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 F4 I88 R1
|
217 |
30.5 |
1742422 |
95.9% |
1670982 |
87.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
552,665 |
T→C |
E178G (GAA→GGA) |
folD ← |
bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 552,665 | 0 | T | C | 100.0%
| 108.6
/ NA
| 30 | E178G (GAA→GGA) | folD | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (15/15); total (15/15) |
TCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTTCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAAC > NZ_CP009273/552587‑552743
|
tCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGTAACCTGCCAGCAGCAGTCCCATGCTCATCg > 1:530731/1‑91 (MQ=255)
tCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCg > 2:864739/1‑91 (MQ=255)
tCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCg > 2:585334/1‑91 (MQ=255)
gCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGggc < 1:228583/91‑1 (MQ=255)
tttCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGcc < 1:864739/91‑1 (MQ=255)
tgaCGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCg > 2:484179/1‑91 (MQ=255)
ttAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATca > 1:132456/1‑91 (MQ=255)
aGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATcacc > 1:725737/1‑91 (MQ=255)
gAAGCAGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCAt > 1:145937/1‑48 (MQ=38)
gAAGCAGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCAt < 2:145937/48‑1 (MQ=38)
aaGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACgg < 2:207036/91‑1 (MQ=255)
cACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCg > 2:745670/1‑91 (MQ=255)
aCTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGa < 2:302044/91‑1 (MQ=255)
aCTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGa < 1:204670/91‑1 (MQ=255)
aCTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGa < 2:379688/91‑1 (MQ=255)
cTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGaa < 1:585334/91‑1 (MQ=255)
tGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAg < 1:484179/91‑1 (MQ=255)
tGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAg < 1:748370/91‑1 (MQ=255)
aGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTa > 1:535888/1‑91 (MQ=255)
aGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTa < 2:420873/91‑1 (MQ=255)
gtggtgCAACCTGCCAGCAGCAGTCCCATGCTCATGGGGCGGCCAACGATATTCGATGCGCCAATCACCACg > 1:536802/1‑72 (MQ=255)
gtggtgCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACg < 2:536802/72‑1 (MQ=255)
tggtgCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATc < 1:509706/91‑1 (MQ=255)
gtgCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCaa > 2:688780/1‑91 (MQ=255)
aaCCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACgg < 1:454069/66‑1 (MQ=255)
aaCCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACgg > 2:454069/1‑66 (MQ=255)
aaCCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACg > 2:298693/1‑65 (MQ=255)
aaCCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACg < 1:298693/65‑1 (MQ=255)
gCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAAc > 1:823549/1‑91 (MQ=255)
gCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAAc > 1:236465/1‑91 (MQ=255)
|
TCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTTCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAAC > NZ_CP009273/552587‑552743
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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
GCCAACGGCAACGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTTCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATA > NZ_CP009273/552565‑552763
|
GCCAACGGCAACGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTC < SRR3722118.61704/101‑1 (MQ=60)
GATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGTAACCTGCCAGCAGCAGTCCCATGCTCATCG > SRR3722118.541988/1‑101 (MQ=60)
GCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGAT < SRR3722118.233202/101‑1 (MQ=60)
TTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTC < SRR3722118.883992/101‑1 (MQ=60)
ACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCA > SRR3722118.134968/1‑101 (MQ=60)
GCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACC > SRR3722118.741666/1‑101 (MQ=60)
GATTTTTAGTGAAGCAGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCtgtctcttatacacatctccgagcccacgaga > SRR3722118.148724/1‑69 (MQ=60)
tgtgtataagagacagGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGC < SRR3722118.304827/85‑1 (MQ=60)
gtgtataagagacagGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCC < SRR3722118.463635/86‑1 (MQ=60)
GAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTA > SRR3722118.547257/1‑101 (MQ=60)
AGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATGGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCtgtctctt > SRR3722118.548192/1‑93 (MQ=60)
ACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAAT < SRR3722118.208760/101‑1 (MQ=60)
CTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATG < SRR3722118.597748/101‑1 (MQ=60)
TGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGT < SRR3722118.494419/101‑1 (MQ=60)
TGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGT < SRR3722118.764800/101‑1 (MQ=60)
TGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAA < SRR3722118.520516/101‑1 (MQ=60)
GGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAAC > SRR3722118.241236/1‑101 (MQ=60)
GGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAAC > SRR3722118.841695/1‑101 (MQ=60)
GTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATA > SRR3722118.738747/1‑101 (MQ=60)
|
GCCAACGGCAACGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTTCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATA > NZ_CP009273/552565‑552763
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
