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 F17 I0 R2
|
276 |
45.3 |
3729697 |
93.0% |
3468618 |
60.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,075,828 |
T→C |
67.3% |
L1159L (TTA→TTG) |
putA ← |
fused DNA‑binding transcriptional regulator, proline dehydrogenase, and pyrroline‑5‑carboxylate dehydrogenase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,075,828 | 0 | T | C | 67.3%
| 69.1
/ 48.3
| 55 | L1159L (TTA→TTG) | putA | fused DNA‑binding transcriptional regulator, proline dehydrogenase, and pyrroline‑5‑carboxylate dehydrogenase |
| Reads supporting (aligned to +/- strand): ref base T (7/11); new base C (19/18); total (26/29) |
| Fisher's exact test for biased strand distribution p-value = 4.07e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.82e-01 |
TCACCCGTCGGCCCCGGCAGCAATCGTTGTGTTCCTGCCTGCGCCAGCTCGCCATATTGCGTACATAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTCAATGC > W3110S.gb/1075763‑1075893
|
tCACCCGTCGGCCCCGGCAGCAATCGTTGTGTTCCTGCCTGCGCCAGCTCGCCATATTGCGTACACAAc < 1:334838/69‑1 (MQ=255)
tCACCCGTCGGCCCCGGCAGCAATCGTTGTGTTCCTGCCTGCGCCAGCTCGCCATATTGCGTACACAAc < 1:3659215/69‑1 (MQ=255)
tCACCCGTCGGCCCCGGCAGCAATCGTTGTGTTCCTGCCTGCGCCAGCTCGCCATATTGCGTACACAAc < 1:419469/69‑1 (MQ=255)
cACCCGTCGGCCCCGGCAGCAATCGTTGTGTTCCTGCCTGCGCCAGCTCGCCATATTGCGTACACAACg > 1:516366/1‑69 (MQ=255)
cccGTCGGCCCCGGCAGCAATCGTTGTGTTCCTGCCTGCGCCAGCTCGCCATATTGCGTACACAACGcc > 1:811974/1‑69 (MQ=255)
cGTTGTGTTCCTGCCTGCGCCAGCTCGCCATATTGCGTACACAACGCCTGCAATTCTGGACGAttt < 1:1589324/66‑1 (MQ=255)
gTTGTGTTCCTGCCTGCGCCAGCTCGCCATATTGCGTACAt < 1:2703745/41‑1 (MQ=255)
gTTGTGTTCCTGCCTGCGCCAGCTCGCCATATTGCGTACAt < 1:2480900/41‑1 (MQ=255)
gTTGTGTTCCTGCCTGCGCCAGCTCGCCATATTGCGTACAt < 1:2472894/41‑1 (MQ=255)
gTTGTGTTCCTGCCTGCGCCAGCTCGCCATATTGCGTACAt < 1:3323301/41‑1 (MQ=255)
tgtgTTCCTGCCTGCGCCAGCTCTCCATATTGCGTACACAACTCCTGCAATTCTGGACGATTTGCTGcc > 1:2972626/1‑69 (MQ=255)
tgtgTTCCTGCCTGCGCCAGCTCGCCATATTGCGTACATAACGCCTGCAATTCTGGACGATTTGCTGcc < 1:1809458/69‑1 (MQ=255)
tgtgTTCCTGCCTGCGCCAGCTCGCCATATTGCGTACATAACGCCTGCAATTCTGGACGATTTGCTGcc < 1:2395678/69‑1 (MQ=255)
tgtgTTCCTGCCTGCGCCAGCTCGCCATATTGCGTACACAACGCCTGCAATTCTGGACGATTTGCTGcc < 1:3194582/69‑1 (MQ=255)
tgtgTTCCTGCCTGCGCCAGCTCGCCATATTGCGTACACAAAGCCTGCAATTCTGGACGATTTGCTGcc < 1:1765599/69‑1 (MQ=255)
gtgtTCCTGCCTGCGCCAGCTCGCCATATTGCGTACATAACGCCTGCAATTCTGGACGATTTGCTGcc < 1:2404778/68‑1 (MQ=255)
gtgtTCCTGCCTGCGCCAGCTCGCCATATTGCGTACACAACGCCTGCAATTCTGGACGAtt > 1:3247279/1‑61 (MQ=255)
gtgtTCCTGCCTGCGCCAGCTCGCCATATTGCGTACACAACGCCTGCAATTCTGGACGAtt > 1:2980159/1‑61 (MQ=255)
gtgtTCCTGCCTGCGCCAGCTCGCCATATTGCGTACACAACGCCTGCAATTCTGGACGATTTGCTGcc < 1:2269093/68‑1 (MQ=255)
ttCCTGCCTGCGCCAGCTCGCCATATTGCGTACACAACGCCTGCAATTCTGGACGATTTGCTGCCCAt < 1:445457/68‑1 (MQ=255)
ttCCTGCCTGCGCCAGCTCGCCATATTGCGTACACAACGCCTGCAATTCTGGACGATTTGCTGCCCAt < 1:827726/68‑1 (MQ=255)
ttCCTGCCTGCGCCAGCTCGCCATATTGCGTACACAACGCCTGCAATTCTGGACGATTTGCTGCCCAt < 1:1808504/68‑1 (MQ=255)
cctgcGCCAGCTCGCCATATTGCGTACACAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCa > 1:144313/1‑69 (MQ=255)
ccAGCTCGCCATATTGCGTACACAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCa < 1:3129239/68‑1 (MQ=255)
ccAGCTCGCCATATTGCGTACACAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCa < 1:1204397/68‑1 (MQ=255)
ccAGCTCGCCATATTGCGTACACAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCa < 1:1570346/68‑1 (MQ=255)
aGCTCGCCATATTGCGTACATAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGc > 1:429147/1‑65 (MQ=255)
aGCTCGCCATATTGCGTACATAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGc < 1:625728/65‑1 (MQ=255)
aGCTCGCCATATTGCGTACATAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGc < 1:2346802/65‑1 (MQ=255)
aGCTCGCCATATTGCGTACACAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCAttt < 1:332626/69‑1 (MQ=255)
cTCGCCATATTGCGTACACAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCATTTAg > 1:3288463/1‑69 (MQ=255)
tCGCCATATTGCGTACACAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCAttt > 1:1670047/1‑66 (MQ=255)
tCGCCATATTGCGTACACAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCAttt > 1:2773088/1‑66 (MQ=255)
cGCCATATTGCGTACACAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCAttt > 1:1005459/1‑65 (MQ=255)
atTGCGTACATAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGa > 1:1983832/1‑68 (MQ=255)
ttGCGTACACAACGCCTGCAATTCTGGACGATTtgctg > 1:2387088/1‑38 (MQ=255)
ttGCGTACACAACGCCTGCAATTCTGGACGATTtgctg > 1:2962198/1‑38 (MQ=255)
ttGCGTACACAACGCCTGCAATTCTGGACGATTtgctg > 1:2223869/1‑38 (MQ=255)
ttGCGTACACAACGCCTGCAATTCTGGACGATTtgctg > 1:650861/1‑38 (MQ=255)
ttGCGTACACAACGCCTGCAATTCTGGACGATTtgc > 1:1001718/1‑36 (MQ=255)
ttGCGTACACAACGCCTGCAATTCTGGACGATTtg > 1:733355/1‑35 (MQ=255)
ttGCGTACACAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGt > 1:3567170/1‑52 (MQ=255)
ttGCGTACACAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGc > 1:351803/1‑54 (MQ=255)
gCGTACATAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTc < 1:2291318/68‑1 (MQ=255)
gCGTACATAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTc < 1:201480/68‑1 (MQ=255)
gCGTACATAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTc < 1:3387483/68‑1 (MQ=255)
gCGTACATAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTCa > 1:1289278/1‑69 (MQ=255)
gCGTACATAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTCa < 1:488010/69‑1 (MQ=255)
gCGTACATAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTCa > 1:2560271/1‑69 (MQ=255)
gCGTACATAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTCa < 1:2074727/69‑1 (MQ=255)
gCGTACATAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTCa > 1:3181386/1‑69 (MQ=255)
gCGTACATAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTCa > 1:2538197/1‑69 (MQ=255)
gCGTACATAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCATTTAGCAGCTGAGTc < 1:3406898/68‑1 (MQ=255)
gCGTACACAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTc < 1:889223/68‑1 (MQ=255)
gCGTACACAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTc < 1:2845465/68‑1 (MQ=255)
gCGTACACAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTc < 1:1155739/68‑1 (MQ=255)
gCGTACACAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTCa > 1:3298366/1‑69 (MQ=255)
cGTACACAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTc < 1:291476/67‑1 (MQ=255)
aCATAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTCAATGc > 1:1969121/1‑69 (MQ=255)
|
TCACCCGTCGGCCCCGGCAGCAATCGTTGTGTTCCTGCCTGCGCCAGCTCGCCATATTGCGTACATAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTCAATGC > W3110S.gb/1075763‑1075893
|
| 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
