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 I194 R1
|
197 |
32.2 |
1845014 |
95.2% |
1756453 |
85.4 |
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%
| 134.8
/ NA
| 37 | 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 (16/21); total (16/21) |
GAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTTCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGT > NZ_CP009273/4367476‑4367641
|
gagaACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCt < 2:237153/90‑1 (MQ=255)
agaACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTa < 2:276788/90‑1 (MQ=255)
agaACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTa < 1:909810/90‑1 (MQ=255)
aaCTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAg < 1:881662/90‑1 (MQ=255)
aCTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAgt > 1:252306/1‑90 (MQ=255)
tGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAgtgt > 1:128858/1‑90 (MQ=255)
tGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAgtgt < 1:131025/90‑1 (MQ=255)
gCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATg < 1:284913/90‑1 (MQ=255)
cAACGACCAGAAATGCAGCTGTCGCTGAGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGGGCAGATGa > 2:526356/1‑90 (MQ=255)
cGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAg > 2:165018/1‑90 (MQ=255)
gCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGc < 2:8637/90‑1 (MQ=255)
aGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCgg > 2:549796/1‑90 (MQ=255)
tGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGgaga > 1:844651/1‑90 (MQ=255)
tGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGgaga > 1:600173/1‑90 (MQ=255)
cGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGaaaa < 1:745532/90‑1 (MQ=255)
cGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGaaaa < 1:299572/90‑1 (MQ=255)
gagGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGAc < 1:447011/55‑1 (MQ=255)
gagGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGAc > 2:447011/1‑55 (MQ=255)
cAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGa > 1:425227/1‑90 (MQ=255)
cAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGa > 1:162249/1‑90 (MQ=255)
aGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGAt < 1:161971/90‑1 (MQ=255)
aGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGAt < 1:783755/90‑1 (MQ=255)
gcgcATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATgg > 1:276617/1‑90 (MQ=255)
cATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAAt < 1:735678/90‑1 (MQ=255)
cATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAAt < 1:31779/90‑1 (MQ=255)
ttCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGa < 1:630066/79‑1 (MQ=255)
ttCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGa > 2:630066/1‑79 (MQ=255)
ttCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTa < 1:165018/90‑1 (MQ=255)
ttCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTa > 1:499890/1‑90 (MQ=255)
tCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTag < 1:369947/90‑1 (MQ=255)
ccTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTaga < 2:320359/90‑1 (MQ=255)
ccTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTaga < 1:115769/90‑1 (MQ=255)
cTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTagag < 2:425227/90‑1 (MQ=255)
ttACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGc < 2:600173/90‑1 (MQ=255)
tACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCg > 2:233918/1‑90 (MQ=255)
tACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCg > 2:911462/1‑90 (MQ=255)
aCTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGt > 2:67264/1‑90 (MQ=255)
|
GAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTTCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGT > NZ_CP009273/4367476‑4367641
|
| 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
GCGTAGGAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTTCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGAA > NZ_CP009273/4367470‑4367647
|
GCGTAGGAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGT > SRR3722072.256577/1‑100 (MQ=60)
GTAGGAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGT > SRR3722072.131187/1‑100 (MQ=60)
AGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATG < SRR3722072.925458/100‑1 (MQ=60)
AACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGAC < SRR3722072.896835/100‑1 (MQ=60)
TGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGC < SRR3722072.133381/100‑1 (MQ=60)
catacgagataatcggacgtctcgtgggctcggagatgtgtataagagacagTAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGA < SRR3722072.353823/48‑1 (MQ=60)
GCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGA < SRR3722072.289798/100‑1 (MQ=60)
gctcggagatgtgtataagagacagGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAA < SRR3722072.455199/75‑1 (MQ=60)
GAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGA > SRR3722072.859268/1‑100 (MQ=60)
GAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGA > SRR3722072.610879/1‑100 (MQ=60)
CGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAA < SRR3722072.758717/100‑1 (MQ=60)
CGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAA < SRR3722072.304772/100‑1 (MQ=60)
CGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGA > SRR3722072.165074/1‑100 (MQ=60)
CGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGA > SRR3722072.432956/1‑100 (MQ=60)
GAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGG > SRR3722072.281346/1‑100 (MQ=60)
AGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTAC < SRR3722072.797488/100‑1 (MQ=60)
AGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTAC < SRR3722072.164793/100‑1 (MQ=60)
GGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGT < SRR3722072.641324/100‑1 (MQ=60)
GCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTA > SRR3722072.508920/1‑100 (MQ=60)
CATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAG < SRR3722072.32341/100‑1 (MQ=60)
CATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAG < SRR3722072.748726/100‑1 (MQ=60)
TTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAG < SRR3722072.167886/100‑1 (MQ=60)
TCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGA < SRR3722072.376521/100‑1 (MQ=60)
CCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGAA < SRR3722072.117899/100‑1 (MQ=60)
|
GCGTAGGAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTTCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGAA > NZ_CP009273/4367470‑4367647
|
| 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: ‑ |
