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 |
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%
| 63.6
/ NA
| 16 | 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 . (9/7); total (9/7) |
AGGGGTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACG > NZ_CP009273/2778841‑2778989
|
aGGGGTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCAtt > 2:333288/1‑90 (MQ=255)
aGGGGTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCAtt > 1:381096/1‑90 (MQ=255)
gATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACtttt < 2:115347/90‑1 (MQ=255)
ataCTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAAt > 2:228468/1‑90 (MQ=255)
ctGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTa > 1:139202/1‑90 (MQ=255)
ggCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACt > 1:115993/1‑90 (MQ=255)
tttATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGAt < 2:324127/90‑1 (MQ=255)
tttATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGAt < 2:145569/90‑1 (MQ=255)
aTCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGa > 2:155045/1‑90 (MQ=255)
cGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATa < 2:115993/90‑1 (MQ=255)
ttAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGt > 1:134000/1‑63 (MQ=255)
ttAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGt < 2:134000/63‑1 (MQ=255)
aTTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATAc < 1:154354/90‑1 (MQ=255)
ttAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGc > 2:217588/1‑90 (MQ=255)
tAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCa > 1:29406/1‑90 (MQ=255)
tCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTgg < 1:279331/90‑1 (MQ=255)
aaGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACg > 2:336265/1‑90 (MQ=255)
aaGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACg > 2:398750/1‑90 (MQ=255)
|
AGGGGTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACG > NZ_CP009273/2778841‑2778989
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AAATGAAGGGGTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAACACCAGCCCTCATTCGAAACCACCCACCG > NZ_CP009273/2778835‑2779026
|
AAATGAAGGGGTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTC < SRR3722091.300008/100‑1 (MQ=60)
TGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTA > SRR3722091.141283/1‑100 (MQ=60)
ATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACT > SRR3722091.117748/1‑100 (MQ=60)
GGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATctgtctcttatacacat > SRR3722091.136014/1‑83 (MQ=60)
GTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCA > SRR3722091.29817/1‑100 (MQ=60)
ATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGG < SRR3722091.156614/100‑1 (MQ=60)
TCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGT < SRR3722091.283957/100‑1 (MQ=60)
GCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAACACCAGCCCTCATTCGAAACCACCCACCG > SRR3722091.56070/1‑100 (MQ=60)
|
AAATGAAGGGGTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAACACCAGCCCTCATTCGAAACCACCCACCG > NZ_CP009273/2778835‑2779026
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
