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 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,814,267 |
A→G |
A368A (GCT→GCC) |
alaS ← |
alanine‑‑tRNA ligase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,814,267 | 0 | A | G | 100.0%
| 50.0
/ NA
| 15 | A368A (GCT→GCC) | alaS | alanine‑‑tRNA ligase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (5/10); total (5/10) |
AGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGAGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAA > NZ_CP009273/2814189‑2814349
|
aGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGctc > 2:436434/1‑90 (MQ=255)
aCCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCttcttc < 1:681296/90‑1 (MQ=255)
aCCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCttcttc < 2:739656/90‑1 (MQ=255)
tATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCa < 1:47142/90‑1 (MQ=255)
ttGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTgcg > 2:423380/1‑90 (MQ=255)
tCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTc < 1:449467/90‑1 (MQ=255)
cAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTtcttcag < 1:444980/47‑1 (MQ=255)
cAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTtcttcag > 2:444980/1‑47 (MQ=255)
gACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCg > 2:576412/1‑90 (MQ=255)
ccGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCa < 1:281679/90‑1 (MQ=255)
cgcgCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCag < 1:665005/90‑1 (MQ=255)
cgcgCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCag < 2:677190/90‑1 (MQ=255)
gcgcTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTCCACCCGCaga > 2:152371/1‑90 (MQ=255)
cgcTCCAGAGTACGGACAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCagag < 2:508386/90‑1 (MQ=255)
gagTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATaa < 1:328389/90‑1 (MQ=255)
|
AGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGAGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAA > NZ_CP009273/2814189‑2814349
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 32 ≤ 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
GTCGTACAGACGGAAAGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGAGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAACGTCGATCAG > NZ_CP009273/2814171‑2814359
|
GTCGTACAGACGGAAAGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCA < SRR3722073.415722/100‑1 (MQ=60)
ACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGC < SRR3722073.695206/100‑1 (MQ=60)
tcgtcggcagcgtcagatgtgtataagagacagCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCAC < SRR3722073.454486/67‑1 (MQ=60)
TATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAAC < SRR3722073.48252/100‑1 (MQ=60)
TCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCAC < SRR3722073.459062/100‑1 (MQ=60)
CCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAA < SRR3722073.287633/100‑1 (MQ=60)
CGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAAC < SRR3722073.678629/100‑1 (MQ=60)
CTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAACGTCG > SRR3722073.532140/1‑100 (MQ=60)
CTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAACGTCG > SRR3722073.693492/1‑100 (MQ=60)
CAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAACGTCGATC < SRR3722073.311739/100‑1 (MQ=60)
GAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAACGTCGATCAG < SRR3722073.335363/100‑1 (MQ=60)
|
GTCGTACAGACGGAAAGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGAGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAACGTCGATCAG > NZ_CP009273/2814171‑2814359
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
