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 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
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 | 85.2%
| 56.6
/ 6.0
| 27 | S52P (TCC→CCC) | yjjQ | response regulator transcription factor |
| Reads supporting (aligned to +/- strand): ref base T (4/0); new base C (15/8); total (19/8) |
| Fisher's exact test for biased strand distribution p-value = 2.85e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AAAGAGGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTTCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTCAC > NZ_CP009273/4593360‑4593528
|
aaaGAGGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTccc < 2:585801/90‑1 (MQ=255)
agGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTTCCGGAt > 1:23495/1‑90 (MQ=255)
agGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGAt > 2:116998/1‑90 (MQ=255)
agGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGAt > 1:773661/1‑90 (MQ=255)
agGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGAt > 1:707969/1‑90 (MQ=255)
ggTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGAtt > 2:181357/1‑90 (MQ=255)
gACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGc < 1:170705/90‑1 (MQ=255)
aCTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTTCCGGATTAGTCATTGCt > 1:83203/1‑90 (MQ=255)
cTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTg > 1:363052/1‑90 (MQ=255)
taataTCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTAAGCCGGTGAAAGTGAAg < 1:142241/90‑1 (MQ=255)
atCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATcc < 1:615993/90‑1 (MQ=255)
ccAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCAc < 1:370304/90‑1 (MQ=255)
gcgcCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTTCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGtt > 1:424635/1‑90 (MQ=255)
gcgcCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGtt > 2:109250/1‑90 (MQ=255)
ctctGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGt > 2:614693/1‑90 (MQ=255)
tctGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGtt > 1:556331/1‑90 (MQ=255)
tctGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGtt > 2:204533/1‑90 (MQ=255)
aggaCCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAAc < 2:624768/90‑1 (MQ=255)
aagaCCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAAc < 2:374254/88‑1 (MQ=255)
ttaccttaTTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACattatt > 2:693146/1‑90 (MQ=255)
ttattaCAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAGGATCCACGTTCTGTTTGTGAACATTATTATTCt > 2:376175/1‑90 (MQ=255)
ttattaCAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCt > 2:552513/1‑90 (MQ=255)
ttattaCAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCt > 1:804095/1‑90 (MQ=255)
attaCAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACa > 2:597550/1‑78 (MQ=255)
attaCAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACa < 1:597550/78‑1 (MQ=255)
aTTACGTCGTTCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAAtctc > 1:690785/1‑90 (MQ=255)
aTTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAAtctc > 2:190242/1‑90 (MQ=255)
tACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTcac < 1:556213/90‑1 (MQ=255)
|
AAAGAGGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTTCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTCAC > NZ_CP009273/4593360‑4593528
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ 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
AAGCAGGGTTAAAAGAGGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTTCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTCACAATATCGGGAAATTCA > NZ_CP009273/4593349‑4593544
|
AAGCAGGGTTAAAAGAGGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCC > SRR3722079.407252/1‑100 (MQ=60)
GGGTTAAAAGAGGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTTCCGGAT > SRR3722079.23662/1‑100 (MQ=60)
GGGTTAAAAGAGGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGAT > SRR3722079.781949/1‑100 (MQ=60)
GGGTTAAAAGAGGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGAT < SRR3722079.348765/100‑1 (MQ=60)
GGGTTAAAAGAGGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGAT > SRR3722079.715488/1‑100 (MQ=60)
AAAAGAGGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTC < SRR3722079.99284/100‑1 (MQ=60)
AAAAGAGGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTC < SRR3722079.263632/100‑1 (MQ=60)
AAAAGAGGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTC < SRR3722079.298681/100‑1 (MQ=60)
GGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTTCCGGATTAGTCATTGCT > SRR3722079.83874/1‑100 (MQ=60)
GTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTG > SRR3722079.365892/1‑100 (MQ=60)
GACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCC < SRR3722079.172191/100‑1 (MQ=60)
ATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTTCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTT > SRR3722079.428297/1‑100 (MQ=60)
TAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTAAGCCGGTGAAAGTGAAGATCCACGTTC < SRR3722079.143451/100‑1 (MQ=60)
ATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTT > SRR3722079.561703/1‑100 (MQ=60)
ATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTT < SRR3722079.622249/100‑1 (MQ=60)
CCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTG < SRR3722079.373270/100‑1 (MQ=60)
GGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCT > SRR3722079.812720/1‑100 (MQ=60)
AGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCT < SRR3722079.603547/100‑1 (MQ=60)
taagagacagCAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATC < SRR3722079.195042/90‑1 (MQ=60)
CCTTATTACAATTACGTCGTTCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTC > SRR3722079.698050/1‑100 (MQ=60)
CAATTACGTCGTCCCGGATTAGTCATTGCTGATTCAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTCACAATATC > SRR3722079.566576/1‑100 (MQ=60)
TACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTCACAATATCGGGA < SRR3722079.561583/100‑1 (MQ=60)
GTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTCACAATATCGGGAAATTCA > SRR3722079.67247/1‑100 (MQ=60)
GTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTCACAATATCGGGAAATTCA > SRR3722079.319294/1‑100 (MQ=60)
|
AAGCAGGGTTAAAAGAGGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTTCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTCACAATATCGGGAAATTCA > NZ_CP009273/4593349‑4593544
|
| 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: ‑ |
