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 |
1,068,442 |
A→C |
G323G (GGT→GGG) |
rutA ← |
pyrimidine utilization protein A |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,068,442 | 0 | A | C | 100.0%
| 57.5
/ NA
| 18 | G323G (GGT→GGG) | rutA | pyrimidine utilization protein A |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (5/13); total (5/13) |
CGCGGCATTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCACCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTACCGC > NZ_CP009273/1068354‑1068525
|
cgcgGCATTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGcccc > 1:667361/1‑91 (MQ=255)
cgcgGCATTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGcccc > 1:68527/1‑91 (MQ=255)
ttGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACg > 2:369453/1‑91 (MQ=255)
tGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCCCGCCTTCGGCCCCAGGCACGCTTGCGACt < 2:821612/91‑1 (MQ=255)
tGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACt < 2:401956/91‑1 (MQ=255)
tGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACt < 1:521026/91‑1 (MQ=255)
gcTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACAt > 2:416565/1‑91 (MQ=255)
cTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATg < 1:369453/91‑1 (MQ=255)
cGAAGGTTTCCATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATgcgcgc < 2:377780/91‑1 (MQ=255)
gTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGacac < 1:801880/91‑1 (MQ=255)
ttCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTg < 2:515969/91‑1 (MQ=255)
cccGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAg > 1:736188/1‑91 (MQ=255)
cgtcgAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGt < 2:329925/91‑1 (MQ=255)
cgAAGGTTAACAGCACGCCTTCGGCCCCTGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTccc < 2:464245/91‑1 (MQ=255)
gTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCCTCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCatat < 1:548420/91‑1 (MQ=255)
gTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCatat < 2:32735/91‑1 (MQ=255)
gCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGtt > 1:358160/1‑91 (MQ=255)
cGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATgcgcgc > 2:398059/1‑46 (MQ=255)
cGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATgcgcgc < 1:398059/46‑1 (MQ=255)
cTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTAccgc < 1:451687/91‑1 (MQ=255)
|
CGCGGCATTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCACCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTACCGC > NZ_CP009273/1068354‑1068525
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 28 ≤ 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
GGTAGATGGGCGCGGCATTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCACCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTACCGCCGAAGTGGGATCGGC > NZ_CP009273/1068344‑1068540
|
GGTAGATGGGCGCGGCATTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCC > SRR3722118.681819/1‑101 (MQ=60)
GGTAGATGGGCGCGGCATTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCC > SRR3722118.69795/1‑101 (MQ=60)
TAGATGGGCGCGGCATTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGGAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAG < SRR3722118.586044/101‑1 (MQ=60)
GCGCGGCATTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCT < SRR3722118.190234/101‑1 (MQ=60)
TGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACA < SRR3722118.532080/101‑1 (MQ=60)
CTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACAC < SRR3722118.377159/101‑1 (MQ=60)
cgtctcgtgggctcggagatgtgtataagagacAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCG < SRR3722118.406409/68‑1 (MQ=60)
GGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAG > SRR3722118.752373/1‑101 (MQ=60)
GTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGA < SRR3722118.819491/101‑1 (MQ=60)
aaaaaaAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACG < SRR3722118.755676/95‑1 (MQ=60)
AAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTT > SRR3722118.365602/1‑101 (MQ=60)
GTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCCTCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTAC < SRR3722118.560052/101‑1 (MQ=60)
CCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTACCGCCGAAGTGGG > SRR3722118.187325/1‑101 (MQ=60)
CCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTACCGCCGAAGTGGG > SRR3722118.253575/1‑101 (MQ=60)
CTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTACCGCCGAAGTGGGA < SRR3722118.461203/101‑1 (MQ=60)
GCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATctgtctcttatacacatctccgagcccacg > SRR3722118.655956/1‑71 (MQ=60)
|
GGTAGATGGGCGCGGCATTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCACCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTACCGCCGAAGTGGGATCGGC > NZ_CP009273/1068344‑1068540
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
