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 |
|
A4 F21 I0 R1
|
1009 |
73.8 |
4146436 |
87.4% |
3623985 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,041,438 |
G→A |
43.1% |
D32N (GAT→AAT) |
yqiI → |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,041,438 | 0 | G | A | 43.1%
| 35.1
/ 89.5
| 72 | D32N (GAT→AAT) | yqiI | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (23/18); new base A (11/20); total (34/38) |
| Fisher's exact test for biased strand distribution p-value = 9.94e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.79e-01 |
TTTTTATGGGTTTTAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATGGTAAAAAAGGTGATAAAATCTG > minE/2041373‑2041508
|
tttttATGGGTTTTAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAAATAcc > 1:137328/1‑71 (MQ=255)
tGGGTTTTAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGt < 1:3158838/70‑1 (MQ=255)
tGGGTTTTAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGt < 1:1144673/70‑1 (MQ=255)
ttAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGgaga > 1:3890484/1‑55 (MQ=255)
ttAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGt > 1:64478/1‑71 (MQ=255)
ttAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGt > 1:321383/1‑71 (MQ=255)
ttAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTGGt > 1:1070941/1‑71 (MQ=255)
tAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGt < 1:999468/70‑1 (MQ=255)
tAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTGGt < 1:1096836/70‑1 (MQ=255)
tAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTGGt < 1:784747/70‑1 (MQ=255)
ttCATTACCTGCATGGGCAATGGACTTCTATGCTGAACATGAAGGTGGAAATACCGTTGTc < 1:1370773/61‑1 (MQ=255)
ttCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTc < 1:428959/61‑1 (MQ=255)
ttCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCAt < 1:3254247/63‑1 (MQ=255)
ttCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTGGTTACg < 1:1924729/71‑1 (MQ=255)
cATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCAt > 1:3312573/1‑61 (MQ=255)
cATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTa > 1:591395/1‑71 (MQ=255)
ttACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGAt < 1:1892457/48‑1 (MQ=255)
aCCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACg > 1:1587069/1‑65 (MQ=255)
aCCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTAcc > 1:722518/1‑69 (MQ=255)
ccTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAg < 1:3352134/71‑1 (MQ=255)
gCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAAt > 1:2204240/1‑71 (MQ=255)
aTGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTGGTTACGTACCAAGAAtct < 1:4036717/71‑1 (MQ=255)
tGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTGGTTACg < 1:1516171/58‑1 (MQ=255)
tGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTGGTTACg < 1:3251476/58‑1 (MQ=255)
tGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTGGTTACg < 1:2710836/58‑1 (MQ=255)
ggCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTa < 1:1888101/71‑1 (MQ=255)
gCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATctct < 1:1511447/69‑1 (MQ=255)
gCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTAt < 1:1499910/71‑1 (MQ=255)
cAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTGGt < 1:1659058/50‑1 (MQ=255)
aTGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATccc > 1:3549086/1‑71 (MQ=255)
tGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATccc > 1:700241/1‑70 (MQ=255)
tGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATccc > 1:1248581/1‑70 (MQ=255)
ggACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTa > 1:3444893/1‑48 (MQ=255)
ggACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATccc > 1:238632/1‑69 (MQ=255)
gACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAg > 1:2072837/1‑71 (MQ=255)
cTGCTATGCTGAACATGAAGGTGGAGATACCGTTGt < 1:2357653/36‑1 (MQ=255)
cTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCg < 1:1751174/71‑1 (MQ=255)
cTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCg < 1:509631/71‑1 (MQ=255)
cTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCg < 1:1758890/71‑1 (MQ=255)
tGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTgg < 1:1507259/41‑1 (MQ=255)
tGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTgg < 1:3387083/41‑1 (MQ=255)
cTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATg > 1:2750324/1‑71 (MQ=255)
cTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATg > 1:834105/1‑71 (MQ=255)
cTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTGGTTACGTACCAAGAAtct > 1:2247830/1‑56 (MQ=255)
tATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGt < 1:128277/39‑1 (MQ=255)
tATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATgg > 1:3044125/1‑71 (MQ=255)
tATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATgg > 1:3450778/1‑71 (MQ=255)
tATGCTGAACATGAAGGTGGAAATACCGTTGTCATTGGTTa < 1:1781259/41‑1 (MQ=255)
gCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGa < 1:3370838/48‑1 (MQ=255)
cTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTAc < 1:3321470/38‑1 (MQ=255)
cTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTAc < 1:1599623/38‑1 (MQ=255)
cTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACg > 1:208792/1‑39 (MQ=255)
cTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTa > 1:1868565/1‑41 (MQ=255)
cTGAACATGAAGGTGGAAATACCGTTGTCATTGGTTACGTACCAAGaa > 1:638641/1‑48 (MQ=255)
cTGAACATGAAGGTGGAAATACCGTTGTCATTGGTTACGTACCAAGaa > 1:2215375/1‑48 (MQ=255)
gAACATGTAGGTGGAAATACCGTTGTCATTGGTTACGTa > 1:1559393/1‑39 (MQ=37)
gAACATGAAGGTGGAGATACCGTTGGCATTGGTTACGTACCaa < 1:630302/43‑1 (MQ=255)
gAACATGAAGGTGGAAATACCGTTGTCATTGGTTACGt > 1:2408200/1‑38 (MQ=255)
gAACATGAAGGTGGAAATACCGTTGTCATTGGTTACGTa > 1:3669564/1‑39 (MQ=255)
gAACATGAAGGTGGAAATACCGTTGTCATTGGTTACGTa > 1:3611642/1‑39 (MQ=255)
aaCATGAAGGTGTAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATGGTaaaa < 1:205329/69‑1 (MQ=255)
aaCATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATGGTaaaa < 1:3467827/69‑1 (MQ=255)
aaCATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATGGTaaaa > 1:2291119/1‑69 (MQ=255)
aaCATGAAGGTGGAAATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATGGTaaaat < 1:702079/70‑2 (MQ=255)
aaCATGAAGGTGGAAATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATGGTaaaaa < 1:2301868/70‑1 (MQ=255)
cATGAAGGTGGAGATACCGTTGTCATTGGTTACGTa > 1:3341063/1‑36 (MQ=255)
cATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGc < 1:1262047/57‑1 (MQ=255)
aTGAAGGTGGAAATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATGGTAAAAAAGGt < 1:1832918/71‑1 (MQ=255)
tGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAAt > 1:1721902/1‑42 (MQ=255)
tGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAAt > 1:911093/1‑42 (MQ=255)
tGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAg > 1:1094359/1‑54 (MQ=255)
tGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATGGTAAAAAAGGt < 1:879512/70‑1 (MQ=255)
ggAAATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATGGTAAAAAAGGTGATAAAAt > 1:2444560/1‑71 (MQ=255)
gagaTACCGTTGTCATTGGTTACGTACCAATAATCTCTATCCCCAGCGATGGTAAAAAAGGTGATAAAATc < 1:4026298/71‑1 (MQ=255)
gaTACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATGGTAAAAAAGGTGATAAAATCTg < 1:2105309/71‑1 (MQ=255)
|
TTTTTATGGGTTTTAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATGGTAAAAAAGGTGATAAAATCTG > minE/2041373‑2041508
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
