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 F3 I95 R1
|
196 |
14.2 |
808436 |
96.0% |
776098 |
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 | . | 100.0%
| 55.6
/ NA
| 14 | coding (984/3474 nt) | bcsC | cellulose synthase complex outer membrane protein BcsC |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (6/8); total (6/8) |
GCTGGATCGCCAGCCAGTAGCGGTTTACTTTCAGCAGACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGCTTTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGCCCAGCGCCCCCAGAGCTTCACTG > NZ_CP009273/3681465‑3681628
|
gctgGATCGCCAGCCAGTAGCGGTTTACTTTCAGCAGACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGGGCGAGGGCttttc > 2:364541/1‑89 (MQ=255)
tAGCGGTTTACTTTCAGCAGACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCAt < 1:19622/90‑1 (MQ=255)
aGCGGTTTACTTTCAGCAGACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCAtt > 2:399718/1‑90 (MQ=255)
gTTTACTTTCAGCAGACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGgcg > 2:324723/1‑90 (MQ=255)
ttCAGCAGACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGc < 1:107523/90‑1 (MQ=255)
gACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTg < 1:225808/90‑1 (MQ=255)
ttCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAAt > 1:173115/1‑90 (MQ=255)
ttCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAAt > 2:142494/1‑90 (MQ=255)
ttCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAAt < 2:362680/90‑1 (MQ=255)
tCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGc > 2:15176/1‑90 (MQ=255)
gttgCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGCCCAgc < 1:142494/90‑1 (MQ=255)
ttgCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGCCCAgcg < 1:245833/90‑1 (MQ=255)
ttgCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGCCCAgcg < 2:301795/90‑1 (MQ=255)
ctgTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGCCCAGCGCCCCCa > 1:49860/1‑90 (MQ=255)
cAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGCCCAGCGCCCCCAGAGCTTCACTg < 2:125666/90‑1 (MQ=255)
|
GCTGGATCGCCAGCCAGTAGCGGTTTACTTTCAGCAGACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGCTTTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGCCCAGCGCCCCCAGAGCTTCACTG > NZ_CP009273/3681465‑3681628
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ 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
TAGCGGTTTACTTTCAGCAGACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGCTTTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGCCCAGCGCCCCCAGAGCTTCACTGTCTTTCGGGTTCGCCCGCAC > NZ_CP009273/3681482‑3681648
|
TAGCGGTTTACTTTCAGCAGACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATC < SRR3722235.19854/100‑1 (MQ=60)
TTCAGCAGACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGA < SRR3722235.108780/100‑1 (MQ=60)
CAGCAGACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAAT > SRR3722235.175102/1‑100 (MQ=60)
GACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCC < SRR3722235.228652/100‑1 (MQ=60)
GTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGCCCAGCGCCCCCA > SRR3722235.50408/1‑100 (MQ=60)
GTTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGCCCAGCGCCCCCAGAG < SRR3722235.144142/100‑1 (MQ=60)
TTGCTGCTGTGCGGGTCCAGTGCGAGGGC‑TTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGCCCAGCGCCCCCAGAGC < SRR3722235.248976/100‑1 (MQ=60)
gcTTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGCCCAGCGCCCCCAGAGCTTCACTGTCTTTCGGGTTCGCCCGCAC < SRR3722235.15351/98‑1 (MQ=60)
gcTTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGCCCAGCGCCCCCAGAGCTTCACTGTCTTTCGGGTTCGCCCGCAC < SRR3722235.314654/98‑1 (MQ=60)
|
TAGCGGTTTACTTTCAGCAGACTGTTCCATTTGTCGTTGTTGCTGCTGTGCGGGTCCAGTGCGAGGGCTTTTTCCAGATTCGCCACTGCATTGGCGCGATCGCCTTTCTGAGAATACGCCTGGCCCAGCGCCCCCAGAGCTTCACTGTCTTTCGGGTTCGCCCGCAC > NZ_CP009273/3681482‑3681648
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
