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 I210 R1
|
226 |
19.6 |
1130256 |
95.4% |
1078264 |
84.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,682,423 |
G→C |
A71G (GCC→GGC) |
fumB ← |
class I fumarate hydratase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,682,423 | 0 | G | C | 100.0%
| 38.6
/ NA
| 13 | A71G (GCC→GGC) | fumB | class I fumarate hydratase |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base C (9/4); total (9/4) |
CCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCATCATGAAACGCCTGGCGCGCCAACAGAGTTAACGC > NZ_CP009273/1682336‑1682499
|
ccTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGccc > 2:381567/1‑90 (MQ=255)
gTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGCCCACCTGTTGTTGGTg < 2:120945/90‑1 (MQ=255)
tACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGccc > 1:293978/1‑68 (MQ=255)
tACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGCCCACCTGTTGTTGGTGCGCCGGAc > 2:130516/1‑90 (MQ=255)
tACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGCCCACCTGTTGTTGGTGCGCCGGAc > 2:316951/1‑90 (MQ=255)
tACGCAGGAATTGCAGCGCCACACATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGccc < 2:293978/68‑1 (MQ=255)
aCGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGCCCACCTGTTGTTGGTGCGCCGGACg < 2:181261/90‑1 (MQ=255)
tGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGCCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAac < 2:428386/90‑1 (MQ=255)
gcCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGCCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGca > 1:82915/1‑90 (MQ=255)
acaTATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGCCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAac < 1:189265/81‑1 (MQ=255)
acaTATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGCCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAac > 2:189265/1‑81 (MQ=255)
tATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGCCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCATCATGAAACg > 2:9886/1‑90 (MQ=255)
tttCGCTGGCCTCCGGGTCACGCAGAATGTCGCCCACCTGTTGTTGGTCCGCCGGACGCAGCATGAACGACGCATCATGAAACGCCCGgc > 1:316379/1‑90 (MQ=255)
ccGGGTCACGCAGAATGTCGCCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCATCATGAAACGCCTGGCGCGCCAACagag > 1:363879/1‑90 (MQ=255)
aCGCAGAATGTCGCCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCATCATGAAACGCCTGGCGCGCCAACAGAGTTAACGc > 1:188697/1‑90 (MQ=255)
aCGCAGAATGTCGCCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCATCATGAAACGCCTGGCGCGCCAACAGAGTTAACGc > 2:134405/1‑90 (MQ=255)
|
CCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCATCATGAAACGCCTGGCGCGCCAACAGAGTTAACGC > NZ_CP009273/1682336‑1682499
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCATCATGAAACGCCTGGCGCGCCAACAGAGTTAACGC > NZ_CP009273/1682348‑1682499
|
ATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGCCCACCTGTTGTTctgtctcttatg > SRR3722092.299108/1‑88 (MQ=60)
GAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGCCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCA > SRR3722092.84332/1‑100 (MQ=60)
TGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGCCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCATCAT < SRR3722092.192411/100‑1 (MQ=60)
TATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGCCCACCTGTTGTTGGTCCGCCGGACGCAGCATGAACGACGCATCATGAAACGCCCGGC > SRR3722092.321972/1‑100 (MQ=60)
TCGCTGGCCTCCGGGTCACGCAGAATGTCGCCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCATCATGAAACGCCTGGCGCGCCAACAGAG > SRR3722092.370650/1‑100 (MQ=60)
CCTCCGGGTCACGCAGAATGTCGCCCACCTGTTGTTGGTGCGCCGGACGCctgtctcttatacacatctgacgctgccgacgaccatcttagtgtagatc > SRR3722092.517958/1‑50 (MQ=60)
CCTCCGGGTCACGCAGAATGTCGCCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCATCATGAAACGCCTGGCGCGCCAACAGAGTTAACGC > SRR3722092.191834/1‑100 (MQ=60)
|
ATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCATCATGAAACGCCTGGCGCGCCAACAGAGTTAACGC > NZ_CP009273/1682348‑1682499
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
