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 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,350,381 |
G→C |
G457G (GGC→GGG) |
cadC ← |
lysine decarboxylation/transport transcriptional activator CadC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,350,381 | 0 | G | C | 97.1%
| 109.4
/ ‑3.4
| 34 | G457G (GGC→GGG) | cadC | lysine decarboxylation/transport transcriptional activator CadC |
| Reads supporting (aligned to +/- strand): ref base G (1/0); new base C (15/18); total (16/18) |
| Fisher's exact test for biased strand distribution p-value = 4.71e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01 |
GTGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTGCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCTTTT > NZ_CP009273/4350298‑4350465
|
gtgtTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGc < 2:37471/90‑1 (MQ=255)
gtgtTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGc < 2:228533/90‑1 (MQ=255)
gtgtTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGc < 1:4318/90‑1 (MQ=255)
tgtTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCa > 2:474012/1‑90 (MQ=255)
gtTTGTCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTGCCAAGCaa > 2:172348/1‑90 (MQ=255)
gtTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCaa < 2:619535/90‑1 (MQ=255)
gtTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCaa > 2:522469/1‑90 (MQ=255)
gtTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCaa < 2:261743/90‑1 (MQ=255)
gttGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAac > 2:644392/2‑90 (MQ=255)
cccTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATa > 2:163428/1‑90 (MQ=255)
cTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAAt > 2:622084/1‑90 (MQ=255)
cTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAAt > 2:604462/1‑90 (MQ=255)
cTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAAt > 2:594214/1‑90 (MQ=255)
gTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGcc < 1:169979/90‑1 (MQ=255)
gTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGcc > 2:44084/1‑90 (MQ=255)
tAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCa > 1:516469/1‑90 (MQ=255)
ggTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAAGACATTTCAAg > 1:521100/1‑90 (MQ=255)
agaTATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCa < 1:594214/90‑1 (MQ=255)
agaTATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCa < 1:189913/90‑1 (MQ=255)
gCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCa < 2:561355/90‑1 (MQ=255)
ttCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGc < 1:209829/90‑1 (MQ=255)
tCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGcc < 1:280945/90‑1 (MQ=255)
gTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTa < 1:712376/90‑1 (MQ=255)
tCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAg < 1:385187/90‑1 (MQ=255)
cATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGTCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTa > 1:516261/1‑87 (MQ=255)
cATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGTCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTa < 2:516261/87‑1 (MQ=255)
tCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACt > 2:635763/1‑90 (MQ=255)
cTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATc < 2:381143/90‑1 (MQ=255)
cTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATc < 2:27415/90‑1 (MQ=255)
ttcatttcatAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCt > 1:244901/1‑90 (MQ=255)
atttcatAAACCTTCCCAAGTAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGtt > 1:259302/1‑90 (MQ=255)
aaCCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGtttt > 1:233202/1‑84 (MQ=255)
aaCCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGtttt < 2:233202/84‑1 (MQ=255)
aCCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGttttacctttt < 1:474012/90‑1 (MQ=255)
|
GTGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTGCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCTTTT > NZ_CP009273/4350298‑4350465
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ 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
CCAGTAAAGGGTGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTGCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCTTTTACCAGAGCAC > NZ_CP009273/4350288‑4350475
|
CCAGTAAAGGGTGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGC < SRR3722112.256251/100‑1 (MQ=60)
GTGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAAT < SRR3722112.4366/100‑1 (MQ=60)
CCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCA > SRR3722112.524040/1‑100 (MQ=60)
GTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTC < SRR3722112.172069/100‑1 (MQ=60)
AATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAAGACATTTCAAG > SRR3722112.528765/1‑100 (MQ=60)
gatctacacattgacattcgtcggcagcgtcagatgtgtataagagacagTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATC < SRR3722112.534373/50‑1 (MQ=60)
AGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTAT < SRR3722112.192240/100‑1 (MQ=60)
AGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTAT < SRR3722112.603298/100‑1 (MQ=60)
CTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGTCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGA > SRR3722112.523827/1‑100 (MQ=60)
TTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGAC < SRR3722112.212367/100‑1 (MQ=60)
TCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACT < SRR3722112.284207/100‑1 (MQ=60)
GTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCT > SRR3722112.247803/1‑100 (MQ=60)
GTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCT < SRR3722112.723513/100‑1 (MQ=60)
TCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGT < SRR3722112.390199/100‑1 (MQ=60)
CATCCCCTTCATTTCATAAACCTTCCCAAGTAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTT > SRR3722112.262358/1‑100 (MQ=60)
TCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCTTT > SRR3722112.235998/1‑100 (MQ=60)
TCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCTTTTACCA > SRR3722112.447801/1‑100 (MQ=60)
ACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCTTTTACCAGAGCAC < SRR3722112.480786/100‑1 (MQ=60)
|
CCAGTAAAGGGTGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTGCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCTTTTACCAGAGCAC > NZ_CP009273/4350288‑4350475
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
