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 I194 R1
|
197 |
32.2 |
1845014 |
95.2% |
1756453 |
85.4 |
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%
| 61.4
/ 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 (7/11); total (7/11) |
CCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTTCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAA > NZ_CP009273/2819016‑2819172
|
ccGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGa < 1:525309/90‑1 (MQ=255)
aCGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCaaa < 2:214699/90‑1 (MQ=255)
gACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATa > 2:288979/1‑90 (MQ=255)
cTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAac < 1:805416/90‑1 (MQ=255)
aactcaactcATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTaa > 1:284900/1‑90 (MQ=255)
aactcaactcATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTaa > 2:75397/1‑90 (MQ=255)
aactcaactcATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTaa > 2:368813/1‑90 (MQ=255)
actcaactcaTTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTaaa < 1:782038/90‑1 (MQ=255)
ttCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATc < 1:906305/90‑1 (MQ=255)
ttCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATc > 2:62957/1‑90 (MQ=255)
ccTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTgat < 1:305611/90‑1 (MQ=255)
ccTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTgat < 2:539733/90‑1 (MQ=255)
tCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATc > 1:76841/1‑78 (MQ=255)
tCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATc < 2:76841/78‑1 (MQ=255)
ttttATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGtt < 1:312041/90‑1 (MQ=255)
aTTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCg > 1:124976/1‑90 (MQ=255)
aaTATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATaa < 1:775896/90‑1 (MQ=255)
aaTATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATaa < 1:578777/90‑1 (MQ=255)
|
CCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTTCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAA > NZ_CP009273/2819016‑2819172
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ 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
CCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTTCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAATCCTGAAGGAGAGAACAATGA > NZ_CP009273/2819016‑2819194
|
CCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAAC < SRR3722072.534759/100‑1 (MQ=60)
GACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAA > SRR3722072.289783/1‑100 (MQ=60)
CTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAAT < SRR3722072.819465/100‑1 (MQ=60)
ACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATC < SRR3722072.795746/100‑1 (MQ=60)
TTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATT < SRR3722072.921906/100‑1 (MQ=60)
CCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTct > SRR3722072.78269/1‑98 (MQ=60)
CCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGT < SRR3722072.310905/100‑1 (MQ=60)
CTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCG > SRR3722072.127244/1‑100 (MQ=60)
TTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGT < SRR3722072.317482/100‑1 (MQ=60)
AATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAATCCTGAAGG < SRR3722072.589119/100‑1 (MQ=60)
AATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAATCCTGAAGG < SRR3722072.789526/100‑1 (MQ=60)
CCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAATCCTGAAGGAGAGAACAATGA < SRR3722072.91802/100‑1 (MQ=60)
|
CCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTTCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAATCCTGAAGGAGAGAACAATGA > NZ_CP009273/2819016‑2819194
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
