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 F3 I96 R1
|
172 |
34.7 |
2005794 |
96.2% |
1929573 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,593,447 |
T→C |
S52P (TCC→CCC) |
yjjQ → |
response regulator transcription factor |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,593,447 | 0 | T | C | 100.0%
| 123.9
/ NA
| 36 | S52P (TCC→CCC) | yjjQ | response regulator transcription factor |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (20/16); total (20/16) |
AGGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTTCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTC > NZ_CP009273/4593364‑4593526
|
agGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGAt > 1:88932/1‑90 (MQ=255)
agGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGAt > 1:514188/1‑90 (MQ=255)
agGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGAt > 1:583791/1‑90 (MQ=255)
ggTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGAtt > 2:636332/1‑90 (MQ=255)
ggACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTg > 2:892950/1‑90 (MQ=255)
gACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGc < 1:183794/90‑1 (MQ=255)
cACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGAt > 1:116600/1‑90 (MQ=255)
tGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCgg > 1:759820/1‑90 (MQ=255)
aaTATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTg < 2:682011/90‑1 (MQ=255)
aaTATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTg > 1:491969/1‑90 (MQ=255)
tatGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGaa > 1:95106/1‑90 (MQ=255)
tatGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGaa > 2:842179/1‑90 (MQ=255)
tatGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGaa < 2:295079/90‑1 (MQ=255)
tGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAg > 1:644182/1‑90 (MQ=255)
taataTCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAg < 2:95106/90‑1 (MQ=255)
taataTCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAg < 1:842179/90‑1 (MQ=255)
atatCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGAt > 1:565709/1‑90 (MQ=255)
ccAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCAc < 2:216650/90‑1 (MQ=255)
aGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGt < 1:636332/90‑1 (MQ=255)
gcgcCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGtt > 1:420370/1‑90 (MQ=255)
gcgcCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGtt > 2:870321/1‑90 (MQ=255)
gcCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCt < 2:322276/90‑1 (MQ=255)
ccTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTg < 1:927792/90‑1 (MQ=255)
aggaCCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAAc < 1:956643/90‑1 (MQ=255)
aggaCCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAAc < 2:362129/90‑1 (MQ=255)
aggaCCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAAc < 1:892950/90‑1 (MQ=255)
ttaccttaTTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACattatt > 2:718229/1‑90 (MQ=255)
accttaTTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACattattat < 2:355853/90‑1 (MQ=255)
aCAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAAt < 2:48468/90‑1 (MQ=255)
aTTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAAtctc > 1:159241/1‑90 (MQ=255)
aTTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAAtctc > 1:947352/1‑90 (MQ=255)
aTTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAAtctc > 1:635089/1‑90 (MQ=255)
aTTACGTCGTCCCGGACTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAAt > 1:956935/1‑87 (MQ=255)
aTTACGTCGTCCCGGACTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAAt < 2:956935/87‑1 (MQ=255)
cgtcgtCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTa < 2:557920/81‑1 (MQ=255)
cgtcgtCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTa > 1:557920/1‑81 (MQ=255)
|
AGGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTTCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTC > NZ_CP009273/4593364‑4593526
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GGGTTAAAAGAGGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTTCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTCACAATATCGGGAAATTCA > NZ_CP009273/4593354‑4593544
|
acagTAAAAGAGGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGAT < SRR3722236.139209/96‑1 (MQ=60)
GGGTTAAAAGAGGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGAT > SRR3722236.90161/1‑100 (MQ=60)
GGGTTAAAAGAGGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGAT > SRR3722236.522002/1‑100 (MQ=60)
GGGTTAAAAGAGGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGAT > SRR3722236.592878/1‑100 (MQ=60)
GGGTTAAAAGAGGTCATGAGGACTCACCTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGAT < SRR3722236.750463/100‑1 (MQ=60)
AAAAGAGGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTC < SRR3722236.860917/100‑1 (MQ=60)
CATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGAT > SRR3722236.118229/1‑100 (MQ=60)
gatctacacctaagccttcgtcgggcagcgtcagatgtgtataagagacAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATT < SRR3722236.890516/51‑1 (MQ=60)
GACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCC < SRR3722236.186514/100‑1 (MQ=60)
CTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGG > SRR3722236.772889/1‑100 (MQ=60)
CACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTG > SRR3722236.499380/1‑100 (MQ=60)
CTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAA > SRR3722236.96432/1‑100 (MQ=60)
TCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAG > SRR3722236.654783/1‑100 (MQ=60)
ATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGAT > SRR3722236.574420/1‑100 (MQ=60)
ATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTT > SRR3722236.426233/1‑100 (MQ=60)
TAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTC < SRR3722236.856933/100‑1 (MQ=60)
AGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTG < SRR3722236.646728/100‑1 (MQ=60)
CCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACA < SRR3722236.944175/100‑1 (MQ=60)
AGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTC < SRR3722236.908659/100‑1 (MQ=60)
AGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTC < SRR3722236.973517/100‑1 (MQ=60)
CCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTC > SRR3722236.964071/1‑100 (MQ=60)
CCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTC > SRR3722236.645458/1‑100 (MQ=60)
CCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTC > SRR3722236.161572/1‑100 (MQ=60)
CCTTATTACAATTACGTCGTCCCGGACTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTC > SRR3722236.973815/1‑100 (MQ=60)
ATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTCACAA > SRR3722236.566504/1‑100 (MQ=60)
CAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTGTTATTCTTTAATCTCACAATATC > SRR3722236.1003491/1‑100 (MQ=60)
CAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTCACAATctg > SRR3722236.911167/1‑97 (MQ=60)
CAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTCACAATATC > SRR3722236.671306/1‑100 (MQ=60)
TACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTCACAATATCGGGA > SRR3722236.257162/1‑100 (MQ=60)
GTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTCACAATATCGGGAAATTCA > SRR3722236.778667/1‑100 (MQ=60)
|
GGGTTAAAAGAGGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTTCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTCACAATATCGGGAAATTCA > NZ_CP009273/4593354‑4593544
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
