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 |
747,264 |
T→C |
D124G (GAT→GGT) |
ybgQ ← |
fimbrial biogenesis outer membrane usher protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 747,264 | 0 | T | C | 100.0%
| 111.9
/ NA
| 30 | D124G (GAT→GGT) | ybgQ | fimbrial biogenesis outer membrane usher protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (19/11); total (19/11) |
GGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGATCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTT > NZ_CP009273/747191‑747347
|
gggAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCAtt > 2:711301/1‑91 (MQ=255)
ggAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCAttt > 1:658575/1‑91 (MQ=255)
gAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTc > 2:684710/1‑91 (MQ=255)
gAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTc > 1:493022/1‑91 (MQ=255)
gAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTc > 2:772631/1‑91 (MQ=255)
gAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGGTGCTGATTGGCTTGTCCGAAATTTAAGAGCTTTTc > 2:563364/1‑91 (MQ=255)
ttttCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCggg < 1:472403/91‑1 (MQ=255)
tCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAACAGCATTTCAGGTCGGGAAc < 2:524366/91‑1 (MQ=255)
cTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACt > 1:867779/1‑91 (MQ=255)
tGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAAt > 2:466994/1‑91 (MQ=255)
ccagccagGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATaca < 2:734618/91‑1 (MQ=255)
cagccagGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATacac < 2:38999/91‑1 (MQ=255)
agccagGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACAcc > 1:64909/1‑91 (MQ=255)
agccagGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACAcc < 1:706657/91‑1 (MQ=255)
aTACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCa > 2:694438/1‑91 (MQ=255)
tCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGaaa < 1:691684/56‑1 (MQ=255)
tCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGaaa > 2:691684/1‑56 (MQ=255)
tCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATc > 1:328852/1‑58 (MQ=255)
tCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATc < 2:328852/58‑1 (MQ=255)
tCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACg > 2:692504/1‑91 (MQ=255)
tCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACg < 1:466994/91‑1 (MQ=255)
tCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACg > 2:109674/1‑91 (MQ=255)
aGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGa < 1:711301/91‑1 (MQ=255)
gTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGat > 2:279223/1‑91 (MQ=255)
gTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGat > 2:633700/1‑91 (MQ=255)
gTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGat > 1:277792/1‑91 (MQ=255)
tGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTg < 1:734331/48‑1 (MQ=255)
tGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTg > 2:734331/1‑48 (MQ=255)
gCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATc > 2:656764/1‑91 (MQ=255)
cTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCt < 1:724257/91‑1 (MQ=255)
ggCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGtttt > 1:238377/1‑91 (MQ=255)
|
GGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGATCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTT > NZ_CP009273/747191‑747347
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 29 ≤ 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
GGCAACACCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGATCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGAC > NZ_CP009273/747164‑747364
|
GGCAACACCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGAC < SRR3722118.206781/101‑1 (MQ=60)
CTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAG < SRR3722118.457578/101‑1 (MQ=60)
TGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTT > SRR3722118.672829/1‑101 (MQ=60)
GTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTC > SRR3722118.503471/1‑101 (MQ=60)
GCGCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACT > SRR3722118.887108/1‑101 (MQ=60)
TTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATC < SRR3722118.482383/101‑1 (MQ=60)
tctcgtgggctcggagatgtgtataagagacagAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATAC < SRR3722118.750464/68‑1 (MQ=60)
gctcggagatgtgtataagagacagATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACT < SRR3722118.706757/76‑1 (MQ=60)
GTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACC > SRR3722118.66116/1‑101 (MQ=60)
AGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTG < SRR3722118.722095/101‑1 (MQ=60)
ATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGActgtctcttatacacatctccga > SRR3722118.335615/1‑78 (MQ=60)
CTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGAT > SRR3722118.283491/1‑101 (MQ=60)
TCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGT < SRR3722118.476844/101‑1 (MQ=60)
AGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTT < SRR3722118.726890/101‑1 (MQ=60)
GTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTT > SRR3722118.243190/1‑101 (MQ=60)
CTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAAC < SRR3722118.740147/101‑1 (MQ=60)
CCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGAC < SRR3722118.490262/101‑1 (MQ=60)
|
GGCAACACCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGATCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGAC > NZ_CP009273/747164‑747364
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
