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 |
2,819,095 |
T→C |
intergenic (‑160/‑96) |
mltB ← / → srlA |
lytic murein transglycosylase B/PTS glucitol/sorbitol transporter subunit IIC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,819,095 | 0 | T | C | 100.0%
| 38.4
/ NA
| 13 | intergenic (‑160/‑96) | mltB/srlA | lytic murein transglycosylase B/PTS glucitol/sorbitol transporter subunit IIC |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (8/5); total (8/5) |
CTGCCCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTTCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAAT > NZ_CP009273/2819012‑2819174
|
cTGCCCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCAtttt > 1:263576/1‑90 (MQ=255)
ccGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGa < 1:132616/90‑1 (MQ=255)
aactcaactcATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTaa > 1:539521/1‑90 (MQ=255)
caactcaTTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTaaa > 1:85616/1‑87 (MQ=255)
caactcaTTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTaaa < 2:85616/87‑1 (MQ=255)
caactcaTTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCt > 1:101233/1‑90 (MQ=255)
actcaTTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCttt > 1:258717/1‑90 (MQ=255)
actcaTTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCttt > 2:319837/1‑90 (MQ=255)
ccTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTgat < 2:238254/90‑1 (MQ=255)
cTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTgattagat < 2:359844/90‑1 (MQ=255)
ttATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGc > 1:223051/1‑90 (MQ=255)
ttATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGc > 2:513363/1‑90 (MQ=255)
tatTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAAt < 2:328065/90‑1 (MQ=255)
|
CTGCCCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTTCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAAT > NZ_CP009273/2819012‑2819174
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GCGGTAGTCACTGCCCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTTCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAATCCTGAAGGA > NZ_CP009273/2819002‑2819183
|
GCGGTAGTCACTGCCCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTT > SRR3722092.267940/1‑100 (MQ=60)
CCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAAC < SRR3722092.134861/100‑1 (MQ=60)
GACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAA > SRR3722092.550357/1‑100 (MQ=60)
TTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCT > SRR3722092.102963/1‑100 (MQ=60)
TTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCT > SRR3722092.87084/1‑100 (MQ=60)
ACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTT > SRR3722092.262950/1‑100 (MQ=60)
CGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGC > SRR3722092.226698/1‑100 (MQ=60)
ATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTctgtctcttatacacatctgacgctgccgacgacc > SRR3722092.264141/1‑65 (MQ=60)
|
GCGGTAGTCACTGCCCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTTCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAATCCTGAAGGA > NZ_CP009273/2819002‑2819183
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
