt > 1:754697/1‑68 (MQ=255)
ctCCAAACGTCCGCTTCTACCACGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTCGATACCt > 1:1369211/1‑68 (MQ=255)
ctCCAAACGTCCGCTTCTACCACGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTCGATACCt > 1:674116/1‑68 (MQ=255)
ctCCAAACGTCCGCTTCTACCACGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTCGATACCt > 1:1396331/1‑68 (MQ=255)
ctCCAAACGTCCGCTTCTACCACGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTCGATACCt > 1:1493032/1‑68 (MQ=255)
ctCCAAACGTCCGCTTCTACCACGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTCGATACCt > 1:344828/1‑68 (MQ=255)
ctCCAAACGTCCGCTTCTACCACGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTCGATACCt > 1:396917/1‑68 (MQ=255)
ctCCAAACGTCCGCTTCTACCACGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTCGATACCt > 1:3387916/1‑68 (MQ=255)
ctCCAAACGTCCGCTTCTACCACGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTCGATACCt > 1:3338289/1‑68 (MQ=255)
ctCCAAACGTCCGCTTCTACCACGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTCGATACCt > 1:2415583/1‑68 (MQ=255)
ctCCAAACGTCCGCTTCTACCACGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTCGATACCt > 1:3229781/1‑68 (MQ=255)
ctCCAAACGTCCGCTTCTACCACGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTCGATACCt > 1:3171644/1‑68 (MQ=255)
ctCCAAACGTCCGCTTCTACCACGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTCGATACCt > 1:3162365/1‑68 (MQ=255)
ctCCAAACGTCCGCTTCTACCACGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTCGATACCt > 1:2387202/1‑68 (MQ=255)
ctCCAAACGTCCGCTTCTACCACGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTAGATACCt > 1:593246/1‑68 (MQ=255)
ctCCAAACGTCCGCTTCT‑ACACGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTCGATACCt > 1:86565/1‑67 (MQ=255)
cGTCCGCTTCTGCCGCGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTCGATACCTGCCAGGTg < 1:2830658/69‑1 (MQ=255)
cGTCCGCTTCTGCCGCGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTCGATACCTGCCAGGTg < 1:976137/69‑1 (MQ=255)
cGTCCGCTTCTGCCGCGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTCGATACCTGCCAGGTg < 1:946624/69‑1 (MQ=255)
cGTCCGCTTCTGCCGCGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTCGATACCTGCCAGGTg < 1:556148/69‑1 (MQ=255)
gTCCGCTTCTGCCGCGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTCGATACCTGCCAGGTg < 1:778832/68‑1 (MQ=255)
gTCCGCTTCTGCCGCGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTCGATACCTGCCAGGTg < 1:1763916/68‑1 (MQ=255)
ccGCTTCTGCCGCGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTc < 1:1700074/51‑1 (MQ=255)
|
AAACAGGCGTTCCTGATCCGCGAACTGAACTCCAAACGTCCGCTTCTGCCGCGCAACTGGCAACCAAGCGCCGAAACGCGCGAAGTGCTCGATACCTGCCAGGTG > minE/2290564‑2290668
|
| 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
