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 I74 R1
|
158 |
13.7 |
815430 |
95.7% |
780366 |
86.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,632,437 |
(T)7→6 |
intergenic (‑71/+8) |
BW25113_RS08135 ← / ← BW25113_RS25620 |
hypothetical protein/hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,632,431 | 0 | T | . | 100.0%
| 28.8
/ NA
| 8 | intergenic (‑65/+14) | BW25113_RS08135/BW25113_RS25620 | hypothetical protein/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (3/5); total (3/5) |
CATTTGGATATTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGA > NZ_CP009273/1632348‑1632471
|
cATTTGGATATTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGAttttttc < 1:175351/90‑2 (MQ=255)
atTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTa < 1:258815/90‑1 (MQ=255)
gCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCgtag < 1:187568/90‑1 (MQ=255)
gCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCgtag > 2:187568/1‑90 (MQ=255)
cATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCgtagt < 2:371326/90‑1 (MQ=255)
aaCTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCgt < 1:369018/75‑1 (MQ=255)
aaCTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCgt > 2:369018/1‑75 (MQ=255)
tCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATc < 1:361362/90‑1 (MQ=255)
cAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGa > 2:17168/1‑90 (MQ=255)
|
CATTTGGATATTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGA > NZ_CP009273/1632348‑1632471
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CATTTGGATATTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAATAGACAC > NZ_CP009273/1632348‑1632479
|
CATTTGGATATTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTAC < SRR3722212.177297/100‑1 (MQ=60)
ATTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATG < SRR3722212.262109/100‑1 (MQ=60)
gacagTGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAG < SRR3722212.374207/95‑1 (MQ=60)
GCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTA < SRR3722212.189679/100‑1 (MQ=60)
GTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGctgtctcttatacacatctcc > SRR3722212.8187/1‑79 (MQ=60)
TCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAATAGACAC < SRR3722212.366429/100‑1 (MQ=60)
|
CATTTGGATATTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAATAGACAC > NZ_CP009273/1632348‑1632479
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
