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 I225 R1
|
227 |
21.4 |
1179702 |
97.1% |
1145490 |
86.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,778,934 |
(T)6→5 |
intergenic (‑564/+187) |
BW25113_RS25705 ← / ← BW25113_RS13825 |
DUF5507 domain‑containing protein/tRNA‑Ile |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,778,929 | 0 | T | . | 100.0%
| 58.8
/ NA
| 15 | intergenic (‑559/+192) | BW25113_RS25705/BW25113_RS13825 | DUF5507 domain‑containing protein/tRNA‑Ile |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (10/5); total (10/5) |
GGGGTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAACACCAGCCCTCATTCG > NZ_CP009273/2778842‑2779013
|
ggggTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCAttt < 2:11062/90‑1 (MQ=255)
aaTGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACt > 2:183520/1‑90 (MQ=255)
aCTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGa > 2:21442/1‑90 (MQ=255)
ctGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTa > 2:584071/1‑90 (MQ=255)
ctGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTa > 2:526896/1‑90 (MQ=255)
ctGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTa > 2:174212/1‑90 (MQ=255)
ctGGCTTTATCGTTAACTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCAt > 1:221812/1‑65 (MQ=255)
ctGGCTTTATCGTTAACTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCAt < 2:221812/65‑1 (MQ=255)
ggCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACt > 1:231507/1‑90 (MQ=255)
tttATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGAt < 2:119215/90‑1 (MQ=255)
tttATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGAt < 2:417747/90‑1 (MQ=255)
ttATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATg > 2:185413/1‑90 (MQ=255)
tATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATgg < 1:21442/90‑1 (MQ=255)
cGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATa < 2:465673/90‑1 (MQ=255)
acaTGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGt > 2:337203/1‑90 (MQ=255)
aaGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACg > 1:242718/1‑90 (MQ=255)
aGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGt < 1:139813/90‑1 (MQ=255)
cAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAACACCAGCCCTCATTCg > 2:513662/1‑90 (MQ=255)
|
GGGGTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAACACCAGCCCTCATTCG > NZ_CP009273/2778842‑2779013
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AATGAAGGGGTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAACACCAGCCCTCATTCGAAACCACCCACCGCAC > NZ_CP009273/2778836‑2779029
|
gatgtgtataagagacagATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTCC < SRR3722109.159762/82‑1 (MQ=60)
ATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACT > SRR3722109.234251/1‑100 (MQ=60)
ACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACnnnnnnnnnnnnnnnnnnnn > SRR3722109.371858/1‑80 (MQ=60)
gcgaccaccgagatctacacattgacattcgtcggcagcgtcagatgtgtataagagacagTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATAC < SRR3722109.302352/39‑1 (MQ=60)
TATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACAT < SRR3722109.21722/100‑1 (MQ=60)
TTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACG > SRR3722109.245575/1‑100 (MQ=60)
AGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAACAC < SRR3722109.141549/100‑1 (MQ=60)
TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCtgtctcttatacacatctgacgctgccgacgaatgtcaatgtgtagat > SRR3722109.574717/1‑52 (MQ=60)
|
AATGAAGGGGTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAACACCAGCCCTCATTCGAAACCACCCACCGCAC > NZ_CP009273/2778836‑2779029
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
