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 |
3,824,374 |
C→T |
100% |
pseudogene (507/687 nt) |
rph → |
ECK3633:JW3618:b3643; ribonuclease PH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,824,374 | 0 | C | T | 100.0%
| 180.0
/ NA
| 63 | pseudogene (507/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (28/35); total (28/35) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
AACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGAT > W3110S.gb/3824306‑3824439
|
aaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGa < 1:3796428/71‑1 (MQ=255)
cGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGa > 1:3934646/1‑69 (MQ=255)
ggCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAg > 1:2153373/1‑70 (MQ=255)
gCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGca < 1:4512878/71‑2 (MQ=255)
cAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGca < 1:2789782/70‑2 (MQ=255)
cTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTg > 1:2994338/1‑71 (MQ=255)
aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGa > 1:2824550/1‑71 (MQ=255)
aaccaaccCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATc > 1:562265/1‑71 (MQ=255)
aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg < 1:2761375/67‑1 (MQ=255)
aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCt > 1:3451634/1‑71 (MQ=255)
ccAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCt < 1:578141/70‑1 (MQ=255)
ccAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTg < 1:2390956/71‑1 (MQ=255)
ccAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTg < 1:4912872/71‑1 (MQ=255)
ccAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTg < 1:5107184/71‑1 (MQ=255)
ccAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTg < 1:4152608/71‑1 (MQ=255)
acccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa < 1:1333910/69‑1 (MQ=255)
ccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACTGTGAAGCAATTTGCGATCTGGAATa > 1:4762662/1‑71 (MQ=255)
ccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATa > 1:173370/1‑71 (MQ=255)
cGATGAAAGGGATGGTAGCCGCAGTTTCCGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATAc < 1:4271093/71‑1 (MQ=255)
gATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACg > 1:90940/1‑71 (MQ=255)
aTGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGca < 1:1937946/51‑2 (MQ=255)
gAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATa > 1:4400866/1‑66 (MQ=255)
gAAAGGGATGGTAGACGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATa > 1:104257/1‑66 (MQ=255)
aaaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg < 1:241735/70‑1 (MQ=255)
aaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg > 1:2291937/1‑69 (MQ=255)
aaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa < 1:634891/71‑1 (MQ=255)
aaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa < 1:2220482/71‑1 (MQ=255)
aGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGca < 1:4760620/46‑2 (MQ=255)
gggATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGa < 1:2845717/71‑1 (MQ=255)
ggATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATAc < 1:3977246/62‑1 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt > 1:4703860/1‑60 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg < 1:3081076/61‑1 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg < 1:4977454/61‑1 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGActcag < 1:509473/70‑3 (MQ=255)
aGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCg > 1:2543418/1‑71 (MQ=255)
gCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGa > 1:4224767/1‑44 (MQ=21)
gCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGa > 1:3760291/1‑44 (MQ=21)
gCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGa > 1:3796225/1‑44 (MQ=21)
ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt < 1:3987026/49‑1 (MQ=25)
ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt < 1:2549385/49‑1 (MQ=25)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCg > 1:3131981/1‑70 (MQ=255)
cTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa < 1:2047520/70‑1 (MQ=255)
cTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa > 1:4284490/1‑70 (MQ=255)
cTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa > 1:4881398/1‑70 (MQ=255)
cTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa > 1:4875778/1‑70 (MQ=255)
cGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATg > 1:3517274/1‑70 (MQ=255)
cGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATg > 1:3211571/1‑70 (MQ=255)
ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa < 1:1137145/68‑1 (MQ=255)
ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa > 1:581693/4‑71 (MQ=255)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACg < 1:1745358/36‑1 (MQ=16)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACg < 1:733189/36‑1 (MQ=16)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc < 1:4725043/49‑1 (MQ=25)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc < 1:2957902/49‑1 (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)
tgtaAACGGTGAAGCAATTTGCGATCTGGAATACg < 1:5094879/35‑1 (MQ=16)
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)
|
AACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGAT > W3110S.gb/3824306‑3824439
|
| 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
