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 F4 I88 R1
|
217 |
30.5 |
1742422 |
95.9% |
1670982 |
87.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
715,111 |
A→G |
I269T (ATC→ACC) |
speF ← |
ornithine decarboxylase SpeF |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 715,111 | 0 | A | G | 100.0%
| 64.3
/ NA
| 18 | I269T (ATC→ACC) | speF | ornithine decarboxylase SpeF |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (9/9); total (9/9) |
ATAAATCGTACCGTCGTAGGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGATCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCATACGGGTTACGT > NZ_CP009273/715023‑715182
|
ataAATCGTACCGTCGTAGGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTc < 1:870116/91‑1 (MQ=255)
gTACCGTCGTAGGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCAc > 1:395030/1‑91 (MQ=255)
tACCGTCGTAGGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACg < 1:124469/91‑1 (MQ=255)
ggTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACtt < 1:846510/91‑1 (MQ=255)
ggTGCCTAACTGAACCACAGGGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACtt < 2:165806/91‑1 (MQ=255)
tGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTttc < 1:170666/91‑1 (MQ=255)
tGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTttc > 2:222671/1‑91 (MQ=255)
tGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAAc < 1:830440/91‑1 (MQ=255)
cacaGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTgc < 1:701886/91‑1 (MQ=255)
gAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCa > 1:207251/1‑91 (MQ=255)
gAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCa > 1:211659/1‑91 (MQ=255)
gAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCa > 1:61763/1‑91 (MQ=255)
gAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCa < 1:766457/91‑1 (MQ=255)
cGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATaa > 2:542029/1‑91 (MQ=255)
aGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAg > 1:132474/1‑91 (MQ=255)
gCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGc > 1:51502/1‑91 (MQ=255)
tctTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCAt < 2:567797/91‑1 (MQ=255)
cTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCATACGGGTTACGt > 2:730464/1‑91 (MQ=255)
|
ATAAATCGTACCGTCGTAGGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGATCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCATACGGGTTACGT > NZ_CP009273/715023‑715182
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 31 ≤ 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
GTTATAAATCGTACCGTCGTAGGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGATCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCATACGGGTTACGTGCCGTTTCCAGATAAACCGGTGTTGCAC > NZ_CP009273/715020‑715210
|
GTTATAAATCGTACCGTCGTAGGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCAC > SRR3722118.403322/1‑101 (MQ=60)
ATAAATCGTACCGTCGTAGGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACCCA < SRR3722118.889504/101‑1 (MQ=60)
TACCGTCGTAGGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTT < SRR3722118.126795/101‑1 (MQ=60)
GGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAAC < SRR3722118.865226/101‑1 (MQ=60)
TGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAG < SRR3722118.174006/101‑1 (MQ=60)
TGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAG < SRR3722118.63310/101‑1 (MQ=60)
TGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATC < SRR3722118.848739/101‑1 (MQ=60)
GAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCA > SRR3722118.211396/1‑101 (MQ=60)
GAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCA > SRR3722118.215906/1‑101 (MQ=60)
GAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCA > SRR3722118.62902/1‑101 (MQ=60)
CACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGC < SRR3722118.717205/101‑1 (MQ=60)
GGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAG > SRR3722118.134986/1‑101 (MQ=60)
GAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGC > SRR3722118.52452/1‑101 (MQ=60)
GAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGC < SRR3722118.783284/101‑1 (MQ=60)
TCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCATACGGGTTACGTGCCGTTTCCAGATAAACCGGTGT > SRR3722118.375784/1‑101 (MQ=60)
TCCGCGGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCATACGGGTTACGTGCCGTTTCCAGATAAACCGGTGT > SRR3722118.393884/1‑101 (MQ=60)
GGTCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCATACGGGTTACGTGCCGTTTCCAGATAAACCGGTGTTGCAC < SRR3722118.179934/101‑1 (MQ=60)
|
GTTATAAATCGTACCGTCGTAGGTGCCTAACTGAATCACAGCGAGGCGGAAAGGACGAGCCTCTTTTGCCCGCTGCGGTGCGACTTCCGCGATCAGCTCACGCAGGTAACTTTCTTCAAAACAGTGCGCATCAATGCCACCGATAAAGCCATACGGGTTACGTGCCGTTTCCAGATAAACCGGTGTTGCAC > NZ_CP009273/715020‑715210
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
