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 I230 R1
|
226 |
18.8 |
1048726 |
96.7% |
1014118 |
86.4 |
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%
| 52.3
/ NA
| 17 | A368A (GCT→GCC) | alaS | alanine‑‑tRNA ligase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (9/8); total (9/8) |
AAGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGAGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGA > NZ_CP009273/2814185‑2814341
|
aaGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACt < 1:398579/90‑1 (MQ=255)
gCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGc < 2:221015/90‑1 (MQ=255)
aGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGctc > 1:286611/1‑90 (MQ=255)
aGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGctc < 1:354687/90‑1 (MQ=255)
aGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGctc > 1:422954/1‑90 (MQ=255)
gCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTtcttcagtcttca > 2:295563/1‑90 (MQ=255)
aTCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCAc < 2:422954/90‑1 (MQ=255)
tCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCAcc > 2:4268/1‑90 (MQ=255)
aGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTc < 1:235747/90‑1 (MQ=255)
aGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTc > 1:486012/1‑90 (MQ=255)
ttGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCGCCTGCTCAACCTgcg > 1:309738/1‑90 (MQ=255)
cAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAg > 2:429531/1‑90 (MQ=255)
gCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGt > 1:190772/1‑90 (MQ=255)
aaCGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCt < 2:258845/90‑1 (MQ=255)
cgcgCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCag < 2:172525/90‑1 (MQ=255)
gcgcTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCaga < 1:483116/90‑1 (MQ=255)
gcgcTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCaga > 1:281955/1‑90 (MQ=255)
|
AAGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGAGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGA > NZ_CP009273/2814185‑2814341
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ 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
GTCGTACAGACGGAAAGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGAGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAACGTCGAT > NZ_CP009273/2814171‑2814356
|
GTCGTACAGACGGAAAGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCA < SRR3722114.329184/100‑1 (MQ=60)
GTCGTACAGACGGAAAGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCA < SRR3722114.369146/100‑1 (MQ=60)
GACGGAAAGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTC > SRR3722114.289631/1‑100 (MQ=60)
GACGGAAAGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTC > SRR3722114.428135/1‑100 (MQ=60)
AAGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTC < SRR3722114.403423/100‑1 (MQ=60)
AGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTC < SRR3722114.358810/100‑1 (MQ=60)
GCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTC > SRR3722114.492095/1‑100 (MQ=60)
CCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCGCCTGCTCAACCTGCG > SRR3722114.313041/1‑100 (MQ=60)
AGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCC < SRR3722114.237980/100‑1 (MQ=60)
TCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGT > SRR3722114.192631/1‑100 (MQ=60)
ACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGA > SRR3722114.284916/1‑100 (MQ=60)
GCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAACG < SRR3722114.489168/100‑1 (MQ=60)
CCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAACGTCGAT > SRR3722114.325255/1‑100 (MQ=60)
|
GTCGTACAGACGGAAAGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGAGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAACGTCGAT > NZ_CP009273/2814171‑2814356
|
| 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: ‑ |
