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 I209 R1
|
216 |
14.4 |
815930 |
96.1% |
784108 |
85.2 |
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 | 100.0%
| 74.1
/ NA
| 23 | G457G (GGC→GGG) | cadC | lysine decarboxylation/transport transcriptional activator CadC |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base C (9/14); total (9/14) |
GTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTGCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCTTTT > NZ_CP009273/4350300‑4350465
|
gtTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCaa > 1:369950/1‑90 (MQ=255)
gtTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCa < 1:191411/89‑1 (MQ=255)
gtTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCa > 2:191411/1‑89 (MQ=255)
cTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAAt > 1:278180/1‑90 (MQ=255)
tGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAAtt < 1:143882/90‑1 (MQ=255)
tGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAAtt < 2:287483/90‑1 (MQ=255)
tGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAAtt < 2:284446/90‑1 (MQ=255)
tGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAAtt < 1:60725/90‑1 (MQ=255)
ttAAAGGCTGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGAc < 1:271364/90‑1 (MQ=255)
aaaGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACAt > 2:118535/1‑90 (MQ=255)
gCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCa < 1:319867/90‑1 (MQ=255)
cGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCaa < 2:278180/90‑1 (MQ=255)
agaTATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCa < 1:350975/90‑1 (MQ=255)
tGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGcc > 2:262600/1‑90 (MQ=255)
tCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTa > 2:228848/1‑90 (MQ=255)
aGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCa < 1:316633/47‑1 (MQ=255)
aGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCa > 2:316633/1‑47 (MQ=255)
ttCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGc > 1:294467/1‑90 (MQ=255)
ttcatAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGtttt < 2:263073/90‑1 (MQ=255)
catAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGttttac > 2:146089/1‑90 (MQ=255)
aCCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGttttacctttt < 1:118535/90‑1 (MQ=255)
aCCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGttttacctttt < 2:294467/90‑1 (MQ=255)
aCCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTCATCGCCTGGTAAGACTCATCTGttttacctttt < 2:255255/90‑1 (MQ=255)
|
GTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTGCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCTTTT > NZ_CP009273/4350300‑4350465
|
| 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
CAGTAAAGGGTGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTGCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCTTTTACCAGAGCAC > NZ_CP009273/4350289‑4350475
|
CAGTAAAGGGTGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCA < SRR3722091.409038/100‑1 (MQ=60)
AGTAAAGGGTGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAA > SRR3722091.376483/1‑100 (MQ=60)
GTGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAAT > SRR3722091.282783/1‑100 (MQ=60)
tcgtcggcagcgtcagatgtgtataagagacagGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATT < SRR3722091.322082/67‑1 (MQ=60)
TGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATT < SRR3722091.194243/100‑1 (MQ=60)
TGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGAC < SRR3722091.146011/100‑1 (MQ=60)
TGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGAC < SRR3722091.61636/100‑1 (MQ=60)
TTAAAGGCTGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGAT < SRR3722091.275815/100‑1 (MQ=60)
GCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGC < SRR3722091.325394/100‑1 (MQ=60)
AGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTAT < SRR3722091.357123/100‑1 (MQ=60)
CATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGC > SRR3722091.299436/1‑100 (MQ=60)
TCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCTTTTACCA > SRR3722091.295765/1‑100 (MQ=60)
ACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCTTTTACCAGAGCAC < SRR3722091.120327/100‑1 (MQ=60)
|
CAGTAAAGGGTGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTGCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCTTTTACCAGAGCAC > NZ_CP009273/4350289‑4350475
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
