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 I207 R1
|
218 |
45.0 |
2482936 |
97.1% |
2410930 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,320,565 |
G→A |
Q521Q (CAG→CAA) |
yciQ → |
DUF2207 domain‑containing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,320,565 | 0 | G | A | 100.0%
| 50.3
/ NA
| 14 | Q521Q (CAG→CAA) | yciQ | DUF2207 domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (5/9); total (5/9) |
GCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAGCAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACAC > NZ_CP009273/1320479‑1320626
|
gCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGAcaacaa < 1:1103057/90‑1 (MQ=255)
gCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGAcaacaa > 1:820148/1‑90 (MQ=255)
gCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGAcaacaa > 2:73332/1‑90 (MQ=255)
cTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTg < 2:22045/90‑1 (MQ=255)
ttGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGc < 1:161379/90‑1 (MQ=255)
ccTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTAt < 2:820148/90‑1 (MQ=255)
gACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGacaaca < 1:608122/63‑1 (MQ=255)
gACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGacaaca > 2:608122/1‑63 (MQ=255)
ccGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTa > 1:392306/1‑90 (MQ=255)
ggTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAAc < 2:596012/90‑1 (MQ=255)
cACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCGCGGTGAAGCTATCGTTAACTATCTTgc > 2:1142690/1‑90 (MQ=255)
ggggTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAaga > 2:345415/1‑90 (MQ=255)
gTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGgc < 1:368079/90‑1 (MQ=255)
gTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGgc < 2:1019805/90‑1 (MQ=255)
atatTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGgcag < 2:85182/90‑1 (MQ=255)
atatTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGgcag < 1:73332/90‑1 (MQ=255)
ttCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAacac < 2:392306/90‑1 (MQ=255)
ttCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAacac > 2:1154438/1‑90 (MQ=255)
ttCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAacac > 1:1112858/1‑90 (MQ=255)
|
GCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAGCAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACAC > NZ_CP009273/1320479‑1320626
|
| 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
GTATATGCCAGCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAGCAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACACACAG > NZ_CP009273/1320469‑1320630
|
GTATATGCCAGCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAA > SRR3722089.831667/1‑100 (MQ=60)
atgtgtataagagacaGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCC < SRR3722089.615677/84‑1 (MQ=60)
GCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCC < SRR3722089.1119737/100‑1 (MQ=60)
GTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTA > SRR3722089.397088/1‑100 (MQ=60)
TTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAAC < SRR3722089.163388/100‑1 (MQ=60)
GGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACAC > SRR3722089.1129712/1‑100 (MQ=60)
GTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACACAC < SRR3722089.372602/100‑1 (MQ=60)
ATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACACACAG < SRR3722089.74224/100‑1 (MQ=60)
|
GTATATGCCAGCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAGCAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACACACAG > NZ_CP009273/1320469‑1320630
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
