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 |
|
A5 F21 I0 R2
|
316 |
65.6 |
5147759 |
97.4% |
5013917 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,824,410 |
T→A |
100% |
pseudogene (543/687 nt) |
rph → |
ECK3633:JW3618:b3643; ribonuclease PH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,824,410 | 0 | T | A | 100.0%
| 212.8
/ NA
| 70 | pseudogene (543/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base A (36/34); total (36/34) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
AGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCAGGGGA > W3110S.gb/3824344‑3824474
|
aGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCg > 1:2543418/1‑71 (MQ=255)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCg > 1:3131981/1‑70 (MQ=255)
cTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa > 1:4881398/1‑70 (MQ=255)
cTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa > 1:4875778/1‑70 (MQ=255)
cTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa > 1:4284490/1‑70 (MQ=255)
cTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa < 1:2047520/70‑1 (MQ=255)
cGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATg > 1:3211571/1‑70 (MQ=255)
cGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATg > 1:3517274/1‑70 (MQ=255)
ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa < 1:1137145/68‑1 (MQ=255)
ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa > 1:581693/4‑71 (MQ=255)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc < 1:2957902/49‑1 (MQ=25)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc < 1:4725043/49‑1 (MQ=25)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCaga < 1:2911979/55‑1 (MQ=255)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCaga < 1:3367154/55‑1 (MQ=255)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg > 1:3687203/1‑69 (MQ=255)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGt < 1:3356189/70‑1 (MQ=255)
gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt > 1:2492810/4‑71 (MQ=255)
gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt > 1:4231358/4‑71 (MQ=255)
taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt < 1:4883736/68‑1 (MQ=255)
aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat < 1:2442030/71‑1 (MQ=255)
aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat > 1:3949146/1‑70 (MQ=255)
gtgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGAc > 1:3633823/3‑70 (MQ=255)
gAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCg < 1:225267/40‑1 (MQ=37)
atttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACgg > 1:4070334/2‑71 (MQ=255)
atttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACgg > 1:522159/2‑71 (MQ=255)
atttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACgg > 1:2385225/2‑71 (MQ=255)
tttGCGATCTGGAATACGTTGAAGACTCAGCCGCaga < 1:1462952/37‑1 (MQ=255)
tttGCGATCTGGAATACGTTGAAGACTCAGCCGCaga < 1:713230/37‑1 (MQ=255)
tttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg < 1:1077072/51‑1 (MQ=255)
tttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCg < 1:4161012/63‑1 (MQ=255)
tttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACg < 1:3395071/69‑1 (MQ=255)
tttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACg < 1:123360/69‑1 (MQ=255)
tttGCGATCTCGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCg < 1:5022339/63‑1 (MQ=255)
ttGCGATCTGGAATACGTTGAAGACTCAGCCGCAgaga > 1:3132839/1‑38 (MQ=255)
ttGCGATCTGGAATACGTTGAAGACTCAGCCGCAgaga > 1:3872654/1‑38 (MQ=255)
ttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACg < 1:730684/68‑1 (MQ=255)
tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAAc > 1:4022226/1‑48 (MQ=255)
tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGa > 1:554123/1‑62 (MQ=255)
tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACggg > 1:3913180/1‑69 (MQ=255)
tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGgcg > 1:583776/1‑71 (MQ=255)
tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGgcg > 1:1606409/1‑71 (MQ=255)
aTCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg < 1:4910911/45‑1 (MQ=255)
aTCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg < 1:2527513/45‑1 (MQ=255)
aTCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg < 1:2235158/45‑1 (MQ=255)
aTCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGaa < 1:2823595/59‑1 (MQ=255)
aTCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGaa < 1:34229/59‑1 (MQ=255)
aTCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGaa < 1:2376026/59‑1 (MQ=255)
tCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcatca > 1:2991954/1‑71 (MQ=255)
cTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtga > 1:216094/1‑49 (MQ=255)
cTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtga > 1:4851668/1‑49 (MQ=255)
cTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGaa > 1:732068/1‑57 (MQ=255)
cTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcatcat > 1:3931378/1‑71 (MQ=255)
cTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcatcat > 1:2463865/1‑71 (MQ=255)
cTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcatcat > 1:339686/1‑71 (MQ=255)
gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcat < 1:2276139/65‑1 (MQ=255)
aTACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAg < 1:4795397/71‑1 (MQ=255)
aTACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAg < 1:4382858/71‑1 (MQ=255)
aTACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAg < 1:2035293/71‑1 (MQ=255)
tACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat < 1:1802085/44‑1 (MQ=255)
tACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTg < 1:4380665/67‑1 (MQ=255)
aCGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGaa < 1:4030700/50‑1 (MQ=255)
cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGaa > 1:2953599/1‑67 (MQ=255)
cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGaa > 1:5061155/1‑67 (MQ=255)
cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAgag > 1:688056/1‑68 (MQ=255)
cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGc < 1:801500/71‑1 (MQ=255)
gAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGaa > 1:3792618/1‑63 (MQ=255)
gAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCAggg > 1:800130/1‑71 (MQ=255)
gAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCAgg > 1:3103271/1‑70 (MQ=255)
aaGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCAggg < 1:1287707/70‑1 (MQ=255)
aCTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCAGGGGa < 1:4785066/69‑1 (MQ=255)
|
AGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCAGGGGA > W3110S.gb/3824344‑3824474
|
| 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
