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 I208 R1
|
222 |
13.1 |
731276 |
96.6% |
706412 |
85.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,673,785 |
T→C |
intergenic (+157/‑29) |
ydgH → / → ydgI |
DUF1471 family protein YdgH/amino acid permease |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,673,785 | 0 | T | C | 100.0%
| 47.3
/ NA
| 14 | intergenic (+157/‑29) | ydgH/ydgI | DUF1471 family protein YdgH/amino acid permease |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (5/9); total (5/9) |
GCATGCAGACACATCTCTTCGTAAAATCCCGCGCTTCAGTGGCAAACTCCATTTTTATGCGTTTTGCCCTAATATTTATTCTTCTTATCACGTTTTAATCACTGGATATCGATGGAAAAGAAACTGGGACTGAGCGCACTCACCGCGCTGGTATTAAGCTCA > NZ_CP009273/1673703‑1673864
|
gcatgcaGACACATCTCTTCGTAAAATCCCGCGCTTCAGTGGCAAACTCCATTTTTATGCGTTTTGCCCTAATATTTATTCTCCTTATCa < 1:49037/90‑1 (MQ=255)
atgcaGACACATCTCTTCGTAAAATCCCGCGCTTCAGTGGCAAACTCCATTTTTATGCGTTTTGCCCTAATATTTATTCTCCTTATCACg > 1:86017/1‑90 (MQ=255)
atgcaGACACATCTCTTCGTAAAATCCCGCGCTTCAGTGGCAAACTCCATTTTTATGCGTTTTGCCCTAATATTTATTCTCCTTATCACg < 2:175347/90‑1 (MQ=255)
aTCTCTTCGTAAAATCCCGCGCTTCAGTGGCAAACTCCATTTTTATGCGTTTTGCCCTAATATTTATTCTCCTTATCACGTTTTAATCAc > 1:274381/1‑90 (MQ=255)
gTAAAATCCCGCGCTTCAGTGGCAAACTCCATTTTTATGCGTTTTGCCCTAATATTTAATCTCCTTATCACGTTTTAATCACTGGATATc < 1:224303/90‑1 (MQ=255)
aaaTCCCGCGCTTCAGTGGCAAACTCCATTTTTATGCGTTTTGCCCTAATATTTATTCTCCTTATCACGTTTTAATCACTGGATATCGAt > 2:222558/1‑90 (MQ=255)
gcgcTTCAGTGGCAAACTCCATTTTTATGCGTTTTGCCCTAATATTTATTCTCCTTATCACGTTTTAATCACTGGATATCGATGGAAAAg < 2:73219/90‑1 (MQ=255)
gcgcTTCAGTGGCAAACTCCATTTTTATGCGTTTTGCCCTAATATTTATTCTCCTTATCACGTTTTAATCACTGGATATCGATGGAAAAg < 2:95808/90‑1 (MQ=255)
gcTTCAGTGGCAAACTCCATTTTTATGCGTTTTGCCCTAATATTTATTCTCCTTATCACGTTTTAATCACTGGATATCGATGGAAAAGaa < 1:42682/90‑1 (MQ=255)
cAGTGGCAAACTCCATTTTTATGCGTTTTGCCCTAATATTTATTCTCCTTATCACGTTTTAATCACTGGATATCGATGGAAAAGAAACTg < 2:154659/90‑1 (MQ=255)
tCCATTTTTATGCGTTTTGCCCTAATATTTATTCTCCTTATCACGTTTTAATCACTGGATATCGATGGAAAAGAAACTGGGACTGAgcgc < 1:121265/90‑1 (MQ=255)
gCGTTTTGCCCTAATATTTATTCTCCTTATCACGTTTTAATCACTGGATATCGATGGAAAAGAAACTGGGACTGAGCGCACTCACCgcgc > 2:348669/1‑90 (MQ=255)
aaTATTTATTCTCCTTATCACGTTTTAATCACTGGATATCGATGGAAAAGAAACTGGGACTGAGCGCACTCACCGCGCTGGTATTAAGCt > 1:18079/1‑90 (MQ=255)
tatttattCTCCTTATCACGTTTTAATCACTGGATATCGATGGAAAAGAAACTGGGACTGAGCGCACTCACCGCGCTGGTATTAAGCTCa < 2:86017/90‑1 (MQ=255)
|
GCATGCAGACACATCTCTTCGTAAAATCCCGCGCTTCAGTGGCAAACTCCATTTTTATGCGTTTTGCCCTAATATTTATTCTTCTTATCACGTTTTAATCACTGGATATCGATGGAAAAGAAACTGGGACTGAGCGCACTCACCGCGCTGGTATTAAGCTCA > NZ_CP009273/1673703‑1673864
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ 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
CGACCATTGCATGCAGACACATCTCTTCGTAAAATCCCGCGCTTCAGTGGCAAACTCCATTTTTATGCGTTTTGCCCTAATATTTATTCTTCTTATCACGTTTTAATCACTGGATATCGATGGAAAAGAAACTGGGACTGAGCGCACTCACCGCGCTGGTATTAAGCTCAATGCTGGGCGCGGGT > NZ_CP009273/1673695‑1673879
|
CGACCATTGCATGCAGACACATCTCTTCGTAAAATCCCGCGCTTCAGTGGCAAACTCCATTTTTATGCGTTTTGCCCTAATATTTATTCTCCTTATCACG > SRR3722090.86965/1‑100 (MQ=60)
GCATGCAGACACATCTCTTCGTAAAATCCCGCGCTTCAGTGGCAAACTCCATTTTTATGCGTTTTGCCCTAATATTTATTCTCCTTATCACGTTTTAATC < SRR3722090.49559/100‑1 (MQ=60)
ATGCAGACACATCTCTTCGTAAAATCCCGCGCTTCAGTGGCAAACTCCATTTTTATGCGTTTTGCCCTAATATTTATTCTCCTTATCACGTTTTAATCAC > SRR3722090.277784/1‑100 (MQ=60)
GTAAAATCCCGCGCTTCAGTGGCAAACTCCATTTTTATGCGTTTTGCCCTAATATTTAATCTCCTTATCACGTTTTAATCACTGGATATCGATGGAAAAG < SRR3722090.226859/100‑1 (MQ=60)
gctcaggagtctcgtgggctcggagatgtgtataagagacagTATTTATTCTCCTTATCACGTTTTAATCACTGGATATCGATGGAAAAGAAACTGGGAC < SRR3722090.195427/58‑1 (MQ=60)
GCTTCAGTGGCAAACTCCATTTTTATGCGTTTTGCCCTAATATTTATTCTCCTTATCACGTTTTAATCACTGGATATCGATGGAAAAGAAACTGGGACTG < SRR3722090.43120/100‑1 (MQ=60)
TCCATTTTTATGCGTTTTGCCCTAATATTTATTCTCCTTATCACGTTTTAATCACTGGATATCGATGGAAAAGAAACTGGGACTGAGCGCACTCACCGCG < SRR3722090.122554/100‑1 (MQ=60)
GTTTTGCCCTAATATTTATTCTCCTTATCACGTTTTAATCACTGGATATCGATGGAAAAGAAACTGGGACTGAGCGCACTCACCGCGCTGGTATTAAGCT > SRR3722090.18278/1‑100 (MQ=60)
ATTCTCCTTATCACGTTTTAATCACTGGATATCGATGGAAAAGAAACTGGGACTGAGCGCACTCACCGCtgtctcttatacacatctccgagcccacgag > SRR3722090.24348/1‑69 (MQ=60)
|
CGACCATTGCATGCAGACACATCTCTTCGTAAAATCCCGCGCTTCAGTGGCAAACTCCATTTTTATGCGTTTTGCCCTAATATTTATTCTTCTTATCACGTTTTAATCACTGGATATCGATGGAAAAGAAACTGGGACTGAGCGCACTCACCGCGCTGGTATTAAGCTCAATGCTGGGCGCGGGT > NZ_CP009273/1673695‑1673879
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
