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 I194 R1
|
197 |
32.2 |
1845014 |
95.2% |
1756453 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,681,554 |
(T)5→4 |
coding (980/3474 nt) |
bcsC ← |
cellulose synthase complex outer membrane protein BcsC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,681,550 | 0 | T | . | 96.7%
| 113.0
/ ‑2.1
| 30 | coding (984/3474 nt) | bcsC | cellulose synthase complex outer membrane protein BcsC |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base . (14/15); total (14/16) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01 |
GCTGGATCGCCAGCCAGTAGCGGTTTACTTTCAGCAGACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGCTTTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGCCCAGCGCCCCCAGAGCTTCACTGTC > NZ_CP009273/3681465‑3681630
|
gctgGATCGCCAGCCAGTAGCGGTTTACTTTCAGCAGACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGCttttc < 2:456136/90‑2 (MQ=255)
aTCGCCAGCCAGTAGCGGTTTACTTTCAGCAGACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGAt > 2:798955/1‑90 (MQ=255)
cGCCAGCCAGTAGCGGTTTACTTTCAGCAGACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTc < 2:183144/90‑1 (MQ=255)
cagccagTAGCGGTTTACTTTCAGCAGACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGcc > 1:225303/1‑90 (MQ=255)
cGGTTTACTTTCAGCAGACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTgg < 1:776988/90‑1 (MQ=255)
aCTTTCAGCAGACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGAt < 2:603335/90‑1 (MQ=255)
tttCAGCAGACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCg < 2:809285/90‑1 (MQ=255)
agcagACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCtt < 1:98605/90‑1 (MQ=255)
gACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTg < 1:557959/90‑1 (MQ=255)
gACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTg > 2:404637/1‑90 (MQ=255)
gACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTg < 2:225303/90‑1 (MQ=255)
gTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGaa > 2:371677/1‑90 (MQ=255)
ttCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCg < 2:261490/77‑1 (MQ=255)
ttCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCg > 1:261490/1‑77 (MQ=255)
ttCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAAt > 1:911054/1‑90 (MQ=255)
ttCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAAt < 2:723024/90‑1 (MQ=255)
ccATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGCTTTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATa < 2:275766/90‑1 (MQ=255)
tGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTg > 2:284716/1‑78 (MQ=255)
tGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTg < 1:284716/78‑1 (MQ=255)
tCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGc > 2:334830/1‑90 (MQ=255)
tCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCCCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGc > 2:447484/1‑90 (MQ=255)
ttgttgCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGCCCa < 2:240237/90‑1 (MQ=255)
gctgTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGCCCAGCGccccc < 2:253940/90‑1 (MQ=255)
ccAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGCCCAGCGCCCCCAGAGCTTCACt < 2:366992/90‑1 (MQ=255)
ccAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGCCCAGCGCCCCCAGAGCTTCACt < 1:61207/90‑1 (MQ=255)
aGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGCCCAGCGccccc > 1:879222/1‑77 (MQ=255)
aGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGCCCAGCGccccc < 2:879222/77‑1 (MQ=255)
aGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGCCCAGCGCCCCCAGAGCTTCACTGt > 2:211339/1‑90 (MQ=255)
aGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGCCCAGCGCCCCCAGAGCTTCACTGt > 2:686116/1‑90 (MQ=255)
aGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGCCCAGCGCCCCCAGAGCTTCACTGt > 2:859493/1‑90 (MQ=255)
gTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGCCCAGCGCCCCCAGAGCTTCACTGTc > 2:791109/1‑90 (MQ=255)
|
GCTGGATCGCCAGCCAGTAGCGGTTTACTTTCAGCAGACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGCTTTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGCCCAGCGCCCCCAGAGCTTCACTGTC > NZ_CP009273/3681465‑3681630
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ 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
GCTGGATCGCCAGCCAGTAGCGGTTTACTTTCAGCAGACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGCTTTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGCCCAGCGCCCCCAGAGCTTCACTGTCTTTCGGGTTCGCCCGCACCGC > NZ_CP009273/3681465‑3681651
|
GCTGGATCGCCAGCCAGTAGCGGTTTACTTTCAGCAGACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCC > SRR3722072.229116/1‑100 (MQ=60)
cgagataatcggacgtctcgtgggctcggagatgtgtataagagacaGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATC < SRR3722072.47094/53‑1 (MQ=60)
CGGTTTACTTTCAGCAGACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCC < SRR3722072.790639/100‑1 (MQ=60)
CAGCAGACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGctg > SRR3722072.265932/1‑97 (MQ=60)
CAGCAGACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAAT > SRR3722072.926716/1‑100 (MQ=60)
AGCAGACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATA < SRR3722072.100428/100‑1 (MQ=60)
agCTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCC < SRR3722072.289595/98‑1 (MQ=60)
GACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCC < SRR3722072.567984/100‑1 (MQ=60)
GTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGCCCAGCGCCCCCAGAGCTTCACctg > SRR3722072.894361/1‑97 (MQ=60)
CCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGCCCAGCGCCCCCAGAGCTTCACTGTCTTTCGGG < SRR3722072.62325/100‑1 (MQ=60)
TTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGCCCAGCGCCCCCAGAGCTTCACTGTCTTTCGGGTTCGCCCGCACCGC < SRR3722072.54106/100‑1 (MQ=60)
|
GCTGGATCGCCAGCCAGTAGCGGTTTACTTTCAGCAGACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGCTTTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGCCCAGCGCCCCCAGAGCTTCACTGTCTTTCGGGTTCGCCCGCACCGC > NZ_CP009273/3681465‑3681651
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
