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 I225 R1
|
227 |
21.4 |
1179702 |
97.1% |
1145490 |
86.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,259,173 |
A→G |
T2A (ACC→GCC) |
hemA → |
glutamyl‑tRNA reductase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,259,173 | 0 | A | G | 100.0%
| 58.9
/ NA
| 19 | T2A (ACC→GCC) | hemA | glutamyl‑tRNA reductase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (14/5); total (14/5) |
GGGCGCTCTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGACCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTCGAT > NZ_CP009273/1259086‑1259256
|
gggCGCTCTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGcc > 2:526887/1‑90 (MQ=255)
gggCGCTCTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGcc > 2:164012/1‑90 (MQ=255)
gggCGCTCTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGcc > 1:388310/1‑90 (MQ=255)
ttATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTc < 1:526887/90‑1 (MQ=255)
tCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCa < 2:488264/90‑1 (MQ=255)
atgCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTg > 1:507981/1‑90 (MQ=255)
tgCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGt > 1:277392/1‑90 (MQ=255)
aGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCg > 1:346962/1‑90 (MQ=255)
aGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCg > 2:338250/1‑90 (MQ=255)
gACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGc > 1:293964/1‑87 (MQ=255)
gACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGc < 2:293964/87‑1 (MQ=255)
aaCCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCgaga < 1:536166/90‑1 (MQ=255)
aCCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGaa > 2:134768/1‑90 (MQ=255)
cTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACgt > 2:202103/1‑90 (MQ=255)
aTCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACgtgt > 1:493954/1‑90 (MQ=255)
cccGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAg > 1:511383/1‑90 (MQ=255)
ccGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGc < 1:463228/81‑1 (MQ=255)
ccGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGc > 2:463228/1‑81 (MQ=255)
gACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTCGAt > 1:187693/1‑90 (MQ=255)
|
GGGCGCTCTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGACCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTCGAT > NZ_CP009273/1259086‑1259256
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CTCCAAAAGGGGGCGCTCTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGACCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTCGAT > NZ_CP009273/1259076‑1259256
|
CTCCAAAAGGGGGCGCTCTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCC > SRR3722109.393866/1‑100 (MQ=60)
TTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACC < SRR3722109.534911/100‑1 (MQ=60)
ATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTG > SRR3722109.515671/1‑100 (MQ=60)
TCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGT > SRR3722109.280885/1‑100 (MQ=60)
GTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCG > SRR3722109.351617/1‑100 (MQ=60)
GATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGC > SRR3722109.297741/1‑100 (MQ=60)
GACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGT > SRR3722109.501414/1‑100 (MQ=60)
AACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCG < SRR3722109.544326/100‑1 (MQ=60)
GGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAG > SRR3722109.519128/1‑100 (MQ=60)
TATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCT < SRR3722109.470181/100‑1 (MQ=60)
ATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTCGAT > SRR3722109.189994/1‑100 (MQ=60)
|
CTCCAAAAGGGGGCGCTCTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGACCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTCGAT > NZ_CP009273/1259076‑1259256
|
| 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: ‑ |
