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 |
1,932,763 |
G→A |
23.3% |
intergenic (‑134/+162) |
yqeF ← / ← lysS |
predicted acyltransferase/lysine tRNA synthetase, constitutive |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,932,763 | 0 | G | A | 23.3%
| 143.4
/ 41.3
| 73 | intergenic (‑134/+162) | yqeF/lysS | predicted acyltransferase/lysine tRNA synthetase, constitutive |
| Reads supporting (aligned to +/- strand): ref base G (36/20); new base A (9/8); total (45/28) |
| Fisher's exact test for biased strand distribution p-value = 4.10e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.88e-01 |
AAAAAAAGTGATTTTTATCACAAAGGAAATATGCCTGAGCAGCAGTCAGAGACATAACTGGCACGTAGGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGATAGGGCGTTAATCTCCCATACTTAACCTGGTT > minE/1932696‑1932831
|
aaaaaaaGTGATTTTTATCACAAAGGAAATATGCCTGAGCAGCAGTCAGAGACATAACTGGCACGTAagg < 1:3439567/70‑1 (MQ=255)
aaaaaaGTGATTTTTATCACAAAGGAAATATGCCTGAGCAGCAGTCAGAGACATAACTGGCACGTAGGGt < 1:1569027/70‑1 (MQ=255)
aaaGTGATTTTTATCACAAAGGAAATATGCCTGAGCAGCAGTCAGAGACATAACTGGCACGTAGGGTTTg > 1:1491432/1‑70 (MQ=255)
aaGTGATTTTTATCACAAAGGAAATATGCCTGAGCAGCAGTCAGAGACATAACTGGCACGTAGGGTTTGc > 1:1402998/1‑70 (MQ=255)
aaGTGATTTTTATCACAAAGGAAATATGCCTGAGCAGCAGTCAGAGACATAACTGGCACGTAAGGTTTGc < 1:2507680/70‑1 (MQ=255)
aaGTGATTTTTATCACAAAGGAAATATGCCTGAGCAGCAGTCAGAGACATAACTGGCACGTAAGGTTTGc > 1:4058779/1‑70 (MQ=255)
aGTGATTTTTATCACAAAGGAAATATGCCTGAGCAGCAGTCAGAGACATAACTGGCACGTAGGGTTTGCaa > 1:2180925/1‑71 (MQ=255)
aGTGATTTTTATCACAAAGGAAATATGCCTGAGCAGCAGTCAGAGACATAACTGGCACGTAGGGTTTGCaa > 1:3930384/1‑71 (MQ=255)
gTGATTTTTATCACAAAGGAAATATGCCTGAGCAGCAGTCAGAGACATAACTGGCACGTAGGGTTTGCAAc < 1:1868208/71‑1 (MQ=255)
gTGATTTTTATCACAAAGGAAATATGCCTGAGCAGCAGTCAGAGACATAACTGGCACGTAAGGTTTGCAAc < 1:3497069/71‑1 (MQ=255)
tGATTTTTATCACAAAGGAAATATGCCTGAGCAGCAGTCAGAGACATAACTGGCTCGTAAGGTTTGc < 1:2502713/67‑1 (MQ=255)
aTTTTTATCACAAAGGAAATATGCCTGAGCAGCAGTCAGAGACATAACTGGCACGTAGGGTTTGCAACCAc > 1:1187111/1‑71 (MQ=255)
aTTTTTATCACAAAGGAAATATGCCTGAGCAGCAGTCAGAGACATAACTGGCACGTAAGGTTTGCAACCAc > 1:1247301/1‑71 (MQ=255)
tttttATCACAAAGGAAATATGCCTGAGCAGCAGTCAGAGACATAACTGGCACGTAGGGTTTGCAACCAc > 1:3490667/1‑70 (MQ=255)
tttttATCACAAAGGAAATATGCCTGAGCAGCAGTCAGAGACATAACTGGCACGTAGGGTTTGCAACCACt < 1:3431402/71‑1 (MQ=255)
ttttATCACAAAGGAAATATGCCTGAGCAGCAGTCAGAGACATAACTGGCACGTAAGGTTTGCAACCACt > 1:701451/1‑70 (MQ=255)
tttATCACAAAGGAAATATGCCTGAGCAGCAGTCAGAGACATAACTGGCACGTAGGGTTTGCAACCACTaa > 1:2346302/1‑71 (MQ=255)
tttATCACAAAGGAAATATGCCTGAGCAGCAGTCAGAGACATAACTGGCACGTAGGGCTTGCAACCa > 1:1529625/1‑67 (MQ=255)
tATCACAAAGGAAATATGCCTGAGCAGCAGTCAGAGACATAACTGGCACGTAGGGTTTGCAACCACTAAcc > 1:3492734/1‑71 (MQ=255)
cacaAAGGAAATATGCCTGAGCAGCAGTCAGAGACATAACTGGCACGTAGGGTTTGCAACCACTAACccac > 1:1076358/1‑71 (MQ=255)
cacaAAGGAAATATGCCTGAGCAGCAGTCAGAGACATAACTGGCACGTAGGGTTTGCAACCACTAACccac > 1:2478804/1‑71 (MQ=255)
caAAGGAAATATGCCTGAGCAGCAGTCAGAGACATAACTGGCACGTAGGGTTTGCAACCACTAACccacc > 1:1124206/1‑70 (MQ=255)
ggAAATATGCCTGAGCAGCAGTCAGAGACATAACTGGCACGTAAGGTTTGCAACCACTAACCCACCAATa < 1:2039530/70‑1 (MQ=255)
gAAATATGCCTGAGCAGCAGTCAGAGACATAACTGGCACGTAGGGTTTGCa < 1:2540283/51‑1 (MQ=255)
aaaTATGCCTGAGCAGCAGTCAGAGACATAACTGGCACGTAGGGTTTGCAACCACTAACCCACCAATagag > 1:3496655/1‑71 (MQ=255)
atGCCTGAGCAGCAGTCAGAGACATAACTGGCACGTAGGGTTTGCAACCACTAACCCACCAATagag > 1:1218107/1‑67 (MQ=255)
atGCCTGAGCAGCAGTCAGAGACATAACTGGCACGTAGGGTTTGCAACCACTAACCCACCAATa > 1:664460/1‑64 (MQ=255)
tGCCTGAGCAGCAGTCAGAGACATAACTGGCACGTAGGGTTTGCAACCACTAACCCACCAATAGAgggg > 1:2335473/1‑69 (MQ=255)
tGCCTGAGCAGCAGTCAGAGACATAACTGGCACGTAAGGTTTGCAACCACTAACCCACCAATa > 1:621268/1‑63 (MQ=255)
ccTGAGCAGCAGTCAGAGACATAACTGGCACGTAGGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGa < 1:2120129/71‑1 (MQ=255)
ccTGAGCAGCAGTCAGAGACATAACTGGCACGTAGGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGa < 1:3130629/71‑1 (MQ=255)
gAGCAGCAGTCAGAGACATAACTGGCACGTAGGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGATAg > 1:3407217/1‑71 (MQ=255)
agcagcAGTCAGAGACATAACTGGCACGTAGGGTTTGCAACCACTAACCCACCAATaga > 1:3286366/1‑59 (MQ=255)
agcagcAGTCAGAGACATAACTGGCACGTAAGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGATAgg > 1:1065714/1‑71 (MQ=255)
gcagcaGTCAGAGACATAACTGGCACGTAGGGTTTGCAACCACTAACCCACCAATa > 1:1612672/1‑56 (MQ=255)
gcagTCAGAGACATAACTGGCACGTAGGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGATAGGGCGt > 1:2584162/1‑71 (MQ=255)
agTCAGAGACATAACTGGCACGTAGGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGATAGGGCGtt > 1:453354/1‑70 (MQ=255)
agTCAGAGACATAACTGGCACGTAGGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGATAGGGCGtt > 1:3455838/1‑70 (MQ=255)
agTCAGAGACATAACTGGCACGTAGGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGATAGGGCGTTa < 1:2605248/71‑1 (MQ=255)
agTCAGAGACATAACTGGCACGTAAGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGATAGGGCGTTa < 1:4141996/71‑1 (MQ=255)
gTCAGAGACATAACTGGCACGTAGGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGATAGGGCGTTaa > 1:1256509/1‑71 (MQ=255)
gTCAGAGACATAACTGGCACGTAGGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGATAGGGCGTTaa > 1:2251381/1‑71 (MQ=255)
gTCAGAGACATAACTGGCACGTAAGGTTTGCAACCACTa < 1:571022/39‑1 (MQ=255)
tCAGAGACATAACTGGCACGTAGGGTTTGCAACCACTAACccacc < 1:3577262/45‑1 (MQ=255)
tCAGAGACATAACTGGCACGTAGGGTTTGCAACCACTAACCCACCAATAGAGGGGTa < 1:3957540/57‑1 (MQ=255)
tCAGAGACATAACTGGCACGTAGGGTTTGCAACCACTAACCCACCAATAGAGGGGTa < 1:2795991/57‑1 (MQ=255)
cAGAGACATAACTGGCACGTAGGGTTTGCAACCACTAACCCACCAATaga > 1:588979/1‑50 (MQ=255)
agagACATAACTGGCACGTAGGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGa > 1:3366054/1‑57 (MQ=255)
agagACATAACTGGCACGTAGGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGa > 1:3375888/1‑57 (MQ=255)
agagACATAACTGGCACGTAGGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGATAGGGCGTTAAtct > 1:1787905/1‑71 (MQ=255)
agagACATAACTGGCACGTAAGGTTTGCAACCACTAACCCACCAATTGAGGGGTAGATAGGGCGTTAAtct < 1:1151723/71‑1 (MQ=255)
agagACATAACTGGCACGTAAGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGATAGGGCGTTAAtct > 1:1094294/1‑71 (MQ=255)
agaCATAACTGGCACGTAGGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGATAGGGCGTTAATCTcc < 1:3003287/71‑1 (MQ=255)
aCATAACTGGCACGTAGGGTTTGCAACCACTAACCCACCaa < 1:1020090/41‑1 (MQ=255)
aCATAACTGGCACGTAGGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGATAGGGCGtt < 1:2639690/62‑1 (MQ=255)
aCATAACTGGCACGTAAGGTTTGCAACCACTAACCCACCAATa > 1:1394042/1‑43 (MQ=255)
cATAACTGGCACGTAGGGTTTGCAACCACTAACCCACCAATAGAGGGGTa > 1:3934314/1‑50 (MQ=255)
cATAACTGGCACGTAGGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGATAGGGCGTTAATCTCCCAt < 1:3430958/71‑1 (MQ=255)
cATAACTGGCACGTAGGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGATAGGGCGTTAATCTCCCAt < 1:3799753/71‑1 (MQ=255)
cATAACTGGCACGTAGGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGATAGGGCGTTAATCTCCCAt < 1:4142878/71‑1 (MQ=255)
aTAACTGGCACGTAGGGTTTGCAACCACTAACCCACCAATa < 1:3441641/41‑1 (MQ=255)
aCTGGCACGTAGGGTTTGCAACCACTAACCCACCAATAGAggg > 1:3024881/1‑43 (MQ=255)
aCTGGCACGTAGGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGATAGGGCGTTAATCTCCCATACt > 1:3861796/1‑70 (MQ=255)
aCTGGCACGTAAGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGATAGGGCGTTAATCTCCCATACtt < 1:3692851/71‑1 (MQ=255)
tGGCACGTAGGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGATAGGGCGTTAATCTCCCATACTTaa > 1:3978271/1‑71 (MQ=255)
gCACGTAAGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGATAGGGCGTTAATCTCCCATACTTAAc > 1:870890/1‑70 (MQ=255)
cACGTAGGGTCTGCAACCACTAACCCACCAATAGAGGGGTAGATAGGGCGTTAATCTCCCATACTTAACCt > 1:2673599/1‑71 (MQ=255)
gTAGGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGATAGGGCGTTa < 1:3724379/50‑1 (MQ=255)
gTAGGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGATAGGGCGTTAATCTCCCATa < 1:3349752/60‑1 (MQ=255)
gTAGGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGATAGGGCGTTAATCTCCCATACTTAACCTGGt > 1:3473111/1‑71 (MQ=255)
gTAAGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGATAGGGCGTTAATCTCCCATACTTAACCTGGt > 1:3217499/1‑71 (MQ=255)
tAGGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGATAGGGCGTTAATCTCCCATACTTAACCTGGtt < 1:3354384/71‑1 (MQ=255)
aGGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGATAGGGCGt > 1:3631091/1‑46 (MQ=255)
aGGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGATAGGGCGTTAATCTcc > 1:857645/1‑54 (MQ=255)
|
AAAAAAAGTGATTTTTATCACAAAGGAAATATGCCTGAGCAGCAGTCAGAGACATAACTGGCACGTAGGGTTTGCAACCACTAACCCACCAATAGAGGGGTAGATAGGGCGTTAATCTCCCATACTTAACCTGGTT > minE/1932696‑1932831
|
| 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
