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 |
1,215,948 |
T→C |
pseudogene (487/2243 nt) |
BW25113_RS25990 → |
autotransporter outer membrane beta‑barrel domain‑containing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,215,948 | 0 | T | C | 100.0%
| 84.6
/ NA
| 24 | pseudogene (487/2243 nt) | BW25113_RS25990 | autotransporter outer membrane beta‑barrel domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (16/8); total (16/8) |
GATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCAAAATAGCACTATTA > NZ_CP009273/1215867‑1216034
|
gATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTc > 1:812688/1‑90 (MQ=255)
atatAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCa > 1:630500/1‑90 (MQ=255)
tataAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCAc < 1:48892/90‑1 (MQ=255)
aaaaaTAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACcgcg > 1:231031/1‑90 (MQ=255)
aaaaaTAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACcgcg > 2:750559/1‑90 (MQ=255)
aaaaaTAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACcgcg > 1:858019/1‑90 (MQ=255)
aTAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTAt > 2:293504/1‑90 (MQ=255)
gTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCaa > 2:169668/1‑90 (MQ=255)
cTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAAc < 1:750559/90‑1 (MQ=255)
cTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAAc > 1:763656/1‑90 (MQ=255)
caacaacaGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATa < 2:147339/90‑1 (MQ=255)
aacaacaGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATaa > 2:559414/1‑90 (MQ=255)
acaacaGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAAc < 1:351145/82‑1 (MQ=255)
acaacaGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAAc > 2:351145/1‑82 (MQ=255)
aacaGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATAAAgg > 2:591322/1‑90 (MQ=255)
ggCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAata < 2:858019/90‑1 (MQ=255)
aaaGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAAtt > 2:791436/1‑90 (MQ=255)
ccccATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGc > 2:378506/1‑90 (MQ=255)
cATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATAAAGGaa > 1:234411/1‑74 (MQ=255)
cATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATAAAGGaa < 2:234411/74‑1 (MQ=255)
cATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATc > 2:218332/1‑90 (MQ=255)
ttGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCaa < 2:901383/90‑1 (MQ=255)
ggtggAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGcc > 1:591405/1‑90 (MQ=255)
tATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCAAAATAGCAc < 1:791436/90‑1 (MQ=255)
tttcCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCAAAATAGCACTATTa < 2:91424/90‑1 (MQ=255)
|
GATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCAAAATAGCACTATTA > NZ_CP009273/1215867‑1216034
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCAAAATAGCACTATTAAGTGT > NZ_CP009273/1215857‑1216039
|
AGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTC > SRR3722072.826847/1‑100 (MQ=60)
GGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCA > SRR3722072.641765/1‑100 (MQ=60)
CATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCG > SRR3722072.234898/1‑100 (MQ=60)
CATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCG > SRR3722072.872831/1‑100 (MQ=60)
TATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCA < SRR3722072.49782/100‑1 (MQ=60)
AAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAAC > SRR3722072.777112/1‑100 (MQ=60)
CTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATAAAGG < SRR3722072.357334/100‑1 (MQ=60)
CTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATAAAGG < SRR3722072.763826/100‑1 (MQ=60)
CTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGActgtct > SRR3722072.238322/1‑94 (MQ=60)
AATATACAATGGTGGAGAGTTATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCC > SRR3722072.601978/1‑100 (MQ=60)
TATTTTTTCCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCAAAATAGCACTATTAAGTGT < SRR3722072.805290/100‑1 (MQ=60)
|
AGGTAACATTGATATAAAAAATAGTTCTATTACAACAACAGGCACTAAAGCCCCCATTGCAAAAATATACAATGGTGGAGAGTTATTTTTTTCCAATGTCACCGCGGTATCAAAACAAGATAAAGGAATATCAATTGATGCATCAAATATCGATTCTCAAGCCAAAATAGCACTATTAAGTGT > NZ_CP009273/1215857‑1216039
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
