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 F5 I102 R1
|
278 |
39.1 |
2251254 |
95.8% |
2156701 |
87.1 |
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%
| 80.0
/ NA
| 25 | G323G (GGT→GGG) | rutA | pyrimidine utilization protein A |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (10/15); total (10/15) |
CGCGGCATTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCACCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTACCGCC > NZ_CP009273/1068354‑1068526
|
cgcgGCATTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGcccc > 1:690742/1‑91 (MQ=255)
gcgGCATTGCATCAGTGGTTGAATGCGCTCGCCGCAGGTTTCGATTCCCGACAGAAACTCGTCGAAGGTTAACAGCCCGCCTTCGGCCCCa > 2:648358/1‑91 (MQ=255)
gcgGCATTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCa > 2:246649/1‑91 (MQ=255)
tCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGc < 2:472198/91‑1 (MQ=255)
ttgTTAAATGCGCTCGCCGAAGGTGTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACt < 1:499722/89‑1 (MQ=255)
tGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACt < 2:990976/91‑1 (MQ=255)
ggTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGTAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACtt > 1:1053487/1‑91 (MQ=255)
ttGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCa > 2:588251/1‑91 (MQ=255)
tGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCAt > 1:266653/1‑91 (MQ=255)
gcgcTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAAc > 2:1096131/1‑91 (MQ=255)
gcTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACAt > 1:157258/1‑91 (MQ=255)
gcTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACAt > 1:685224/1‑91 (MQ=255)
cTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATg < 2:157258/91‑1 (MQ=255)
cGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATgcgcgc < 1:352365/91‑1 (MQ=255)
cGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATgcgcgc < 1:305417/91‑1 (MQ=255)
aCAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAAcc < 1:861681/91‑1 (MQ=255)
aTCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAAc < 1:760133/91‑1 (MQ=255)
gtcgAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTc > 2:1072298/1‑91 (MQ=255)
cgAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTccc < 2:75214/91‑1 (MQ=255)
cgAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTccc < 2:803051/91‑1 (MQ=255)
cgAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCAACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTccc < 2:672640/91‑1 (MQ=255)
cACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGttt < 2:690742/91‑1 (MQ=255)
aCGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTa > 1:430722/1‑91 (MQ=255)
cGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTAc > 1:846831/1‑91 (MQ=255)
cGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTAc < 1:690336/91‑1 (MQ=255)
cTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTAccgc < 2:314327/91‑1 (MQ=255)
ttCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTAccgcc < 1:509105/91‑1 (MQ=255)
|
CGCGGCATTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCACCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTACCGCC > NZ_CP009273/1068354‑1068526
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ 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
GGTAGATGGGCGCGGCATTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCACCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTACCGCCGAAGTGGGAT > NZ_CP009273/1068344‑1068536
|
GGTAGATGGGCGCGGCATTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCC > SRR3722125.705630/1‑101 (MQ=60)
TTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGTAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTT > SRR3722125.1077152/1‑101 (MQ=60)
CATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCAT > SRR3722125.272020/1‑101 (MQ=60)
TTGTTAAATGCGCTCGCCGAAGGTGTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACA < SRR3722125.510299/101‑1 (MQ=60)
GGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACAT > SRR3722125.160264/1‑101 (MQ=60)
GGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACAT > SRR3722125.700008/1‑101 (MQ=60)
CGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCG < SRR3722125.311677/101‑1 (MQ=60)
CGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCG < SRR3722125.359738/101‑1 (MQ=60)
ACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTC < SRR3722125.880689/101‑1 (MQ=60)
ATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATAT < SRR3722125.776590/101‑1 (MQ=60)
GGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTA > SRR3722125.439800/1‑101 (MQ=60)
GTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTAC > SRR3722125.865464/1‑101 (MQ=60)
CGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTACCGCCGAAGTG < SRR3722125.705216/101‑1 (MQ=60)
TTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTACCGCCGAAGTGGGAT < SRR3722125.519905/101‑1 (MQ=60)
|
GGTAGATGGGCGCGGCATTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCACCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTACCGCCGAAGTGGGAT > NZ_CP009273/1068344‑1068536
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
