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 I229 R1
|
214 |
17.4 |
943020 |
97.5% |
919444 |
87.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,527,151 |
T→C |
Q87Q (CAA→CAG) |
nanS ← |
9‑O‑acetyl‑N‑acetylneuraminic acid deacetylase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,527,151 | 0 | T | C | 100.0%
| 92.5
/ NA
| 30 | Q87Q (CAA→CAG) | nanS | 9‑O‑acetyl‑N‑acetylneuraminic acid deacetylase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (14/16); total (14/16) |
ATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTTTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAGTGGAATAATGTCGTTAA > NZ_CP009273/4527074‑4527236
|
aTCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGtt < 1:229835/90‑1 (MQ=255)
cccTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGc > 1:457523/1‑90 (MQ=255)
cccTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGc > 2:40071/1‑90 (MQ=255)
cTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCa > 1:93219/1‑90 (MQ=255)
ttATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGa < 2:371738/90‑1 (MQ=255)
aTCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATg < 1:224142/90‑1 (MQ=255)
aTCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATg > 1:174880/1‑90 (MQ=255)
gAATGAAGGGCAGTAATTTCCGTGCAATATGGAGTGCCTGGCCAATGGGGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTggg > 1:245471/1‑88 (MQ=255)
gAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGAt < 1:40071/90‑1 (MQ=255)
gAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGAt < 2:150356/90‑1 (MQ=255)
gAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAAcc < 2:169298/90‑1 (MQ=255)
aaGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAAccc < 2:171408/90‑1 (MQ=255)
gCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCa < 2:196840/90‑1 (MQ=255)
gCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCa < 2:14929/90‑1 (MQ=255)
aGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCata < 2:133822/90‑1 (MQ=255)
aGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCata < 2:457523/90‑1 (MQ=255)
ttCCGTGCAATATGCGGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGGTAACCCTGCATATCCTGa > 1:342741/1‑90 (MQ=255)
ttCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGa > 1:403691/1‑90 (MQ=255)
cGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACa < 1:112358/90‑1 (MQ=255)
tGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATg > 2:137665/1‑63 (MQ=255)
tGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATg < 1:137665/63‑1 (MQ=255)
tGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATc > 1:11909/1‑90 (MQ=255)
tGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATc < 2:216115/90‑1 (MQ=255)
gTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGAt > 2:172541/1‑57 (MQ=255)
gTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGAt < 1:172541/57‑1 (MQ=255)
gCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGa > 2:157632/1‑90 (MQ=255)
tGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTc < 2:118941/90‑1 (MQ=255)
gtgtCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAGTGGAATAATGTCGTTaa > 1:238024/1‑90 (MQ=255)
gtgtCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAGTGGAATAATGTCGTTaa > 1:161054/1‑90 (MQ=255)
gtgtCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAGTGGAATAATGTCGTTaa > 2:61143/1‑90 (MQ=255)
|
ATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTTTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAGTGGAATAATGTCGTTAA > NZ_CP009273/4527074‑4527236
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ACGGCAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTTTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAGTGGAATAATGTCGTTAAAG > NZ_CP009273/4527052‑4527238
|
aagacggcatacgagattcgccttagtctcgtgggctcggagatgtgtataagagacagGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTC < SRR3722113.448745/41‑1 (MQ=60)
ACGACAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTC < SRR3722113.126372/100‑1 (MQ=60)
CGATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGC > SRR3722113.462360/1‑100 (MQ=60)
ATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCA > SRR3722113.94058/1‑100 (MQ=60)
ATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGAT < SRR3722113.231756/100‑1 (MQ=60)
TCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATG > SRR3722113.176274/1‑100 (MQ=60)
GCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGGAGTGCCTGGCCAATGGGGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGgg > SRR3722113.247595/1‑98 (MQ=60)
atgtgtataagagacagGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCC < SRR3722113.138814/83‑1 (MQ=60)
ATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCC < SRR3722113.225981/100‑1 (MQ=60)
tcggagatgtgtataagagacagGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCAT < SRR3722113.173924/77‑1 (MQ=60)
GAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCAT < SRR3722113.40406/100‑1 (MQ=60)
GGGCAGTAATTTCCGTGCAATATGCGGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGGTAACCCTGCATATCCTGA > SRR3722113.346232/1‑100 (MQ=60)
GGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGA > SRR3722113.407920/1‑100 (MQ=60)
GTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATC > SRR3722113.12016/1‑100 (MQ=60)
CGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGC < SRR3722113.113338/100‑1 (MQ=60)
cgtgggctcggagatgtgtataagagacagGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAG < SRR3722113.357386/70‑1 (MQ=60)
GTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAGTGGAATAATGTCGTTAA > SRR3722113.240052/1‑100 (MQ=60)
GTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAGTGGAATAATGTCGTTAA > SRR3722113.162375/1‑100 (MQ=60)
GCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAGTGGAATAATGTCGTTAAAG > SRR3722113.395833/1‑100 (MQ=60)
|
ACGGCAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTTTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAGTGGAATAATGTCGTTAAAG > NZ_CP009273/4527052‑4527238
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
