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 |
564,951 |
G→A |
E198E (GAG→GAA) |
ybcK → |
recombinase family protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 564,951 | 0 | G | A | 100.0%
| 80.8
/ NA
| 22 | E198E (GAG→GAA) | ybcK | recombinase family protein |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (9/13); total (9/13) |
ATGACGGCGTCTTGTCCGAGATGGCTCTCCTTAGATGACAAAAGAACGGCTTTTGTTCCAGACCCCGACAGGGTGAAAACTATTGAGCTAATTTTTAAACTCAGGATGGAAAGGCGCTCATTGAATGCAATAGCCAAGTATTTAAATGATCATGCTGTAAAGAATTTCTCA > NZ_CP009273/564865‑565035
|
aTGACGGCGTCTTGTCCGAGATGGCTCTCCTTAGATGACAAAAGAACGGCTTTTGTTCCAGACCCCGACAGGGTGAAAACTATTGAACTa < 2:47693/90‑1 (MQ=255)
aTGACGGCGTCTTGTCCGAGATGGCTCTCCTTAGATGACAAAAGAACGGCTTTTGTTCCAGACCCCGACAGGGTGAAAACTATTGAACTa < 2:245202/90‑1 (MQ=255)
gccGGCGTCTTGTCCGAGATGGCTCTCCTTAGATGACAAAAGAACGGCTTTTGTTCCAGACCCCGACAGGGTGAAAACTATTGAACTAAt < 1:159832/88‑1 (MQ=255)
gACGGCGTCTTGTCCGAGATGGCTCTCCTTAGATGACAAAAGAACGGCTTTTGTTCCAGACCCCGACAGGGTGAAAACTATTGAACTAAt > 2:398239/1‑90 (MQ=255)
tGTCCGAGATGGCTCTCCTTAGATGACAAAAGAACGGCTTTTGTTCCAGACCCCGACAGGGTGAAAACTATTGAACTAATTTTTAAACTc < 2:73062/90‑1 (MQ=255)
tGTCCGAGATGGCTCTCCTTAGATGACAAAAGAACGGCTTTTGTTCCAGACCCCGACAGGGTGAAAACTATTGAACTAATTTTTAAACTc < 1:398239/90‑1 (MQ=255)
cGAGATGGCTCTCCTTAGATGACAAAAGAACGGCTTTTGTTCCAGACCCCGACAGGGTGAAAACTATTGAACTAATTTTTAAACTCAGGa < 2:10348/90‑1 (MQ=255)
gCTCTCCTTAGATGACAAAAGAACGGCTTTTGTTCCAGACCCCGACAGGGTGAAAACTATTGAACTAATTTTTAAACTCAGGATGGAAAg < 1:104408/90‑1 (MQ=255)
ccTTAGATGACAAAAGAACGGCTTTTGTTCCAGACCCCGACAGGGTGAAAACTATTGAACTAATTTTTAAACTCAGGATGGAAAGGCGCt < 2:406418/90‑1 (MQ=255)
tAGATGACAAAAGAACGGCTTTTGTTCCAGACCCCGACAGGGTGAAAACTATTGAACTAATTTTTAAACTCAGGATGGAAAGGCGCTCAt > 2:504269/1‑90 (MQ=255)
cAAAAGAACGGCTTTTGTTCCAGACCCCGACAGGGTGAAAACTATTGAACTAATTTTTAAACTCAGGATGGAAAGGCGCTCATTGaa > 1:401536/1‑87 (MQ=255)
cAAAAGAACGGCTTTTGTTCCAGACCCCGACAGGGTGAAAACTATTGAACTAATTTTTAAACTCAGGATGGAAAGGCGCTCATTGaa < 2:401536/87‑1 (MQ=255)
cAAAAGAACGGCTTTTGTTCCAGACCCCGACAGGGTGAAAACTATTGAACTAATTTTTAAACTCAGGATGGAAAGGCGCTCATTGAATGc > 1:156353/1‑90 (MQ=255)
cAAAAGAACGGCTTTTGTTCCAGACCCCGACAGGGTGAAAACTATTGAACTAATTTTTAAACTCAGGATGGAAAGGCGCTCATTGAATGc > 2:155807/1‑90 (MQ=255)
cGGCTTTTGTTCCAGACCCCGACAGGGTGAAAACTATTGAACTAATTTTTAAACTCAGGATGGAAAGGCGCTCATTGAATGCAATAGCCa < 2:2123/90‑1 (MQ=255)
cGGCTTTTGTTCCAGACCCCGACAGGGTGAAAACTATTGAACTAATTTTTAAACTCAGGATGGAAAGGCGCTCATTGAATGCAATAGCCa < 2:322945/90‑1 (MQ=255)
ttttGTTCCAGACCCCGACAGGGTGAAAACTATTGAACTAATTTTTAAACTCAGGATGGAAAGGCGCTCATTGAATGCAATAGCCAAGTa > 1:333849/1‑90 (MQ=255)
ttCCAGACCCCGACAGGGTGAAAACTATTGAACTAATTTTTAAACTCAGGATGGAAAGGCGCTCATTGAATGCAATAGCCAAGTATTTaa < 2:53095/90‑1 (MQ=255)
gggTGAAAACTATTGAACTAATTTTTAAACTCAGGATGGAAAGGCGCTCATTGAATGCAATAGCCAAGTATTTAAATGATCATGCTGTaa > 1:410056/1‑90 (MQ=255)
tATTGAACTAATTTTTAAACTCAGGATGGAAAGGCGCTCATTGAATGCAATAGCCAAGTATTTAAATGATCATGCTGTAAAGAATTtctc > 2:211564/1‑90 (MQ=255)
tATTGAACTAATTTTTAAACTCAGGATGGAAAGGCGCTCATTGAATGCAATAGCCAAGTATTTAAATGATCATGCTGTAAAGAATTtctc < 1:491225/90‑1 (MQ=255)
aTTGAACTAATTTTTAAACTCAGGATGGAAAGGCGCTCATTGAATGCAATAGCCAAGTATTTAAATGATCATGCTGTAAAGAATTTCTCa > 1:90209/1‑90 (MQ=255)
|
ATGACGGCGTCTTGTCCGAGATGGCTCTCCTTAGATGACAAAAGAACGGCTTTTGTTCCAGACCCCGACAGGGTGAAAACTATTGAGCTAATTTTTAAACTCAGGATGGAAAGGCGCTCATTGAATGCAATAGCCAAGTATTTAAATGATCATGCTGTAAAGAATTTCTCA > NZ_CP009273/564865‑565035
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ 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
GACGGCGTCTTGTCCGAGATGGCTCTCCTTAGATGACAAAAGAACGGCTTTTGTTCCAGACCCCGACAGGGTGAAAACTATTGAGCTAATTTTTAAACTCAGGATGGAAAGGCGCTCATTGAATGCAATAGCCAAGTATTTAAATGATCATGCTGTAAAGAATTTCTCAGGAAAAGAA > NZ_CP009273/564867‑565044
|
GCCGGCGTCTTGTCCGAGATGGCTCTCCTTAGATGACAAAAGAACGGCTTTTGTTCCAGACCCCGACAGGGTGAAAACTATTGAACTAATTTTTAAACTC < SRR3722114.161430/100‑1 (MQ=60)
TGTCCGAGATGGCTCTCCTTAGATGACAAAAGAACGGCTTTTGTTCCAGACCCCGACAGGGTGAAAACTATTGAACTAATTTTTAAACTCAGGATGGAAA < SRR3722114.403076/100‑1 (MQ=60)
GCTCTCCTTAGATGACAAAAGAACGGCTTTTGTTCCAGACCCCGACAGGGTGAAAACTATTGAACTAATTTTTAAACTCAGGATGGAAAGGCGCTCATTG < SRR3722114.105508/100‑1 (MQ=60)
CCTTAGATGACAAAAGAACGGCTTTTGTTCCAGACCCCGACAGGGTGAAAACTATTGAACTAATTTTTAAACTCAGGATGGAAAGGCGCTCATTGAATGC > SRR3722114.157923/1‑100 (MQ=60)
CCTTAGATGACAAAAGAACGGCTTTTGTTCCAGACCCCGACAGGGTGAAAACTATTGAACTAATTTTTAAACTCAGGATGGAAAGGCGCTCATTGAATGC > SRR3722114.406419/1‑100 (MQ=60)
AAAGAACGGCTTTTGTTCCAGACCCCGACAGGGTGAAAACTATTGAACTAATTTTTAAACTCAGGATGGAAAGGCGCTCATTGAATGCAATAGCCAAGTA > SRR3722114.337579/1‑100 (MQ=60)
GACCCCGACAGGGTGAAAACTATTGAACTAATTTTTAAACTCAGGATGGAAAGGCGCTCATTGAATGCAATAGCCAAGTATTTAAATGATCATGCTGTAA > SRR3722114.415073/1‑100 (MQ=60)
GGTGAAAACTATTGAACTAATTTTTAAACTCAGGATGGAAAGGCGCTCATTGAATGCAATAGCCAAGTATTTAAATGATCATGCTGTAAAGAATTTCTCA > SRR3722114.91161/1‑100 (MQ=60)
TATTGAACTAATTTTTAAACTCAGGATGGAAAGGCGCTCATTGAATGCAATAGCCAAGTATTTAAATGATCATGCTGTAAAGAATTTCTCAGGAAAAGAA < SRR3722114.497369/100‑1 (MQ=60)
|
GACGGCGTCTTGTCCGAGATGGCTCTCCTTAGATGACAAAAGAACGGCTTTTGTTCCAGACCCCGACAGGGTGAAAACTATTGAGCTAATTTTTAAACTCAGGATGGAAAGGCGCTCATTGAATGCAATAGCCAAGTATTTAAATGATCATGCTGTAAAGAATTTCTCAGGAAAAGAA > NZ_CP009273/564867‑565044
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
