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 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
86.4 |
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%
| 77.7
/ NA
| 19 | 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 . (8/11); total (8/11) |
GGCATAGTTTGCGTCAAACCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGGAAAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGCCAGGAATGAACAAAACGCTAATCGCCGCAGCTG > NZ_CP009273/1060894‑1061068
|
ggCATAGTTTGCGTCAAACCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGGa > 2:186890/1‑90 (MQ=255)
gTTTGCGTCAAACCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGGaaaaagt > 1:684274/1‑88 (MQ=255)
ttGCGTCAAACCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGGaaaaagtca > 1:649918/1‑86 (MQ=255)
gCGTCAAACCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCata > 2:173094/1‑90 (MQ=255)
gCGTCAAACCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCata > 1:667166/1‑90 (MQ=255)
gCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCacac < 1:299289/90‑1 (MQ=255)
gCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCacac < 2:266805/90‑1 (MQ=255)
gCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCacac < 2:171932/90‑1 (MQ=255)
gCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCacac < 2:136101/90‑1 (MQ=255)
gCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCacac < 1:564457/90‑1 (MQ=255)
gATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGtgattg < 2:116717/90‑1 (MQ=255)
aTGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGtgattga > 1:218493/1‑90 (MQ=255)
gAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTcac > 1:374837/1‑65 (MQ=255)
gAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTcac < 2:374837/65‑1 (MQ=255)
aaaaCAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAagag > 1:443817/1‑90 (MQ=255)
aaaCAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGtgattga < 1:527380/78‑1 (MQ=255)
aaaCAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGtgattga > 2:527380/1‑78 (MQ=255)
cGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCttt < 1:572842/62‑1 (MQ=255)
cGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCttt > 2:572842/1‑62 (MQ=255)
ttGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGCCAGGAATGAACAAAACGCTa < 1:404856/90‑1 (MQ=255)
gAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGCCAGGAATGAACAAAACGCTAATcg > 2:654585/1‑90 (MQ=255)
cccGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGCCAGGAATGAACAAAACGCTAATCGCCGCAGCtg < 1:486645/90‑1 (MQ=255)
|
GGCATAGTTTGCGTCAAACCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGGAAAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGCCAGGAATGAACAAAACGCTAATCGCCGCAGCTG > NZ_CP009273/1060894‑1061068
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CAGGCATAGTTTGCGTCAAACCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGGAAAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGCCAGGAATGAACAAAACGCTAATCGCCGCAGCTGTGGCAGGGAT > NZ_CP009273/1060892‑1061078
|
CAGGCATAGTTTGCGTCAAACCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCA > SRR3722112.660043/1‑100 (MQ=60)
GGCATAGTTTGCGTCAAACCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATA > SRR3722112.677575/1‑100 (MQ=60)
GCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGA < SRR3722112.302740/100‑1 (MQ=60)
GCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGA < SRR3722112.573030/100‑1 (MQ=60)
GTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGA > SRR3722112.221128/1‑100 (MQ=60)
gatgtgtataagagacagGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGAT < SRR3722112.581571/82‑1 (MQ=60)
GATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTctgtctcttatacac > SRR3722112.379680/1‑85 (MQ=60)
AGGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGA < SRR3722112.535171/100‑1 (MQ=60)
TGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAG > SRR3722112.449971/1‑100 (MQ=60)
TTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGCCAGGAATGAACAAAACGCTAATCGCCGCAG < SRR3722112.410198/100‑1 (MQ=60)
CCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGCCAGGAATGAACAAAACGCTAATCGCCGCAGCTGTGGCAGGGAT < SRR3722112.493657/100‑1 (MQ=60)
|
CAGGCATAGTTTGCGTCAAACCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGGAAAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGCCAGGAATGAACAAAACGCTAATCGCCGCAGCTGTGGCAGGGAT > NZ_CP009273/1060892‑1061078
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
