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 I224 R1
|
7 |
23.0 |
1302986 |
97.5% |
1270411 |
87.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,512,090 |
+GC |
coding (334/522 nt) |
aroK ← |
shikimate kinase AroK |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,512,088 | 1 | . | G | 100.0%
| 43.1
/ NA
| 13 | A112A (GCA→GCC) | aroK | shikimate kinase AroK |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (5/8); total (5/8) |
| * | NZ_CP009273 | 3,512,088 | 2 | . | C | 100.0%
| 43.9
/ NA
| 13 | A112A (GCA→GCG) | aroK | shikimate kinase AroK |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (5/8); total (5/8) |
TTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGTTTTTTATCACGCTGCGTGCGT‑‑GCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACGAGCGGAAAGACGGTTACGCGTTTCACGGGATTT > NZ_CP009273/3512002‑3512168
||
ttGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGTTTTTTATCACGCTGCgtgcgt‑‑gcg > 2:437212/1‑89 (MQ=255)
aaCGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGTTTTTTATCACGCTGCGTGCGTGCGCAAGTTGCTTTTCGa < 1:271016/90‑1 (MQ=255)
ttCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGTTTTTTATCACGCTGCGTGCGTGCGCAAGTTGCTTTTCGATGGTc < 1:352375/90‑1 (MQ=255)
ttCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGTTTTTTATCACGCTGCGTGCGTGCGCAAGTTGCTTTTCGATGGTc < 1:482810/90‑1 (MQ=255)
gAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGTTTTTTATCACGCTGCGTGCGTGCGCAAGTTGCTTTTCGATGGTCGTTTc < 1:166742/90‑1 (MQ=255)
ttCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGTTTTTTATCACGCTGCGTGCGTGCGCAAGTTGCTTTTCGATGGTCGTTTCAAGa > 2:357863/1‑90 (MQ=255)
tCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGTTTTTTATCACGCTGCGTGCGTGCGCAAGTTGCTTTTCGATGGTCGTTTCAAGAt < 2:120080/90‑1 (MQ=255)
gtgtTTCAACGTGCAGCAACGGGCGTTGTTTATCACGCTTCGTGCGTGCGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAAc > 1:400414/1‑90 (MQ=255)
cGTGCAGCAACGGGCGTTTTTTATCACGCTGCGTGCGTGCGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACGAGc < 1:84384/90‑1 (MQ=255)
gTGCAGCAACGGGCGTTTTTTATCACGCTGCGTGCGTGCGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACGAGCg > 2:34553/1‑90 (MQ=255)
aaCGGGCGTTTTTTATCACGCTGCGTGCGTGCGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACGAGCGGAAAGAc < 1:138441/90‑1 (MQ=255)
gggCGTTTTTTATCACGCTGCGTGCGTGCGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACGAGCGGAAAGACGGt > 1:109953/1‑90 (MQ=255)
gggCGTTTTTTATCACGCTGCGTGCGTGCGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACGAGCGGAAAGACGGt > 1:565356/1‑90 (MQ=255)
aCGCTGCGTGCGTGCGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACGAGCGGAAAGACGGTTACGCGTTTCACgg < 2:385507/90‑1 (MQ=255)
gcgtgcgtgcGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACGAGCGGAAAGACGGTTACGCGTTTCACGGGAttt > 1:27508/1‑90 (MQ=255)
||
TTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGTTTTTTATCACGCTGCGTGCGT‑‑GCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACGAGCGGAAAGACGGTTACGCGTTTCACGGGATTT > NZ_CP009273/3512002‑3512168
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 31 ≤ 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
GGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGTTTTTTATCACGCTGCGTGC‑‑GT‑‑GCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACGAGCGGAAAGACGGTTACGCGTTTCACGGGATTTCACAGA > NZ_CP009273/3511999‑3512174
|
GGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGTTTTTTATCACGCTGCGTGC‑‑GTGCGCAAGTTG > SRR3722108.589590/1‑100 (MQ=60)
AACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGTTTTTTATCACGCTGCGTGC‑‑GTGCGCAAGTTGCTTTTCGATGGTCGTTTC < SRR3722108.273976/100‑1 (MQ=60)
TTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGTTTTTTATCACGCTGCGTGC‑‑GTGCGCAAGTTGCTTTTCGATGGTCGTTTCAAGAT < SRR3722108.356653/100‑1 (MQ=60)
TTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGTTTTTTATCACGCTGCGTGC‑‑GTGCGCAAGTTGCTTTTCGATGGTCGTTTCAAGAT < SRR3722108.489501/100‑1 (MQ=60)
GAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGTTTTTTATCACGCTGCGTGC‑‑GTGCGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACG < SRR3722108.168674/100‑1 (MQ=60)
TCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGTTGTTTATCACGCTTCGTGC‑‑GTGCGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAAC > SRR3722108.405508/1‑100 (MQ=60)
ACGTGCAGCAACGAGCGGTTTTTTTCACGCTTCGTGCGAGC‑‑GCAAGTTGCTTTTCGATGGACGTTTCAAGATAAAagaaaacgccgtatccgtaaacacg > SRR3722108.483686/1‑75 (MQ=30)
CGTGCAGCAACGGGCGTTTTTTATCACGCTGCGTGC‑‑GTGCGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACGAGCGGAAAGACGG < SRR3722108.85337/100‑1 (MQ=60)
GTGCAGCAACGGGCGTTTTTTATCACGCTGCGTGC‑‑GTGCGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACGAGCGGAAAGACGGT > SRR3722108.111229/1‑100 (MQ=60)
GTGCAGCAACGGGCGTTTTTTATCACGCTGCGTGC‑‑GTGCGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACGAGCGGAAAGACGGT > SRR3722108.573503/1‑100 (MQ=60)
AACGGGCGTTTTTTATCACGCTGCGTGC‑‑GTGCGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACGAGCGGAAAGACGGTTACGCGT < SRR3722108.140073/100‑1 (MQ=60)
TTATCACGCTGCGTGC‑‑GTGCGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACGAGCGGAAAGACGGTTACGCGTTTCACGGGATTT > SRR3722108.27831/1‑100 (MQ=60)
CGCTGCGTGC‑‑GTGCGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACGAGCGGAAAGACGGTTACGCGTTTCACGGGATTTCACAGA > SRR3722108.37219/1‑100 (MQ=60)
|
GGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGTTTTTTATCACGCTGCGTGC‑‑GT‑‑GCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACGAGCGGAAAGACGGTTACGCGTTTCACGGGATTTCACAGA > NZ_CP009273/3511999‑3512174
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
