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 I205 R1
|
220 |
17.5 |
961422 |
97.1% |
933540 |
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%
| 51.3
/ NA
| 16 | T2A (ACC→GCC) | hemA | glutamyl‑tRNA reductase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (9/7); total (9/7) |
GGGCGCTCTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGACCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCG > NZ_CP009273/1259086‑1259235
|
gggCGCTCTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGcc < 1:3771/90‑1 (MQ=255)
gATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTAt > 1:168791/1‑90 (MQ=255)
tCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCa < 1:227365/90‑1 (MQ=255)
tCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCa < 2:479786/90‑1 (MQ=255)
ccTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAAc < 2:168791/90‑1 (MQ=255)
tATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCa < 2:293932/90‑1 (MQ=255)
atgCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCa < 1:441762/86‑1 (MQ=255)
atgCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCa > 2:441762/1‑86 (MQ=255)
atgCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTCTAGCACTCGGTATCAAACATAAAACGGCACCTg > 2:217825/1‑90 (MQ=255)
aGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCg > 1:354107/1‑90 (MQ=255)
cAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCt > 1:252919/1‑90 (MQ=255)
gACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCAt < 1:60426/68‑1 (MQ=255)
gACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCAt > 2:60426/1‑68 (MQ=255)
aTCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACgtgt > 2:164824/1‑90 (MQ=255)
aTCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACgtgt > 2:425159/1‑90 (MQ=255)
aCGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCg > 1:140144/1‑90 (MQ=255)
|
GGGCGCTCTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGACCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCG > NZ_CP009273/1259086‑1259235
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ 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
GGGCGCTCTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGACCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTCGATCAGGCGCTTGACAGCC > NZ_CP009273/1259086‑1259272
|
GGGCGCTCTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCAC < SRR3722087.3808/100‑1 (MQ=60)
CTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTAT > SRR3722087.170327/1‑100 (MQ=60)
TCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAAC < SRR3722087.229438/100‑1 (MQ=60)
tataagagacagGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCAC < SRR3722087.60947/88‑1 (MQ=60)
GTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCG > SRR3722087.358084/1‑100 (MQ=60)
TATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGC < SRR3722087.446922/100‑1 (MQ=60)
ATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCT > SRR3722087.255368/1‑100 (MQ=60)
AACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCG > SRR3722087.141442/1‑100 (MQ=60)
GCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTCGATCAGGCGCTTGACAGCC < SRR3722087.97203/100‑1 (MQ=60)
|
GGGCGCTCTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGACCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTCGATCAGGCGCTTGACAGCC > NZ_CP009273/1259086‑1259272
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
