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 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,818,956 |
T→G |
K80T (AAA→ACA) |
ves ← |
environmental stress‑induced protein Ves |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,818,956 | 0 | T | G | 75.0%
| 17.5
/ 3.9
| 12 | K80T (AAA→ACA) | ves | environmental stress‑induced protein Ves |
| Reads supporting (aligned to +/- strand): ref base T (1/2); new base G (2/7); total (3/9) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.07e-01 |
TGATGTTGAAATCCATCGACATCTGCCCTGCCGTCAGTTTCGCTTTTACCACCTGGTCCGCTGCAAAGGCAAAAGGCTGGAACGGTTTTAAGGTATGGTTAAAGCGGTCTGCGCTTTCAAGGAGCATCTCGCCGCCTTCCAGCAACGTCAC > NZ_CP009273/1818870‑1819020
|
tgatgTTGAAATCCATCGACATCTGCCCTGCCGTCAGTTTCGCTTTTACCACCTGGTCCGCTGC‑AAGGCAAAAGGCTGGAACGGTGTTaa > 1:730566/1‑90 (MQ=255)
ttGAAATCCATCGACATCTGCCCTGCCGTCAGTTTCGCTTTTACCACCTGGTCCGCTGCAAAGGCAAAAGGCTGGAACGGTTTTAAGGTa < 1:27172/90‑1 (MQ=255)
ttGAAATCCATCGACATCTGCCCTGCCGTCAGTTTCGCTTTTACCACCTGGTCCGCTGCAAAGGCAAAAGGCTGGAACGGTGTTAAGGTa < 1:176288/90‑1 (MQ=255)
aTCGACATCTGCCCTGCCGTCAGTTTCGCCTTTACCACCTGGTCCGCTGCAAAGGCAAAAGGCTGGAACGGTGTTAAGGTATGGTTAAAg < 1:727831/90‑1 (MQ=255)
gccctgccGTCAGTTTCGCTTTTACCACCTGGTCCGCTGCAAAGGCAAAAGGCTGGAACGGTGTTAAGGTATGGTTAAAGCGGTCTgcgc < 1:221708/90‑1 (MQ=255)
tgccGTCAGTTTCGCTTTTACCACCTGGTCCGCTGCAAAGGCAAAAGGCTGGAACGGTGTTAAGGTATGGTTAAAGCGGTCTGCGCTTTc > 2:260436/1‑90 (MQ=255)
cTTTTACCACCTGGTCCGCTGC‑AAGGCAAAAGGCTGGAACGGTGTTAAGGTATGGTTAAAGCGGTCTGCGCTTTCAAGGAGCATCTcgcc < 2:730566/90‑1 (MQ=255)
ccTGGTCCGCTGCAAAGGCAAAAGGCTGGAACGGTTTTAAGGTATGGTTAAAGCGGTCTGCGCTTTCAAGGAGCATCTCGCCGCCTTCCa > 2:478099/1‑90 (MQ=255)
ggTCCGCTGCAAAGGCAAAAGGCTGGAACGGTGTTAAGGTATGGTTAAAGCGGTCTGCGCTTTCAAGGAGCATCTCGCCGCCTTCCAGCa < 2:241811/90‑1 (MQ=255)
tGCAAAGGCAAAAGGCTGGAACGGTTTTAAGGTATGGTTAAAGCGGTCTGCGCTTTCAAGGAGCATCTCGCCGCCTTCCAGCAACGTCAc < 2:707341/90‑1 (MQ=255)
tGCAAAGGCAAAAGGCTGGAACGGTGTTAAGGTATGGTTAAAGCGGTCTGCGCTTTCAAGGAGCATCTCGCCGCCTTCCAGCAACGTCAc < 1:260436/90‑1 (MQ=255)
tGCAAAGGCAAAAGGCTGGAACGGTGTTAAGGTATGGTTAAAGCGGTCTGCGCTTTCAAGGAGCATCTCGCCGCCTTCCAGCAACGTCAc < 2:150895/90‑1 (MQ=255)
|
TGATGTTGAAATCCATCGACATCTGCCCTGCCGTCAGTTTCGCTTTTACCACCTGGTCCGCTGCAAAGGCAAAAGGCTGGAACGGTTTTAAGGTATGGTTAAAGCGGTCTGCGCTTTCAAGGAGCATCTCGCCGCCTTCCAGCAACGTCAC > NZ_CP009273/1818870‑1819020
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ 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
AGGCGTGTCATGATGTTGAAATCCATCGACATCTGCCCTGCCGTCAGTTTCGCTTTTACCACCTGGTCCGCTGCAAAGGCAAAAGGCTGGAACGGTTTTAAGGTATGGTTAAAGCGGTCTGCGCTTTCAAGGAGCATCTCGCCGCCTTCCAGCAACGTCACTATCCTTTCCATGCCGGGAAACAAAGAAAACTC > NZ_CP009273/1818860‑1819053
|
AGGCGTGTCATGATGTTGAAATCCATCGACATCTGCCCTGCCGTCAGTTTCGCTTTTACCACCTGGTCCGCTGC‑AAGGCAAAAGGCTGGAACGGTGTTAA > SRR3722079.738381/1‑100 (MQ=60)
TGTCATGATGTTGAAATCCATCGACATCTGCCCTGCCGTCAGTTTCGCTTTTACCACCTGGTCCGCTGCAAAGGCAAAAGGCTGGAACGGTGTTAAGGTA < SRR3722079.183151/100‑1 (MQ=60)
TTGAAATCCATCGACATCTGCCCTGCCGTCAGTTTCGCTTTTACCACCTGGTCCGCTGCAAAGGCAAAAGGCTGGAACGGTTTTAAGGTATGGTTAAAGC < SRR3722079.27367/100‑1 (MQ=60)
TTGAAATCCATCGACATCTGCCCTGCCGTCAGTTTCGCTTTTACCACCTGGTCCGCTGCAAAGGCAAAAGGCTGGAACGGTGTTAAGGTATGGTTAAAGC < SRR3722079.177825/100‑1 (MQ=60)
ATCGACATCTGCCCTGCCGTCAGTTTCGCCTTTACCACCTGGTCCGCTGCAAAGGCAAAAGGCTGGAACGGTGTTAAGGTATGGTTAAAGCGGTCTGCGC < SRR3722079.735614/100‑1 (MQ=60)
GCCCTGCCGTCAGTTTCGCTTTTACCACCTGGTCCGCTGCAAAGGCAAAAGGCTGGAACGGTGTTAAGGTATGGTTAAAGCGGTCTGCGCTTTCAAGGAG < SRR3722079.223598/100‑1 (MQ=60)
TGCAAAGGCAAAAGGCTGGAACGGTGTTAAGGTATGGTTAAAGCGGTCTGCGCTTTCAAGGAGCATCTCGCCGCCTTCCAGCAACGTCACTATCCTTTCC < SRR3722079.262621/100‑1 (MQ=60)
GTTTTAAGGTATGGTTAAAGCGGTCTGCGCTTTCAAGGAGCATCTCGCCGCCTTCCAGCAACGTCACTATCCTTTCCATGCCGGGAAACAAAGAAAACTC > SRR3722079.136707/1‑100 (MQ=60)
GTGTTAAGGTATGGTTAAAGCGGTCTGCGCTTTCAAGGAGCATCTCGCCGCCTTCCAGCAACGTCACTATCCTTTCCATGCCGGGAAACAAAGAAAACTC > SRR3722079.353404/1‑100 (MQ=60)
GTGTTAAGGTATGGTTAAAGCGGTCTGCGCTTTCAAGGAGCATCTCGCCGCCTTCCAGCAACGTCACTATCCTTTCCATGCCGGGAAACAAAGAAAACTC > SRR3722079.625940/1‑100 (MQ=60)
|
AGGCGTGTCATGATGTTGAAATCCATCGACATCTGCCCTGCCGTCAGTTTCGCTTTTACCACCTGGTCCGCTGCAAAGGCAAAAGGCTGGAACGGTTTTAAGGTATGGTTAAAGCGGTCTGCGCTTTCAAGGAGCATCTCGCCGCCTTCCAGCAACGTCACTATCCTTTCCATGCCGGGAAACAAAGAAAACTC > NZ_CP009273/1818860‑1819053
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
