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 F3 I142 R1
|
10 |
30.9 |
1778688 |
96.4% |
1714655 |
84.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,754,231 |
G→T |
R127S (CGC→AGC) |
selA ← |
L‑seryl‑tRNA(Sec) selenium transferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,754,231 | 0 | G | T | 100.0%
| 154.2
/ NA
| 39 | R127S (CGC→AGC) | selA | L‑seryl‑tRNA(Sec) selenium transferase |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base T (15/24); total (15/24) |
CATTGTTATTGACGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCGTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGCCTGCGCAACGGCTTCCACCGCGGCTTCCGCCTG > NZ_CP009273/3754150‑3754312
|
cATTGTTATTGACGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGcgt < 2:328791/90‑1 (MQ=255)
cATTGTTATTGACGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGcgt < 2:470176/90‑1 (MQ=255)
ttACTGACGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTcc < 2:803088/90‑1 (MQ=255)
aTTGACGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAg < 2:600808/90‑1 (MQ=255)
tGACGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGAt < 2:567998/90‑1 (MQ=255)
aCGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCa < 2:3557/90‑1 (MQ=255)
cGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCAt < 2:797425/90‑1 (MQ=255)
aTACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATAc > 2:109951/1‑90 (MQ=255)
aTACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATAc > 1:705889/1‑90 (MQ=255)
aTCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGt > 1:563690/1‑90 (MQ=255)
cTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCa > 2:624542/1‑90 (MQ=255)
ttCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCAc < 1:396427/90‑1 (MQ=255)
ccGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTg < 2:171155/90‑1 (MQ=255)
ccccGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGa < 1:402537/90‑1 (MQ=255)
ccccGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGa < 2:563690/90‑1 (MQ=255)
ccccGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGa < 1:379328/90‑1 (MQ=255)
ccccGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGa < 1:280486/90‑1 (MQ=255)
ccccGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGa < 1:18514/90‑1 (MQ=255)
ccGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCAt < 1:203698/69‑1 (MQ=255)
ccGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCAt > 2:203698/1‑69 (MQ=255)
cGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACg > 2:427372/1‑90 (MQ=255)
cGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACg > 2:318342/1‑90 (MQ=255)
tAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCa < 1:624542/90‑1 (MQ=255)
cGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGcc < 2:814820/90‑1 (MQ=255)
cGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGcc < 1:212068/90‑1 (MQ=255)
gCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGcgt > 2:329390/1‑47 (MQ=255)
gCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGcgt > 1:108440/1‑47 (MQ=255)
gCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGcgt < 2:108440/47‑1 (MQ=255)
gCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGcgt < 1:76656/47‑1 (MQ=255)
gCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGcgt < 1:329390/47‑1 (MQ=255)
gCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGcgt > 2:76656/1‑47 (MQ=255)
gCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAg > 1:656192/1‑54 (MQ=255)
gCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAg < 2:656192/54‑1 (MQ=255)
gCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGCCTg > 2:119858/1‑90 (MQ=255)
gcagcTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGCCTGCGCaa > 2:142074/1‑90 (MQ=255)
tGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGCCTGCGCAACGGCt > 1:437814/1‑90 (MQ=255)
gATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGCCTGCGCAACGGCTTCCACCGCGGCtt < 2:655473/90‑1 (MQ=255)
cgcgATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGCCTGCGCAACGGCTTCCACCGCGGCTTCCg < 2:470077/90‑1 (MQ=255)
aTGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGCCTGCGCAACGGCTTCCACCGCGGCTTCCGCCTg > 1:160928/1‑90 (MQ=255)
|
CATTGTTATTGACGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCGTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGCCTGCGCAACGGCTTCCACCGCGGCTTCCGCCTG > NZ_CP009273/3754150‑3754312
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ 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
CACCGCCGCCGCATTGTTATTGACGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCGTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGCCTGCGCAACGGCTTCCACCGCGGCTTCCGCCTGTAAAGCTCGCCCAAGG > NZ_CP009273/3754139‑3754328
|
CACCGCCGCCGCATTGTTATTGACGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCG < SRR3722011.162032/100‑1 (MQ=60)
CACCGCCGCCGCATTGTTATTGACGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCG < SRR3722011.344083/100‑1 (MQ=60)
tcgtcggcagcgtcagatgtgtataagagacagCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATC < SRR3722011.77743/67‑1 (MQ=60)
tcgtcggcagcgtcagatgtgtataagagacagCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATC < SRR3722011.334030/67‑1 (MQ=60)
GTTATTGACGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATAC > SRR3722011.718159/1‑100 (MQ=60)
ataagagacagTCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGT < SRR3722011.206740/89‑1 (MQ=60)
CGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGT > SRR3722011.572964/1‑100 (MQ=60)
TTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGC < SRR3722011.402088/100‑1 (MQ=60)
CCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGCC < SRR3722011.384616/100‑1 (MQ=60)
CCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGCC < SRR3722011.408350/100‑1 (MQ=60)
CCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGCC < SRR3722011.284499/100‑1 (MQ=60)
CCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGCC < SRR3722011.18796/100‑1 (MQ=60)
CCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCctgtctcttatacacatctgacgctgccgacga > SRR3722011.110022/1‑67 (MQ=60)
CCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGctgtctcttatacacatctgacgccg > SRR3722011.667470/1‑74 (MQ=60)
TAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATCCTCGAGGGTCACTGGCGAACGCATAGCCTGCGC < SRR3722011.635137/100‑1 (MQ=60)
CGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAAntcatnnnnnnnnnnannn > SRR3722011.582646/1‑81 (MQ=60)
CGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGCCTGCGCAACGG < SRR3722011.215210/100‑1 (MQ=60)
GCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGCCTGCGCAACGGCT > SRR3722011.444460/1‑100 (MQ=60)
CCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGCCTGCGCAACGGCTTCCACCGCGGCTTCCGCCTG > SRR3722011.163319/1‑100 (MQ=60)
GCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGCCTGCGCAACGGCTTCCACCGCGGCTTCCGCCTGTAAAGCTCGCCCAAGG < SRR3722011.144184/100‑1 (MQ=60)
|
CACCGCCGCCGCATTGTTATTGACGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCGTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGCCTGCGCAACGGCTTCCACCGCGGCTTCCGCCTGTAAAGCTCGCCCAAGG > NZ_CP009273/3754139‑3754328
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
