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 I209 R1
|
216 |
14.4 |
815930 |
96.1% |
784108 |
85.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,367,563 |
T→C |
intergenic (‑24/+65) |
blc ← / ← ampC |
lipocalin Blc/BlaEC family class C beta‑lactamase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,367,563 | 0 | T | C | 100.0%
| 63.6
/ NA
| 20 | intergenic (‑24/+65) | blc/ampC | lipocalin Blc/BlaEC family class C beta‑lactamase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (12/8); total (12/8) |
ACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTTCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAA > NZ_CP009273/4367480‑4367644
|
aCTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAgt > 2:170154/1‑90 (MQ=255)
aCTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAgt > 1:106051/1‑90 (MQ=255)
aGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGa > 2:312162/1‑90 (MQ=255)
aGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGa > 2:299770/1‑90 (MQ=255)
ggCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGAt < 1:123676/90‑1 (MQ=255)
cAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGa > 2:42341/1‑90 (MQ=255)
aaTGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGaaa < 1:67046/90‑1 (MQ=255)
tGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGgaga > 2:133135/1‑90 (MQ=255)
cGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGaaaa > 1:367024/1‑90 (MQ=255)
cGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGaaaa < 1:142604/90‑1 (MQ=255)
aGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGAt < 2:182171/90‑1 (MQ=255)
aGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGAt < 2:363249/90‑1 (MQ=255)
ggCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATg > 2:199678/1‑90 (MQ=255)
gcgcATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATgg > 2:2649/1‑90 (MQ=255)
ccTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTaga < 2:66491/90‑1 (MQ=255)
cTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTagag < 1:84140/90‑1 (MQ=255)
cTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTagag < 1:312162/90‑1 (MQ=255)
tACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCg > 1:346412/1‑90 (MQ=255)
cTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGtt > 1:67033/1‑90 (MQ=255)
ggTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCAGACCCGATGGAATTTTACTGTAGAGCGTTaa > 1:386562/1‑90 (MQ=255)
|
ACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTTCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAA > NZ_CP009273/4367480‑4367644
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ 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
GCGTAGGAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTTCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGAAT > NZ_CP009273/4367470‑4367648
|
GCGTAGGAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGT > SRR3722091.107677/1‑100 (MQ=60)
GGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGG < SRR3722091.125543/100‑1 (MQ=60)
AATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAA < SRR3722091.68058/100‑1 (MQ=60)
ATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAA > SRR3722091.373493/1‑100 (MQ=60)
CGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAA < SRR3722091.144713/100‑1 (MQ=60)
AATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCG > SRR3722091.352479/1‑100 (MQ=60)
TGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTT > SRR3722091.68045/1‑100 (MQ=60)
TTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCAGACCCGATGGAATTTTACTGTAGAGCGTTAA > SRR3722091.393384/1‑100 (MQ=60)
CTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGAAT < SRR3722091.317513/100‑1 (MQ=60)
CTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGAAT < SRR3722091.85443/100‑1 (MQ=60)
|
GCGTAGGAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTTCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGAAT > NZ_CP009273/4367470‑4367648
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
