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 |
3,597,860 |
C→T |
T36T (ACC→ACT) |
rsmD → |
16S rRNA (guanine(966)‑N(2))‑methyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,597,860 | 0 | C | T | 82.3%
| 37.2
/ ‑0.1
| 17 | T36T (ACC→ACT) | rsmD | 16S rRNA (guanine(966)‑N(2))‑methyltransferase |
| Reads supporting (aligned to +/- strand): ref base C (2/1); new base T (10/4); total (12/5) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GGCCAAATCCGCATTATTGGCGGGCAGTGGCGAGGCCGTAAACTCCCGGTTCCTGATAGCCCAGGTCTGCGCCCCACCACCGACCGCGTACGCGAAACGTTGTTTAACTGGCTGGCTCCGGTCATTGTTGACGCCCAATGTCTGGATTGCTTCGCCGG > NZ_CP009273/3597780‑3597937
|
ggCCAAATCCGCATTATTGGCGGGCAGTGGCGAGGCCGTAAACTCCCGGTTCCTGATAGCCCAGGTCTGCGCCCCACCACTGACCGCGTa < 1:348851/90‑1 (MQ=255)
ccGCATTATTGGCGGGCAGTGGCGAGGCCGTAAACTCCCGGTTCCTGATAGCCCAGGTCTGCGCCCCACCACTGACCGCGTACGCGAAAc < 2:901140/90‑1 (MQ=255)
ggCGGGCAGTGGCGAGGCCGGAAACTCCCGGTTCCTGATAACCCCGGGCTGCGCCCCACCCCTGACCCCGTACGCGAAACGTTGTTTAAc > 2:808734/1‑90 (MQ=255)
gggCAGGGGCGAGGCCCTAAACTCCCGGGTCCTTAAAGCCCACGGCTTCGCCCCACCACCGACCGCGGACGCGGAACGCTTTTTTAatgg > 2:331545/1‑90 (MQ=255)
gCAGTGGCGAGGCCGTAAACTCCCGGTTCCTGATAGCCCAGGTCTGCGCCCCACCACTGACCGCGTACGCGAAACGTTGTTTAActggct < 1:78183/90‑1 (MQ=255)
gTGGCGAGGCCGTAAACTCCCGGTTCCTGATAGCCCAGGTCTGCGCCCCACCACTGACCGCGTACGCGAAACGTTGTTTAACtggctggc > 1:834068/1‑90 (MQ=255)
ggCGAGGCCGTAAACTCCCGGTTCCTGATAGCCCAGGTCTGCGCCCCACCACTGACCGCGTACGCGAAACGTTGTTTAACTGGCTGGCTc > 2:607096/1‑90 (MQ=255)
ggCCGTAAACTCCCGGTTCCTGATAGCCCAGGTCTGCGCCCCACCACCGACCGCGTACGCGAAACGTTGTTTAACTGGCTGGCTCCGGTc > 1:794972/1‑90 (MQ=255)
tAAACTCCCGGTTCCTGATAGCCCAGGTCTGCGCCCCACCACTGACCGCGTACGCGAAACGTTGTTTAACTGGCTGGCTCCGGTCAttgt > 1:610115/1‑90 (MQ=255)
ccGGTTCCTGATAGCCCAGGTCTGCGCCCCACCACTGACCGCGTACGCGAAACGTTGTTTAACTGGCTGGCTCCGGTCATTGTTGACGcc > 1:177679/1‑90 (MQ=255)
ggTTCCTGATAGCCCAGGTCTGCGCCCCACCACTGACCGCGTACGCGAAACGTTGTTTAACTGGCTGGCTCCGGTCATTGTTGACGCCCa < 1:448103/90‑1 (MQ=255)
tCCTGATAGCCCAGGTCTGCGCCCCACCACCGACCGCGTACGCGAAACGTTGTTTAACTGGCTGGCTCCGGTCATTGTTGACGCCCAATg < 2:794972/90‑1 (MQ=255)
gCCCAGGTCTGCGCCCCACCACTGACCGCGTACGCGAAACGTTGTTTAACTGGCTGGCCCCGGTCATTGTTGACGCCCAATGTCTGGAtt > 2:41981/1‑90 (MQ=255)
cAGGTCTGCGCCCCACCACTGACCGCGTACGCGAAACGTTGTTTAACTGGCTGGCTCCGGTCATTGTTGACGCCCAATGTCTGGATTGCt > 2:684980/1‑90 (MQ=255)
aGGTCTGCGCCCCACCACTGACCGCGTACGCGAAACGTTGTTCAACTGGCTGGCTCCGGTCATTGTTGACGCCCAATGTCTGGATTGCtt > 2:790117/1‑90 (MQ=255)
gcgcCCCACCACTGACCGCGTACGCGAAACGTTGTTTAACTGGCTGGCTCCGGTCATTGTTGACGCCCAATGTCTGGATTGCTTCGCCgg > 2:115307/1‑90 (MQ=255)
gcgcCCCACCACTGACCGCGTACGCGAAACGTTGTTTAACTGGCTGGCTCCGGTCATTGTTGACGCCCAATGTCTGGATTGCTTCGCCgg > 1:249820/1‑90 (MQ=255)
|
GGCCAAATCCGCATTATTGGCGGGCAGTGGCGAGGCCGTAAACTCCCGGTTCCTGATAGCCCAGGTCTGCGCCCCACCACCGACCGCGTACGCGAAACGTTGTTTAACTGGCTGGCTCCGGTCATTGTTGACGCCCAATGTCTGGATTGCTTCGCCGG > NZ_CP009273/3597780‑3597937
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GGCCAAATCCGCATTATTGGCGGGCAGTGGCGAGGCCGTAAACTCCCGGTTCCTGATAGCCCAGGTCTGCGCCCCACCACCGACCGCGTACGCGAAACGTTGTTTAACTGGCTGGCTCCGGTCATTGTTGACGCCCAATGTCTGGATTGCTTCGCCGGGAGCGGCGCGCTGGGGCT > NZ_CP009273/3597780‑3597955
|
GGCCAAATCCGCATTATTGGCGGGCAGTGGCGAGGCCGTAAACTCCCGGTTCCTGATAGCCCAGGTCTGCGCCCCACCACTGACCGCGTACGCGAAACGT < SRR3722072.354999/100‑1 (MQ=60)
TTGGCGGGCAGTGGCGAGGCCGTAAACTCCCGGTTCCTGATAGCCCAGGTCTGCGCCCCACCACTGACCGCGTACGCGAAACGTTGTTTAACTGGCTGGC > SRR3722072.848522/1‑100 (MQ=60)
GCAGTGGCGAGGCCGTAAACTCCCGGTTCCTGATAGCCCAGGTCTGCGCCCCACCACTGACCGCGTACGCGAAACGTTGTTTAACTGGCTGGCTCCGGTC < SRR3722072.79634/100‑1 (MQ=60)
GCAGTGGCGAGGCCGTAAACTCCCGGTTCCTGATAGCCCAGGTCTGCGCCCCACCACCGACCGCGTACGCGAAACGTTGTTTAACTGGCTGGCTCCGGTC > SRR3722072.808874/1‑100 (MQ=60)
GGCGAGGCCGTAAACTCCCGGTTCCTGATAGCCCAGGTCTGCGCCCCACCACTGACCGCGTACGCGAAACGTTGTTTAACTGGCTGGCTCCGGTCATTGT > SRR3722072.620988/1‑100 (MQ=60)
CCGTAAACTCCCGGTTCCTGATAGCCCAGGTCTGCGCCCCACCACTGACCGCGTACGCGAAACGTTGTTTAACTGGCTGGCTCCGGTCATTGTTGACGCC > SRR3722072.180754/1‑100 (MQ=60)
GGTTCCTGATAGCCCAGGTCTGCGCCCCACCACTGACCGCGTACGCGAAACGTTGTTTAACTGGCTGGCTCCGGTCATTGTTGACGCCCAATGTCTGGAT < SRR3722072.456305/100‑1 (MQ=60)
GCCCAGGTCTGCGCCCCACCACTGACCGCGTACGCGAAACGTTGTTTAACTGGCTGGCTCCGGTCATTGTTGACGCCCAATGTCTGGATTGCTTCGCCGG > SRR3722072.254040/1‑100 (MQ=60)
CCCCACCACTGACCGCGTACGCGAAACGTTGTTTAACctgtctcttatacacatctccgagcccacgagacgtccgattatctcgtatgccgtcttctgc > SRR3722072.11597/1‑37 (MQ=60)
ACCACTGACCGCGTACGCGAAACGTTGTTTAACTGGCTGGCTCCGGTCATTGTTGACGCCCAATGTCTGGATctgtctcttatacacatctccgagccca > SRR3722072.463966/1‑72 (MQ=60)
CCACTGACCGCGTACGCGAAACGTTGTTTAACTGGCTGGCTCCGGTCATTGTTGACGCCCAATGTCTGGATTGCTTCGCCGGGAGCGGCGCGCTGGGGCT > SRR3722072.445764/1‑100 (MQ=60)
|
GGCCAAATCCGCATTATTGGCGGGCAGTGGCGAGGCCGTAAACTCCCGGTTCCTGATAGCCCAGGTCTGCGCCCCACCACCGACCGCGTACGCGAAACGTTGTTTAACTGGCTGGCTCCGGTCATTGTTGACGCCCAATGTCTGGATTGCTTCGCCGGGAGCGGCGCGCTGGGGCT > NZ_CP009273/3597780‑3597955
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
