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 |
4,591,162 |
C→A |
15.6% |
V112V (GTG→GTT) |
hsdR ← |
endonuclease R |
|
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
* | W3110S.gb | 4,591,162 | 0 | C | A | 15.6%
| 155.3
/ 10.0
| 51 | V112V (GTG→GTT) | hsdR | endonuclease R |
Reads supporting (aligned to +/- strand): ref base C (28/15); new base A (4/4); total (32/19) |
Fisher's exact test for biased strand distribution p-value = 4.50e-01 |
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.90e-01 |
AGACAGCCAGGCGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACAGAGAGGATGTTGTCATCAACAAA > W3110S.gb/4591095‑4591224
|
aGACAGCCAGGCGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGc < 1:2535162/68‑1 (MQ=255)
aGACAGCCAGGCGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGc < 1:2458485/68‑1 (MQ=255)
aCAGCCAGGCGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGAAcc < 1:2294010/69‑1 (MQ=255)
cAGCCAGGCGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCg > 1:1236075/1‑69 (MQ=255)
aGGCGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGCCTg > 1:2379811/1‑68 (MQ=255)
ggCGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGAACCGCCTGGt < 1:1185565/69‑1 (MQ=255)
ggCGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGAACCGCCTGGt < 1:1061659/69‑1 (MQ=255)
ggCGGAACCCGACTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGAACCGCCTGGt < 1:758563/69‑1 (MQ=255)
gCGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGCCTGGtt < 1:3075281/69‑1 (MQ=255)
cGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCAc < 1:2625639/59‑1 (MQ=255)
gAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTAcc < 1:2411205/69‑1 (MQ=255)
cccGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGc < 1:3582503/52‑1 (MQ=255)
ggCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAAtt < 1:1708500/69‑1 (MQ=255)
cacaTCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGcc > 1:2087234/1‑45 (MQ=255)
cacaTCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGcc > 1:2881265/1‑45 (MQ=255)
acaTCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTtg > 1:1328292/1‑68 (MQ=255)
acaTCTGGGCATCGTTGAGATCGTTATGATATTCGTGAACCga > 1:1596852/1‑42 (MQ=255)
acaTCTGGGCATCGTTGAGATCGTTATGATATTCGTGAACCGCCTGGTTACCAATGCGGCGTAATTtg > 1:573120/1‑68 (MQ=255)
acaTCTGGGCATCGTTGAGATCGTTATGATATTCGTGAACCGCCTGGTTACCAATGCGGCGTAATTtg > 1:2379162/1‑68 (MQ=255)
cTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGaaa > 1:2136027/1‑69 (MQ=255)
tGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGcc > 1:3276370/1‑39 (MQ=255)
tGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGcc > 1:660159/1‑39 (MQ=255)
tGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGcc > 1:691332/1‑39 (MQ=255)
cATCGTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACa < 1:1690730/68‑1 (MQ=255)
tCGTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACagag < 1:1907772/69‑1 (MQ=255)
gTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGa < 1:795588/58‑1 (MQ=255)
gTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGa < 1:3058945/58‑1 (MQ=255)
gTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACagagag > 1:2353308/1‑69 (MQ=255)
gTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACagagag > 1:1565030/1‑69 (MQ=255)
gTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACagagag > 1:3085475/1‑69 (MQ=255)
gTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACagagag > 1:315118/1‑69 (MQ=255)
gTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACagagag > 1:404524/1‑69 (MQ=255)
gTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACagagag > 1:3485298/1‑69 (MQ=255)
gTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACagagag > 1:3489527/1‑69 (MQ=255)
gTTGAGATCGTTATGATATTCGTGAACCGCCTGGTTAcc > 1:2690967/1‑39 (MQ=255)
tGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCa > 1:2244316/1‑38 (MQ=255)
gagaTCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGt > 1:1366066/1‑46 (MQ=255)
gagaTCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGt > 1:703686/1‑46 (MQ=255)
gagaTCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGt > 1:3463762/1‑46 (MQ=255)
gagaTCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACAGAGAGGAt > 1:2180255/1‑69 (MQ=255)
gagaTCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACAGAGAGGAt > 1:3398812/1‑69 (MQ=255)
tCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACagagag > 1:1205755/1‑62 (MQ=255)
tCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACagagag > 1:1846197/1‑62 (MQ=255)
cGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACAGAGAGGAtgttgt > 1:2032394/1‑69 (MQ=255)
cGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACAGAGAGGAtgttgt > 1:3219229/1‑69 (MQ=255)
cGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACAGAGAGGAtgttgt > 1:670942/1‑69 (MQ=255)
atTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACAGAGAGGATGTTGTCATcaaca < 1:3639041/68‑1 (MQ=255)
atTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACAGAGAGGATGTTGTCATcaaca < 1:471595/68‑1 (MQ=255)
atTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACAGAGAGGATGTTGTCATcaaca < 1:3173079/68‑1 (MQ=255)
atTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACAGAGAGGATGTTGTCATcaaca < 1:1746771/68‑1 (MQ=255)
atTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACAGAGAGGATGTTGTCATcaaca < 1:3065935/68‑1 (MQ=255)
atTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACAGAGAGGATGTTGTCATcaaca < 1:3053722/68‑1 (MQ=255)
atTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACAGAGAGGATGTTGTCATcaaca < 1:2856893/68‑1 (MQ=255)
ttCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACAGAGAGGATGTTGTCATCAACaaa > 1:2875913/1‑69 (MQ=255)
|
AGACAGCCAGGCGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACAGAGAGGATGTTGTCATCAACAAA > W3110S.gb/4591095‑4591224
|
Alignment Legend |
---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A