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 F2 I230 R1
|
226 |
18.8 |
1048726 |
96.7% |
1014118 |
86.4 |
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%
| 57.9
/ NA
| 19 | S52P (TCC→CCC) | yjjQ | response regulator transcription factor |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (14/5); total (14/5) |
AGGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTTCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTC > NZ_CP009273/4593364‑4593526
|
agGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTTCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGAt < 1:401900/90‑1 (MQ=255)
agGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGAt > 2:6838/1‑90 (MQ=255)
ggTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGATCTTACCTTATTACAATTACGTCGTCCCGGAtt < 1:193963/90‑1 (MQ=255)
aCTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCt > 2:195116/1‑90 (MQ=255)
tGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCgg > 1:204998/1‑90 (MQ=255)
tatGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGaa > 1:197829/1‑90 (MQ=255)
cAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACg > 2:176514/1‑90 (MQ=255)
gcgcCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCTGGTGAAAGTGAAGATCCACGtt > 1:337010/1‑90 (MQ=255)
ccTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTg > 1:198617/1‑90 (MQ=255)
ggaggaCCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGa < 2:204998/90‑1 (MQ=255)
ttaccttaTTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATc > 1:365569/1‑66 (MQ=255)
ttaccttaTTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATc < 2:365569/66‑1 (MQ=255)
ttaccttaTTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACattatt > 1:451719/1‑90 (MQ=255)
ttaccttaTTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACattatt > 2:147502/1‑90 (MQ=255)
ttaccttaTTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACattatt > 2:15832/1‑90 (MQ=255)
taccttaTTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACattatta < 2:209579/90‑1 (MQ=255)
tattaCAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCtt > 2:400916/1‑90 (MQ=255)
attaCAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCttt > 1:57451/1‑90 (MQ=255)
aTTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAAtctc > 1:6285/1‑90 (MQ=255)
|
AGGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTTCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTC > NZ_CP009273/4593364‑4593526
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AGGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTTCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTCACAATATCGGGAAATTCAC > NZ_CP009273/4593364‑4593545
|
AGGTCATGAGGACTCACTTCCCTGAATTTGAAATAATATCCAGCGCCTCTTCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGC < SRR3722114.406793/100‑1 (MQ=60)
GGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGATCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCT < SRR3722114.195859/100‑1 (MQ=60)
CTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGG > SRR3722114.206994/1‑100 (MQ=60)
CTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAA > SRR3722114.199761/1‑100 (MQ=60)
cgagatctagtacggtctcgtgggctcggagatgtgtataagagacagCAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAG < SRR3722114.14404/52‑1 (MQ=60)
ATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCTGGTGAAAGTGAAGATCCACGTT > SRR3722114.340799/1‑100 (MQ=60)
ATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTG > SRR3722114.200559/1‑100 (MQ=60)
GCGGAGGTCCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTctgtctcttataca > SRR3722114.369901/1‑86 (MQ=60)
GCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATT > SRR3722114.457353/1‑100 (MQ=60)
ACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTT > SRR3722114.58018/1‑100 (MQ=60)
CCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTC > SRR3722114.6348/1‑100 (MQ=60)
GTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCtgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgccgt > SRR3722114.256837/1‑45 (MQ=60)
TCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTCACAATATCGGGAAATTCAC < SRR3722114.67850/100‑1 (MQ=60)
|
AGGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTTCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTCACAATATCGGGAAATTCAC > NZ_CP009273/4593364‑4593545
|
| 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: ‑ |
