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 I230 R1
|
226 |
18.8 |
1048726 |
96.7% |
1014118 |
86.4 |
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%
| 56.7
/ NA
| 18 | 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 (11/7); total (11/7) |
CTGCCCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTTCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAATCCTGAAG > NZ_CP009273/2819012‑2819181
|
cTGCCCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCAtttt > 2:304773/1‑90 (MQ=255)
tGCCCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTg > 1:7373/1‑90 (MQ=255)
gATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATc < 2:504600/90‑1 (MQ=255)
gATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATc < 1:54994/90‑1 (MQ=255)
aTACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCa > 2:496001/1‑90 (MQ=255)
aaCTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATa > 2:74865/2‑90 (MQ=255)
aactcaactcATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTaa > 2:183320/1‑90 (MQ=255)
aactcaactcATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTaa > 1:506156/1‑90 (MQ=255)
aactcaactcATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTaa > 1:419593/1‑90 (MQ=255)
caactcaTTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCt > 2:479281/1‑90 (MQ=255)
caactcaTTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCt > 1:356922/1‑90 (MQ=255)
caactcaTTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCt > 1:224518/1‑90 (MQ=255)
ttCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATc < 1:226364/90‑1 (MQ=255)
ccTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTgat < 2:506156/90‑1 (MQ=255)
tttATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTg > 1:500712/1‑90 (MQ=255)
aaaTATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATa < 1:183320/90‑1 (MQ=255)
aaaTATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATa < 2:326438/90‑1 (MQ=255)
cTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAATCCTGAAg < 2:224518/90‑1 (MQ=255)
|
CTGCCCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTTCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAATCCTGAAG > NZ_CP009273/2819012‑2819181
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CGGTAGTCACTGCCCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTTCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAATCCTGAAGGAGAGAACAATGA > NZ_CP009273/2819003‑2819194
|
CGGTAGTCACTGCCCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTG > SRR3722114.7446/1‑100 (MQ=60)
GATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACAC < SRR3722114.55540/100‑1 (MQ=60)
GACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAA > SRR3722114.424739/1‑100 (MQ=60)
GACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAA > SRR3722114.512495/1‑100 (MQ=60)
TTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCT > SRR3722114.226651/1‑100 (MQ=60)
TTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCT > SRR3722114.361093/1‑100 (MQ=60)
TTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATT < SRR3722114.228512/100‑1 (MQ=60)
TCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTG > SRR3722114.506990/1‑100 (MQ=60)
AAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAATCCTGAAG < SRR3722114.185127/100‑1 (MQ=60)
CCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAATCCTGAAGGAGAGAACAATGA < SRR3722114.308022/100‑1 (MQ=60)
|
CGGTAGTCACTGCCCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTTCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAATCCTGAAGGAGAGAACAATGA > NZ_CP009273/2819003‑2819194
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
