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 I206 R1
|
206 |
23.7 |
1314362 |
96.8% |
1272302 |
86.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,060,988 |
(A)6→5 |
intergenic (+240/‑53) |
yccE → / → agp |
YccE family protein/bifunctional glucose‑1‑phosphatase/inositol phosphatase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,060,983 | 0 | A | . | 100.0%
| 72.9
/ NA
| 18 | intergenic (+235/‑58) | yccE/agp | YccE family protein/bifunctional glucose‑1‑phosphatase/inositol phosphatase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base . (8/10); total (8/10) |
GCGTCAAACCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGGAAAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGCCAGGAATGAACAAAACGCTAATCGCC > NZ_CP009273/1060904‑1061061
|
gCGTCAAACCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCata > 1:124734/1‑90 (MQ=255)
gCGTCAAACCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCata > 1:435801/1‑90 (MQ=255)
aaCCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTg > 2:539969/1‑90 (MQ=255)
aCCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGt < 1:604023/90‑1 (MQ=255)
gATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGtgattg < 2:124734/90‑1 (MQ=255)
gATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGtgattg < 2:108314/90‑1 (MQ=255)
gAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTc > 1:7830/1‑59 (MQ=255)
gAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTc < 2:7830/59‑1 (MQ=255)
gAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAag > 1:488570/1‑90 (MQ=255)
aaaCAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAgg > 1:249661/1‑90 (MQ=255)
aaaCAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAgg > 2:62660/1‑90 (MQ=255)
aCAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGGaaaa < 2:168825/43‑1 (MQ=255)
aCAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGGaaaa > 1:168825/1‑43 (MQ=255)
aGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGcc < 1:62660/90‑1 (MQ=255)
aGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGcc < 2:453491/90‑1 (MQ=255)
cGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGCCAgg > 2:617860/1‑90 (MQ=255)
aGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGCCAGGAATGAACaa < 1:54927/90‑1 (MQ=255)
cGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGCCAGGAATGAACAAAACGCTAATc < 1:136921/90‑1 (MQ=255)
aCCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGCCAGGAATGAACAAAACGCTAATcgcc < 2:249661/90‑1 (MQ=255)
aCCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGCCAGGAATGAACAAAACGCTAATcgcc < 2:107048/90‑1 (MQ=255)
|
GCGTCAAACCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGGAAAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGCCAGGAATGAACAAAACGCTAATCGCC > NZ_CP009273/1060904‑1061061
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ 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
GGCATAGTTTGCGTCAAACCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGGAAAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGCCAGGAATGAACAAAACGCTAATCGCCGCAGCTG > NZ_CP009273/1060894‑1061068
|
GGCATAGTTTGCGTCAAACCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATA > SRR3722088.126028/1‑100 (MQ=60)
GGCATAGTTTGCGTCAAACCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATA > SRR3722088.440796/1‑100 (MQ=60)
ACCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTT < SRR3722088.611461/100‑1 (MQ=60)
GATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCctgtctcttatacacatctcc > SRR3722088.7929/1‑79 (MQ=60)
GATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAG > SRR3722088.494391/1‑100 (MQ=60)
GTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGG > SRR3722088.252099/1‑100 (MQ=60)
ATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCtcttatacacatctccgagcccacgagaccgt > SRR3722088.170525/1‑68 (MQ=60)
AGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGCCAGGAATGAAC < SRR3722088.63318/100‑1 (MQ=60)
AGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGCCAGGAATGAACAAAACGCTAATC < SRR3722088.55514/100‑1 (MQ=60)
CGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGCCAGGAATGAACAAAACGCTAATCGCCGCAGCTG < SRR3722088.138332/100‑1 (MQ=60)
|
GGCATAGTTTGCGTCAAACCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGGAAAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGCCAGGAATGAACAAAACGCTAATCGCCGCAGCTG > NZ_CP009273/1060894‑1061068
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
