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 I208 R1
|
222 |
13.1 |
731276 |
96.6% |
706412 |
85.9 |
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%
| 39.8
/ NA
| 12 | T2A (ACC→GCC) | hemA | glutamyl‑tRNA reductase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (6/6); total (6/6) |
GATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGACCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTC > NZ_CP009273/1259103‑1259253
|
gATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTAt > 1:293670/1‑90 (MQ=255)
tCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCa < 1:187169/90‑1 (MQ=255)
tCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCa < 1:37593/90‑1 (MQ=255)
ttACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAAc > 1:135516/1‑90 (MQ=255)
tCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATaaaa > 1:357260/1‑90 (MQ=255)
tATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCa < 2:293670/90‑1 (MQ=255)
tgatgCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACGTGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCAcc < 1:203725/90‑1 (MQ=255)
aaGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATc < 2:125960/90‑1 (MQ=255)
aTCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACgtgt > 2:18556/1‑90 (MQ=255)
aTCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACgtgt > 2:73890/1‑90 (MQ=255)
tttCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGAt < 1:18556/90‑1 (MQ=255)
gCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTc > 1:73677/1‑90 (MQ=255)
|
GATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGACCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTC > NZ_CP009273/1259103‑1259253
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CTCCAAAAGGGGGCGCTCTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGACCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTCGATCAGGCGCTTG > NZ_CP009273/1259076‑1259266
|
CTCCAAAAGGGGGCGCTCTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCC < SRR3722090.65600/100‑1 (MQ=60)
CTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTAT > SRR3722090.297362/1‑100 (MQ=60)
TTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAAC > SRR3722090.136940/1‑100 (MQ=60)
ATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAA > SRR3722090.361913/1‑100 (MQ=60)
TCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAAC < SRR3722090.189192/100‑1 (MQ=60)
TCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAAC < SRR3722090.37980/100‑1 (MQ=60)
TGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACGTGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTG < SRR3722090.205986/100‑1 (MQ=60)
ATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTC > SRR3722090.74496/1‑100 (MQ=60)
TTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTCGATC < SRR3722090.18759/100‑1 (MQ=60)
GACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTCGATCAGGCGCTTG > SRR3722090.113761/1‑100 (MQ=60)
|
CTCCAAAAGGGGGCGCTCTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGACCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTCGATCAGGCGCTTG > NZ_CP009273/1259076‑1259266
|
| 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: ‑ |
