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 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
86.4 |
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 | 89.5%
| 46.0
/ ‑0.8
| 19 | T2A (ACC→GCC) | hemA | glutamyl‑tRNA reductase |
| Reads supporting (aligned to +/- strand): ref base A (0/2); new base G (12/5); total (12/7) |
| Fisher's exact test for biased strand distribution p-value = 1.23e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01 |
GGGCGCTCTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGACCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTCGATCAGGC > NZ_CP009273/1259086‑1259261
|
gggCGCTCTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGcc > 2:532499/1‑90 (MQ=255)
gggCGCTCTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGcc > 2:265068/1‑90 (MQ=255)
gcTCTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCttt > 2:56592/1‑90 (MQ=255)
ttATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGACCCTTTTAGCACTc < 1:128688/90‑1 (MQ=255)
gATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTAt > 2:698602/1‑90 (MQ=255)
gATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTAt > 2:208891/1‑90 (MQ=255)
gATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTAt > 1:7666/1‑90 (MQ=255)
tCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCa < 2:559462/90‑1 (MQ=255)
tCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCa < 2:629194/90‑1 (MQ=255)
cTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACg < 1:142216/90‑1 (MQ=255)
tATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCa < 2:577805/90‑1 (MQ=255)
gatgCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCt > 1:203442/1‑90 (MQ=255)
gACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGc > 2:28329/1‑90 (MQ=255)
cccTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAAc < 1:368062/90‑1 (MQ=255)
aTCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACgtgt > 1:423769/1‑90 (MQ=255)
aTCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACgtgt > 2:449883/1‑90 (MQ=255)
aTCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACgtgt > 2:623753/1‑90 (MQ=255)
ccGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGc > 2:107081/1‑90 (MQ=255)
gACCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTCGATCAGgc < 1:286976/90‑1 (MQ=255)
|
GGGCGCTCTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGACCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTCGATCAGGC > NZ_CP009273/1259086‑1259261
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ 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
CTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGACCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTCGATCAGGCGCTTGACAGC > NZ_CP009273/1259093‑1259271
|
CTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTAT > SRR3722112.7763/1‑100 (MQ=60)
TTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGACCCTTTTAGCACTCGGTATCAACC < SRR3722112.130285/100‑1 (MQ=60)
GATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCT > SRR3722112.205915/1‑100 (MQ=60)
CTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTAT < SRR3722112.143998/100‑1 (MQ=60)
GACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGT > SRR3722112.429423/1‑100 (MQ=60)
CCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTT < SRR3722112.372796/100‑1 (MQ=60)
CATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTCGATCAGGCGCTTGAC > SRR3722112.39257/1‑100 (MQ=60)
GACCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTCGATCAGGCGCTTGACAGC < SRR3722112.290309/100‑1 (MQ=60)
|
CTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGACCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTCGATCAGGCGCTTGACAGC > NZ_CP009273/1259093‑1259271
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
