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 I175 R1
|
221 |
18.5 |
1047116 |
95.1% |
995807 |
84.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,548,194 |
Δ1 bp |
coding (1150/1173 nt) |
iadA ← |
beta‑aspartyl‑peptidase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,548,192 | 0 | T | . | 95.5%
| 82.3
/ ‑1.6
| 22 | coding (1152/1173 nt) | iadA | beta‑aspartyl‑peptidase |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base . (11/10); total (11/11) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.86e-01 |
ACGTTTTACTCTGTCAGCCGCCCTTGCGGGCATTCTACGTCCATTCGGGCGGCTGACAACCGTTTAAGCCGTTTCAAACGTTCCTTTCACGCAGGCTTTGCCGTCTTTGACCATCAGTTTGCCGCGAGCGTATACCTGCTCAATGCGCAGTTCTGGCGTCATGA > NZ_CP009273/4548108‑4548271
|
aCGTTTTACTCTGTCAGCCGCCCTTGCGGGCATTCTACGTCCATTCGGGCGGCTGACAACCGTTTAAGCCGTTTCAAACGTTCCttcacg > 1:147196/1‑86 (MQ=255)
gTTTTACTCTGTCAGCCGCCCTTGCGGGCATTCTACGTCCATTCGGGCGGCTGACAACCGTTTAAGCCGTTTCAAACGTTCC‑TTCACGCa < 1:312631/90‑1 (MQ=255)
ttACTCTGTCAGCCGCCCTTGCGGGCATTCTACGTCCATTCGGGCGGCTGACAACCGTTTAAGCCGTTTCAAACGTTCC‑TTCACGCAGGc > 1:298477/1‑90 (MQ=255)
gTCAGCCGCCCTTGCGGGCATTCTACGTCCATTCGGGCGGCTGACAACCGTTTAAGCCGTTTCAAACGTTCC‑TTCACGCAGGCTTTGCCg > 1:12424/1‑90 (MQ=255)
gTCAGCCGCCCTTGCGGGCATTCTACGTCCATTCGGGCGGCTGACAACCGTTTAAGCCGTTTCAAACGTTCC‑TTCACGCAGGCTTTGCCg > 2:489185/1‑90 (MQ=255)
ccgccCTTGCGGGCATTCTACGTCCATTCGGGCGGCTGACAACCGTTTAAGCCGTTTCAAACGTTCC‑TTCACGCAGGCTTTGCCGTCttt < 1:21122/90‑1 (MQ=255)
cccTTGCGGGCATTCTACGTCCATTCGGGCGGCTGACAACCGTTTAAGCCGTTTCAAACGTTCC‑TTCACGCAGGCTTTGCCGTCTTTGAc > 1:515467/1‑90 (MQ=255)
cTTGCGGGCATTCTACGTCCATTCGGGCGGCTGACAACCGTTTAAGCCGTTTCAAACGTTCC‑TTCACGCAGGCTTTGCCGTCTTTGACCa > 1:390374/1‑90 (MQ=255)
ttGCGGGCATTCTACGTCCATTCGGGCGGCTGACAACCGTTTAAGCCGTTTCAAACGTTCC‑TTCACGCAGGCTTTGCCGTCTTTGACCAt > 1:88025/1‑90 (MQ=255)
cATTCTACGTCCATTCGGGCGGCTGACAACCGTTTAAGCCGTTTCAAACGTTCC‑TTCACGCAGGCTTTGCCGTCTTTGACCATCAGTTTg > 1:443261/1‑90 (MQ=255)
cTACGTCCATTCGGGCGGCTGACAACCGTTTAAGCCGTTTCAAACGTTCC‑TTCACGCAGGCTTTGCCGTCTTTGACCATCAGTTTGCcgc < 2:515467/90‑1 (MQ=255)
tACGTCCATTCGGGCGGCTGACAACCGTTTAAGCCGTTTCAAACGTTCC‑TTCACGCAGGCTTTGCCGTCTTTGACCATCAGTTTGCcgcg < 2:147196/90‑1 (MQ=255)
aCGTCCATTCGGGCGGCTGACAACCGTTTAAGCCGTTTCAAACGTTCCTTTCACGCAGGCTTTGCCGTCTTTGACCATCAGTTTGCcgcg < 2:306713/90‑1 (MQ=255)
ccATTCGGGCGGCTGACAACCGTTTAAGCCGTTTCAAACGTTCC‑TTCACGCAGGCTTTGCCGTCTTTGACCATCAGTTTGCCGCGAGCGt < 2:88025/90‑1 (MQ=255)
aTTCGGGCGGCTGACAACCGTTTAAGCCGTTTCAAACGTTCC‑TTCACGCAGGCTTTGCCGTCTTTGACCATCAGTTTGCCGCGAGCGtat > 1:64373/1‑90 (MQ=255)
aTTCGGGCGGCTGACAACCGTTTAAGCCGTTTCAAACGTTCC‑TTCACGCAGGCTTTGCCGTCTTTGACCATCAGTTTGCCGCGAGCGtat > 1:235339/1‑90 (MQ=255)
tGACAACCGTTTAAGCCGTTTCAAACGTTCC‑TTCACGCAGGCTTTGCCGTCTTTGACCATCAGTTTGCCGCGAGCGTATACCTGCTCAAt > 1:451699/1‑90 (MQ=255)
aaCCGTTTAAGCCGTTTCAAACGTTCC‑TTCACGCAGGCTTTGCCGTCTTTGACCATCAGTTTGCCGCGAGCGTATACCTGCTCAATgcgc < 2:453264/90‑1 (MQ=255)
aaCCGTTTAAGCCGTTTCAAACGTTCC‑TTCACGCAGGCTTTGCCGTCTTTGACCATCAGTTTGCCGCGAGCGTATACCTGCTCAATgcgc < 2:518527/90‑1 (MQ=255)
gTTTAAGCCGTTTCAAACGTTCC‑TTCACGCAGGCTTTGCCGTCTTTGACCATCAGTTTGCCGCGAGCGTATACCTGCTCAATGCGCAGtt > 2:86999/1‑90 (MQ=255)
aaGCCGTTTCAAACGTTCC‑TTCACGCAGGCTTTGCCGTCTTTGACCATCAGTTTGCCGCGAGCGTATACCTGCTCAATGCGCAGTTCTgg < 1:64898/90‑1 (MQ=255)
tCAAACGTTCC‑TTCACGCAGGCTTTGCCGTCTTTGACCATCAGTTTGCCGCGAGCGTATACCTGCTCAATGCGCAGTTCTGGCGTCATGa < 1:489185/90‑1 (MQ=255)
tCAAACGTTCC‑TTCACGCAGGCTTTGCCGTCTTTGACCATCAGTTTGCCGCGAGCGTATACCTGCTCAATGCGCAGTTCTGGCGTCATGa < 1:13065/90‑1 (MQ=255)
|
ACGTTTTACTCTGTCAGCCGCCCTTGCGGGCATTCTACGTCCATTCGGGCGGCTGACAACCGTTTAAGCCGTTTCAAACGTTCCTTTCACGCAGGCTTTGCCGTCTTTGACCATCAGTTTGCCGCGAGCGTATACCTGCTCAATGCGCAGTTCTGGCGTCATGA > NZ_CP009273/4548108‑4548271
|
| 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
GTCATCCATTACGTTTTACTCTGTCAGCCGCCCTTGCGGGCATTCTACGTCCATTCGGGCGGCTGACAACCGTTTAAGCCGTTTCAAACGTTCCTTTCACGCAGGCTTTGCCGTCTTTGACCATCAGTTTGCCGCGAGCGTATACCTGCTCAATGCGCAGTTCTGGCGTCATGACCAGCAAGTCAGCATCA > NZ_CP009273/4548098‑4548288
|
GTCATCCATTACGTTTTACTCTGTCAGCCGCCCTTGCGGGCATTCTACGTCCATTCGGGCGGCTGACAACCGTTTAAGCCGTTTCAAACGTTCC‑TTCACG > SRR3722048.149325/1‑100 (MQ=60)
CCATTACGTTTTACTCTGTCAGCCGCCCTTGCGGGCATTCTACGTCCATTCGGGCGGCTGACAACCGTTTAAGCCGTTTCAAACGTTCC‑TTCACGCAGGC > SRR3722048.302944/1‑100 (MQ=60)
GTTTTACTCTGTCAGCCGCCCTTGCGGGCATTCTACGTCCATTCGGGCGGCTGACAACCGTTTAAGCCGTTTCAAACGTTCC‑TTCACGCAGGCTTTGCCG > SRR3722048.12582/1‑100 (MQ=60)
GTTTTACTCTGTCAGCCGCCCTTGCGGGCATTCTACGTCCATTCGGGCGGCTGACAACCGTTTAAGCCGTTTCAAACGTTCC‑TTCACGCAGGCTTTGCCG < SRR3722048.317348/100‑1 (MQ=60)
CTGTCAGCCGCCCTTGCGGGCATTCTACGTCCATTCGGGCGGCTGACAACCGTTTAAGCCGTTTCAAACGTTCC‑TTCACGCAGGCTTTGCCGTCTTTGAC > SRR3722048.523987/1‑100 (MQ=60)
GTCAGCCGCCCTTGCGGGCATTCTACGTCCATTCGGGCGGCTGACAACCGTTTAAGCCGTTTCAAACGTTCC‑TTCACGCAGGCTTTGCCGTCTTTGACCA > SRR3722048.396682/1‑100 (MQ=60)
TCAGCCGCCCTTGCGGGCATTCTACGTCCATTCGGGCGGCTGACAACCGTTTAAGCCGTTTCAAACGTTCC‑TTCACGCAGGCTTTGCCGTCTTTGACCAT > SRR3722048.89291/1‑100 (MQ=60)
CCGCCCTTGCGGGCATTCTACGTCCATTCGGGCGGCTGACAACCGTTTAAGCCGTTTCAAACGTTCC‑TTCACGCAGGCTTTGCCGTCTTTGACCATCAGT < SRR3722048.21411/100‑1 (MQ=60)
CCCTTGCGGGCATTCTACGTCCATTCGGGCGGCTGACAACCGTTTAAGCCGTTTCAAACGTTCC‑TTCACGCAGGCTTTGCCGTCTTTGACCATCAGTTTG > SRR3722048.450535/1‑100 (MQ=60)
TTCTACGTCCATTCGGGCGGCTGACAACCGTTTAAGCCGTTTCAAACGTTCC‑TTCACGCAGGCTTTGCCGTCTTTGACCATCAGTTTGCCGCGAGCGTAT > SRR3722048.238628/1‑100 (MQ=60)
TTCTACGTCCATTCGGGCGGCTGACAACCGTTTAAGCCGTTTCAAACGTTCC‑TTCACGCAGGCTTTGCCGTCTTTGACCATCAGTTTGCCGCGAGCGTAT > SRR3722048.65287/1‑100 (MQ=60)
TTCGGGCGGCTGACAACCGTTTAAGCCGTTTCAAACGTTCC‑TTCACGCAGGCTTTGCCGTCTTTGACCATCAGTTTGCCGCGAGCGTATACCTGCTCAAT > SRR3722048.459140/1‑100 (MQ=60)
gaggtctcgtgggctcggagatgtgtataagagacagccTTCACGCAGGCTTTGCCGTCTTTGACCATCAGTTTGCCGCGAGCGTATACCTGCTCAATGC < SRR3722048.133783/61‑1 (MQ=60)
AAGCCGTTTCAAACGTTCC‑TTCACGCAGGCTTTGCCGTCTTTGACCATCAGTTTGCCGCGAGCGTATACCTGCTCAATGCGCAGTTCTGGCGTCATGACC < SRR3722048.65818/100‑1 (MQ=60)
TTTCAAACGTTCC‑TTCACGCAGGCTTTGCCGTCTTTGACCATCAGTTTGCCGCGAGCGTATACCTGtctcttatacacatctccgagcccacgagacctc > SRR3722048.156567/1‑66 (MQ=60)
TTTCAAACGTTCC‑TTCACGCAGGCTTTGCCGTCTTTGACCATCAGTTTGCCGCGAGCGTATACCTGCTCAATGCGCAGTTCTGGCGTCATGACCAGCAAG > SRR3722048.281138/1‑100 (MQ=60)
TCAAACGTTCC‑TTCACGCAGGCTTTGCCGTCTTTGACCATCAGTTTGCCGCGAGCGTATACCTGCTCAATGCGCAGTTCTGGCGTCATGACCAGCAAGTC < SRR3722048.497273/100‑1 (MQ=60)
TCAAACGTTCC‑TTCACGCAGGCTTTGCCGTCTTTGACCATCAGTTTGCCGCGAGCGTATACCTGCTCAATGCGCAGTTCTGGCGTCATGACCAGCAAGTC < SRR3722048.13229/100‑1 (MQ=60)
TTCC‑TTCACGCAGGCTTTGCCGTCTTTGACCATCAGTTTGCCGCGAGCGTATACCTGCTCAATGCGCAGTTCTGGCGTCATGACCAGCAAGTCAGCATCA > SRR3722048.30134/1‑100 (MQ=60)
TTCC‑TTCACGCAGGCTTTGCCGTCTTTGACCATCAGTTTGCCGCGAGCGTATACCTGCTCAATGCGCAGTTCTGGCGTCATGACCAGCAAGTCAGCATCA > SRR3722048.60088/1‑100 (MQ=60)
|
GTCATCCATTACGTTTTACTCTGTCAGCCGCCCTTGCGGGCATTCTACGTCCATTCGGGCGGCTGACAACCGTTTAAGCCGTTTCAAACGTTCCTTTCACGCAGGCTTTGCCGTCTTTGACCATCAGTTTGCCGCGAGCGTATACCTGCTCAATGCGCAGTTCTGGCGTCATGACCAGCAAGTCAGCATCA > NZ_CP009273/4548098‑4548288
|
| 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: ‑ |
