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 I78 R1
|
12 |
11.6 |
697012 |
95.6% |
666343 |
85.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,527,045 |
A→C |
S123A (TCG→GCG) |
nanS ← |
9‑O‑acetyl‑N‑acetylneuraminic acid deacetylase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,527,045 | 0 | A | C | 100.0%
| 84.4
/ NA
| 25 | S123A (TCG→GCG) | nanS | 9‑O‑acetyl‑N‑acetylneuraminic acid deacetylase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (11/14); total (11/14) |
GCGGAGTATCCGTTCCCCAACGACAAGCATCATGGCTGGCTCCGTGCCGTTCTGAATATGTCCCTTCGCTGCCCGCGGTAAAAGCCGATCCGCCACGGCAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATAT > NZ_CP009273/4526958‑4527119
|
gCGGAGTATCCGTTCCCCAACGACAAGCATCATGGCTGGCTCCGTGCCGTTCTGAATATGTCCCTTCGCTGCCCGCGGTAAAAGCCGCTc > 2:304923/1‑90 (MQ=255)
gTATCCGTTCCCCAACGACAAGCATCATGGCTGGCTCCGTGCCGTTCTGAATATGTCCCTTCGCTGCCCGCGGTAAAAGCCGCTCCGCCa > 2:181011/1‑90 (MQ=255)
tCCGTTCCCCAACGACAAGCATCATGGCTGGCTCCGTGCCGTTCTGAATATGTCCCTTCGCTGCCCGCGGTAAAAGCCGCTCCGCCACgg < 2:326079/90‑1 (MQ=255)
cGTTCCCCAACGACAAGCATCATGGCTGGCTCCGTGCCGTTCTGAATATGTCCCTTCGCTGCCCGCGGTAAAAGCCGCTCCGCCACGGCa > 2:260810/1‑90 (MQ=255)
cGTTCCCCAACGACAAGCATCATGGCTGGCTCCGTGCCGTTCTGAATATGTCCCTTCGCTGCCCGCGGTAAAAGCCGCTCCGCCACGGCa > 2:197388/1‑90 (MQ=255)
ccccAACGACAAGCATCATGGCTGGCTCCGTGCCGTTCTGAATATGTCCCTTCGCTGCCCGCGGTAAAAGCCGCTCCGCCACGGCAacac < 1:236952/90‑1 (MQ=255)
cAACGACAAGCATCATGGCTGGCTCCGTGCCGTTCTGAATATGTCCCTTCGCTGCCCGCGGTAAAAGCCGCTCCGCCACGGCAACACGGa > 2:58235/1‑90 (MQ=255)
cAACGACAAGCATCATGGCTGGCTCCGTGCCGTTCTGAATATGTCCCTTCGCTGCCCGCGGTAAAAGCCGCTCCGCCACGGCAACACGGa < 2:273609/90‑1 (MQ=255)
aaCGACAAGCATCATGGCTGGCTCCGTGCCGTTCTGAATATGTCCCTTCGCTGCCCGCGGTAAAAGCCGCTCCGCCACGGCAACACGGaa > 2:324648/1‑90 (MQ=255)
gCATCATGGCTGGCTCCGTGCCGTTCTGAATATGTCCCTTCGCTGCCCGCGGTAAAAGCCGCTCCGCCACGGCAACACGGAACGATAAGa < 1:109892/90‑1 (MQ=255)
tggctggcTCCGTGCCGTTCTGAATATGTCCCTTCGCTGCCCGCGGTAAAAGCCGCTCCGCCACGGCAACACGGAACGATAAGAATCCCt < 1:87366/90‑1 (MQ=255)
tCCGTGCCGTTCTGAATATGTCCCTTCGCTGCCCGCGGTAAAAGCCGCTCCGCCACGGCAACACGGAACGATAAGAATCCCTGCATTATc < 1:181011/90‑1 (MQ=255)
tCCGTGCCGTTCTGAATATGTCCCTTCGCTGCCCGCGGTAAAAGCCGCTCCGCCACGGCAACACGGAACGATAAGAATCCCTGCATTATc < 1:61979/90‑1 (MQ=255)
gTTCTGAATATGTCCCTTCGCTGCCCGCGGTAAAAGCCGCTCCGCCACGGCAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGa < 1:214371/90‑1 (MQ=255)
tGTCCCTTCGCTGCCCGCGGTAAAAGCCGCTCCGCCACGGCAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTaa > 2:144476/1‑90 (MQ=255)
tGTCCCTTCGCTGCCCGCGGTAAAAGCCGCTCCGCCACGGCAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTaa > 2:225455/1‑90 (MQ=255)
cTTCGCTGCCCGCGGTAAAAGCCGCTCCGCCACGGCAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTcc > 1:98415/1‑90 (MQ=255)
ttCGCTGCCCGCGGTAAAAGCCGCTCCGCCACGGCAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCg < 1:199331/90‑1 (MQ=255)
cGCTGCCCGCGGTAAAAGCCGCTCCGCCACGGCAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTg < 1:197388/90‑1 (MQ=255)
cGCTGCCCGCGGTAAAAGCCGCTCCGCCACGGCAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTg < 1:133072/90‑1 (MQ=255)
cGCTGCCCGCGGTAAAAGCCGCTCCGCCACGGCAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTg < 2:98415/90‑1 (MQ=255)
tGCCCGCGGTAAAAGCCGCTCCGCCACGGCAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCaa < 2:203366/90‑1 (MQ=255)
tGCCCGCGGTAAAAGCCGCTCCGCCACGGCAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCaa > 1:105608/1‑90 (MQ=255)
gCCCGCGGTAAAAGCCGCTCCGCCACGGCAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAat < 1:324648/90‑1 (MQ=255)
ccGCGGTAAAAGCCGCTCCGCCACGGCAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAatat > 2:156683/1‑90 (MQ=255)
|
GCGGAGTATCCGTTCCCCAACGACAAGCATCATGGCTGGCTCCGTGCCGTTCTGAATATGTCCCTTCGCTGCCCGCGGTAAAAGCCGATCCGCCACGGCAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATAT > NZ_CP009273/4526958‑4527119
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ 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
TCCTGGTACAGCGGAGTATCCGTTCCCCAACGACAAGCATCATGGCTGGCTCCGTGCCGTTCTGAATATGTCCCTTCGCTGCCCGCGGTAAAAGCCGATCCGCCACGGCAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCC > NZ_CP009273/4526948‑4527127
|
TCCTGGTACAGCGGAGTATCCGTTCCCCAACGACAAGCATCATGGCTGGCTCCGTGCCGTTCTGAATATGTCCCTTCGCTGCCCGCGGTAAAAGCCGCTC > SRR3722216.72052/1‑100 (MQ=60)
AGCGGAGTATCCGTTCCCCAACGACAAGCATCATGGCTGGCTCCGTGCCGTTCTGAATATGTCCCTTCGCTGCCCGCGGTAAAAGCCGCTCCGCCACGGC < SRR3722216.52899/100‑1 (MQ=60)
CCCCAACGACAAGCATCATGGCTGGCTCCGTGCCGTTCTGAATATGTCCCTTCGCTGCCCGCGGTAAAAGCCGCTCCGCCACGGCAACACGGAACGATAA < SRR3722216.240216/100‑1 (MQ=60)
GCATCATGGCTGGCTCCGTGCCGTTCTGAATATGTCCCTTCGCTGCCCGCGGTAAAAGCCGCTCCGCCACGGCAACACGGAACGATAAGAATCCCTGCAT < SRR3722216.111236/100‑1 (MQ=60)
TGGCTGGCTCCGTGCCGTTCTGAATATGTCCCTTCGCTGCCCGCGGTAAAAGCCGCTCCGCCACGGCAACACGGAACGATAAGAATCCCTGCATTATCAG < SRR3722216.88437/100‑1 (MQ=60)
naatgcctagtcnggtnnnannnnnnnnnnnnnnaagngaaagngnanaagaaGATCCGCCACGGCAACACGGAACGATAAGAATCCCTGCATTANCAGG < SRR3722216.102350/47‑1 (MQ=60)
TCCGTGCCGTTCTGAATATGTCCCTTCGCTGCCCGCGGTAAAAGCCGCTCCGCCACGGCAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAG < SRR3722216.183287/100‑1 (MQ=60)
TCCGTGCCGTTCTGAATATGTCCCTTCGCTGCCCGCGGTAAAAGCCGCTCCGCCACGGCAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAG < SRR3722216.62725/100‑1 (MQ=60)
GTTCTGAATATGTCCCTTCGCTGCCCGCGGTAAAAGCCGCTCCGCCACGGCAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTAA < SRR3722216.217169/100‑1 (MQ=60)
GAATATGTCCCTTCGCTGCCCGCGGTAAAAGCCGCTCCGCCACGGCAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCC > SRR3722216.99620/1‑100 (MQ=60)
GTCCCTTCGCTGCCCGCGGTAAAAGCCGCTCCGCCACGGCAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAA > SRR3722216.106904/1‑100 (MQ=60)
TTCGCTGCCCGCGGTAAAAGCCGCTCCGCCACGGCAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGC < SRR3722216.201882/100‑1 (MQ=60)
CGCTGCCCGCGGTAAAAGCCGCTCCGCCACGGCAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAG < SRR3722216.134648/100‑1 (MQ=60)
CGCTGCCCGCGGTAAAAGCCGCTCCGCCACGGCAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAG < SRR3722216.199915/100‑1 (MQ=60)
GCCCGCGGTAAAAGCCGCTCCGCCACGGCAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCC < SRR3722216.329439/100‑1 (MQ=60)
|
TCCTGGTACAGCGGAGTATCCGTTCCCCAACGACAAGCATCATGGCTGGCTCCGTGCCGTTCTGAATATGTCCCTTCGCTGCCCGCGGTAAAAGCCGATCCGCCACGGCAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCC > NZ_CP009273/4526948‑4527127
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
