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 I197 R1
|
189 |
12.7 |
697584 |
97.1% |
677354 |
86.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,526,050 |
A→G |
T95A (ACC→GCC) |
cysK → |
cysteine synthase A |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,526,050 | 0 | A | G | 100.0%
| 42.2
/ NA
| 14 | T95A (ACC→GCC) | cysK | cysteine synthase A |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (10/4); total (10/4) |
GAACCGACCAGCGGTAATACCGGGATTGCACTGGCCTATGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAACCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGACGGAAGGTGCTAAAGGCATGAAA > NZ_CP009273/2525966‑2526130
|
gAACCGACCAGCGGTAATACCGGGATTGCACTGGCCTATGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAGCCATg < 1:131463/90‑1 (MQ=255)
aaTACCGGGATTGCACTGGCCTATGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAGCCATGAGTATTGAAcgccgc > 2:212789/1‑90 (MQ=255)
ggCCTATGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGtt > 2:199094/1‑90 (MQ=255)
aTGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTg > 1:169016/1‑90 (MQ=255)
cGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGGTATGTGCAAACCTGGt > 1:208002/1‑90 (MQ=255)
tCACCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGACGGAAGGTGCTa < 1:199094/90‑1 (MQ=255)
cACCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGACGGAAGGTGCTaa > 1:260161/1‑90 (MQ=255)
cACCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGACGGAAGGTGCTaa < 1:272922/90‑1 (MQ=255)
gACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGACGGAAGGTGCTAAAGGCAt > 2:160542/1‑90 (MQ=255)
aTGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGACGGAAGGTGCTAAAGGCATGaaa > 1:148899/1‑90 (MQ=255)
aTGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGACGGAAGGTGCTAAAGGCATGaaa > 1:259545/1‑90 (MQ=255)
aTGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGACGGAAGGTGCTAAAGGCATGaaa > 1:596/1‑90 (MQ=255)
gCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGa < 1:258222/38‑1 (MQ=38)
gCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGa > 2:258222/1‑38 (MQ=38)
|
GAACCGACCAGCGGTAATACCGGGATTGCACTGGCCTATGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAACCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGACGGAAGGTGCTAAAGGCATGAAA > NZ_CP009273/2525966‑2526130
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ 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
GAACCGACCAGCGGTAATACCGGGATTGCACTGGCCTATGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAACCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGACGGAAGGTGCTAAAGGCATGAAA > NZ_CP009273/2525966‑2526130
|
GAACCGACCAGCGGTAATACCGGGATTGCACTGGCCTATGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAGCCATGAGTATTGAAC < SRR3722076.133002/100‑1 (MQ=60)
cgaccgccatcgtcggcagcgtcagatgtgtataagagacagCCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGG < SRR3722076.261944/58‑1 (MQ=60)
nnnnnnngnnnnnnnnnnnnncgtcagatgtgtataagagacagGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTG < SRR3722076.62970/56‑1 (MQ=60)
GCACTGGCCTATGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTG > SRR3722076.171113/1‑100 (MQ=60)
ATGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGGTATGTGCAAACCTGGT > SRR3722076.210710/1‑100 (MQ=60)
GTTACAAACTCACCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGACGGAAGGTGCTAA > SRR3722076.263919/1‑100 (MQ=60)
TCACCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGACGGAAGGTGCTAAAGGCATGAA < SRR3722076.201641/100‑1 (MQ=60)
CACCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGACGGAAGGTGCTAAAGGCATGAAA > SRR3722076.150601/1‑100 (MQ=60)
CACCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGACGGAAGGTGCTAAAGGCATGAAA > SRR3722076.263290/1‑100 (MQ=60)
CACCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGACGGAAGGTGCTAAAGGCATGAAA < SRR3722076.276927/100‑1 (MQ=60)
CACCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGACGGAAGGTGCTAAAGGCATGAAA > SRR3722076.604/1‑100 (MQ=60)
|
GAACCGACCAGCGGTAATACCGGGATTGCACTGGCCTATGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAACCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGACGGAAGGTGCTAAAGGCATGAAA > NZ_CP009273/2525966‑2526130
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
