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 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
86.4 |
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%
| 93.0
/ NA
| 29 | 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 (17/12); total (17/12) |
AGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTTCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGAA > NZ_CP009273/4367477‑4367647
|
agaACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTa < 1:229172/90‑1 (MQ=255)
aaCTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAg > 1:648220/1‑90 (MQ=255)
aCTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAgt > 1:18369/1‑90 (MQ=255)
aCTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAgt > 2:449105/1‑90 (MQ=255)
gCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTa > 2:641643/1‑90 (MQ=255)
aGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGa > 1:94943/1‑90 (MQ=255)
aGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGa > 2:70658/1‑90 (MQ=255)
gCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATg < 1:570743/90‑1 (MQ=255)
gCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATg < 1:144018/90‑1 (MQ=255)
cGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAg > 2:32325/1‑90 (MQ=255)
gCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGc < 2:699783/90‑1 (MQ=255)
gCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGc > 2:365379/1‑90 (MQ=255)
aGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCgg > 2:591451/1‑90 (MQ=255)
tGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGgaga > 1:633932/1‑90 (MQ=255)
gagaGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAAtt > 1:215543/1‑90 (MQ=255)
aGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGAccc > 1:403278/1‑90 (MQ=255)
ggCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATg > 2:305002/1‑90 (MQ=255)
cgcATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGa > 1:649607/1‑90 (MQ=255)
gcATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGC‑AGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAAt < 2:577437/90‑1 (MQ=255)
cATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAAt < 1:722713/90‑1 (MQ=255)
cATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAAt < 1:39281/90‑1 (MQ=255)
cATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAAt < 1:449105/90‑1 (MQ=255)
aTAAATGTTTCCTTACTGG‑TTTTTCCTAAGGGGAAATGGAAGCAAGGAAAAAGGGGGAAAAAGGCCGGAAAATTGGGCCCCATTGGAttt > 2:311653/1‑90 (MQ=255)
tAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAAttt < 1:123030/90‑1 (MQ=255)
tAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAAttt < 1:633746/90‑1 (MQ=255)
tttCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGt > 2:388390/1‑90 (MQ=255)
tCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCAGACCCGATGGAATTTTACTGTag > 2:530588/1‑90 (MQ=255)
ccTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTaga < 1:641643/90‑1 (MQ=255)
cTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTagag < 2:470811/90‑1 (MQ=255)
tttttcCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGaa < 2:215543/90‑1 (MQ=255)
|
AGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTTCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGAA > NZ_CP009273/4367477‑4367647
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ 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
GGCGTAGGAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTTCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGAA > NZ_CP009273/4367469‑4367647
|
GGCGTAGGAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAG > SRR3722112.658321/1‑100 (MQ=60)
GCGTAGGAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGT > SRR3722112.18599/1‑100 (MQ=60)
GGAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGA > SRR3722112.96126/1‑100 (MQ=60)
AGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATG < SRR3722112.231926/100‑1 (MQ=60)
GCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGA < SRR3722112.145810/100‑1 (MQ=60)
GCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGA < SRR3722112.579437/100‑1 (MQ=60)
GAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGA > SRR3722112.643754/1‑100 (MQ=60)
CTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATT > SRR3722112.218140/1‑100 (MQ=60)
AACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCC > SRR3722112.408603/1‑100 (MQ=60)
AGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGA > SRR3722112.659730/1‑100 (MQ=60)
CATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAG < SRR3722112.39761/100‑1 (MQ=60)
CATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAG < SRR3722112.455368/100‑1 (MQ=60)
CATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAG < SRR3722112.733993/100‑1 (MQ=60)
TAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAG < SRR3722112.124553/100‑1 (MQ=60)
TAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAG < SRR3722112.643563/100‑1 (MQ=60)
CCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGAA < SRR3722112.651622/100‑1 (MQ=60)
|
GGCGTAGGAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTTCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGAA > NZ_CP009273/4367469‑4367647
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
