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 |
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%
| 98.9
/ NA
| 30 | 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 (11/19); total (11/19) |
GAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTTCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGAA > NZ_CP009273/4367476‑4367647
|
gagaACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCt < 1:224314/90‑1 (MQ=255)
agaACTGCAGGCACCGCCCAGAAATGCAGCTGTCGCTGCGGCCACGAGAGGGAGCAGGCGCATAAATGTTTCCTTGCTGGTTTTTTCCTa < 1:458253/90‑1 (MQ=255)
agaACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTa < 2:113096/90‑1 (MQ=255)
aCTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAgt > 2:136678/1‑90 (MQ=255)
aCTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAgt > 1:245219/1‑90 (MQ=255)
aCTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAgt > 1:514827/1‑90 (MQ=255)
gCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATg < 2:462778/90‑1 (MQ=255)
gCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATg < 2:313111/90‑1 (MQ=255)
gCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATg < 2:166485/90‑1 (MQ=255)
aCCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCa > 1:430310/1‑90 (MQ=255)
aaaTGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGaa < 1:341311/90‑1 (MQ=255)
aaTGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGaaa < 1:21303/90‑1 (MQ=255)
gCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGc < 2:90722/90‑1 (MQ=255)
gCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGc < 2:124755/90‑1 (MQ=255)
tGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAg < 2:168232/67‑1 (MQ=255)
tGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAg > 1:168232/1‑67 (MQ=255)
tGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGgaga > 1:265301/1‑90 (MQ=255)
aGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGAt > 1:235413/1‑90 (MQ=255)
aGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGAt < 1:178601/90‑1 (MQ=255)
aGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGAt < 2:431423/90‑1 (MQ=255)
ggCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATg < 2:56103/90‑1 (MQ=255)
cATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAAt < 2:245219/90‑1 (MQ=255)
aTAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAAtt > 1:396823/1‑90 (MQ=255)
tAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAAttt < 1:136678/90‑1 (MQ=255)
tAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAAttt < 2:150182/90‑1 (MQ=255)
tAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAAttt < 2:488692/90‑1 (MQ=255)
ttCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTa > 1:339597/1‑90 (MQ=255)
ccTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTaga < 1:435059/90‑1 (MQ=255)
tACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCg > 1:181803/1‑90 (MQ=255)
tACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCg > 2:123065/1‑90 (MQ=255)
tttttcCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCAGGTGGAATTTTACTGTAGAGCGTTAAGaa < 1:44478/90‑1 (MQ=255)
|
GAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTTCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGAA > NZ_CP009273/4367476‑4367647
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GGCGTAGGAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTTCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGAATCTGCCAGGC > NZ_CP009273/4367469‑4367657
|
GGCGTAGGAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAG < SRR3722114.126547/100‑1 (MQ=60)
GCGTAGGAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGT > SRR3722114.521281/1‑100 (MQ=60)
GCGTAGGAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGT > SRR3722114.247593/1‑100 (MQ=60)
GAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGAT < SRR3722114.226444/100‑1 (MQ=60)
AGAACTGCAGGCACCGCCCAGAAATGCAGCTGTCGCTGCGGCCACGAGAGGGAGCAGGCGCATAAATGTTTCCTTGCTGGTTTTTTCCTAAGTGTAGATG < SRR3722114.463974/100‑1 (MQ=60)
GCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCA > SRR3722114.435607/1‑100 (MQ=60)
GAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAActgtctcttatac > SRR3722114.169891/1‑87 (MQ=60)
GAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGA > SRR3722114.268011/1‑100 (MQ=60)
AAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAA < SRR3722114.345181/100‑1 (MQ=60)
AATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAA < SRR3722114.21513/100‑1 (MQ=60)
GAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGAT > SRR3722114.237645/1‑100 (MQ=60)
GAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATT > SRR3722114.401638/1‑100 (MQ=60)
AGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTAC < SRR3722114.180372/100‑1 (MQ=60)
GCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTA > SRR3722114.343431/1‑100 (MQ=60)
TAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAG < SRR3722114.138091/100‑1 (MQ=60)
AATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCG > SRR3722114.183595/1‑100 (MQ=60)
CCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGAA < SRR3722114.440413/100‑1 (MQ=60)
TTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCAGGTGGAATTTTACTGTAGAGCGTTAAGAATCTGCCAGGC < SRR3722114.44915/100‑1 (MQ=60)
|
GGCGTAGGAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTTCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGAATCTGCCAGGC > NZ_CP009273/4367469‑4367657
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
