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 |
|
A23 F18 I1 R1
|
18 |
29.5 |
1031908 |
94.0% |
969993 |
141.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913_3_pae_tpiA |
2,679,525 |
G→T |
A1074D (GCT→GAT) |
yphG ← |
DUF4380 domain‑containing TPR repeat protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913_3_pae_tpiA | 2,679,525 | 0 | G | T | 96.0%
| 70.7
/ NA
| 27 | A1074D (GCT→GAT) | yphG | DUF4380 domain‑containing TPR repeat protein |
| Reads supporting (aligned to +/- strand): ref base G (1/0); new base T (13/11); total (16/11) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TTTTATTAACAACGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCG‑TCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAGTCAGG > NC_000913_3_pae_tpiA/2679385‑2679667
|
ttttATTAACAACGGCTTATTCTAATTATATTGTGATGAGCGGCAGCGCATGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGAGAAAAATCCCGCCTTCGGCCAACCCCGATTa > 2:23108/1‑149 (MQ=255)
aacGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCG‑TCa > 2:353908/1‑149 (MQ=255)
ttCTTATTAGTTTGTTATGTTCTGCAGCGAGTGCCGCTCATATATTACAGTTAATAGGGTTTAGTGAATGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCG‑TCAATTCAgcgc < 2:168597/149‑1 (MQ=255)
cTAATGATTGTGTTAGTAGCGTCAGCGCGTGCCGCACAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATCATGCAGTTAGAGGCCAAACCGGATTAATCGCCG‑TCAATTCAGCGCGa > 2:366544/1‑149 (MQ=255)
tAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCG‑TCAATTCAGCGCGAg > 2:396966/1‑149 (MQ=255)
tttGTGATGAGTGGTAGCGTGTTATTCGCTGATATTATATTTAAAATGGTTTAGTTAACGCGTTTAAAAATAAAAGGCTTCTCGGTGGTGAAGAATGCCGCTTTCGGCCAATCCGGATTATTCGCCG‑TCAATTCAGCGCGAGCAGAcgc < 2:492032/149‑3 (MQ=255)
tgaGCGGAAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTGAAAAATAAATGGCATCACGATGGTGAATAATTACGCTTTCGGCCAAGCGGGATACATCGCCT‑GCGATGTCGCGGGAGCGGCCTCATGTTgc > 2:86923/1‑149 (MQ=255)
gCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTCAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCG‑TCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTccc > 1:448791/1‑149 (MQ=255)
aGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCG‑TCAATTCAGCGCGAGCAGACTCATATTGCGCACCCTCCCCGAGTCCCGCGGACGCCAgac > 2:275689/1‑147 (MQ=255)
ttAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCG‑TCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATc < 1:300510/149‑1 (MQ=255)
ttAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCG‑TCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATc > 1:332003/1‑149 (MQ=255)
aTAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCG‑TCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGcc > 1:319809/1‑149 (MQ=255)
aTAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGGGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCG‑TCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAATCCCGCGGACGCCAGCATCgac > 2:393887/1‑147 (MQ=255)
ggTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCG‑TCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGccacca > 2:198683/1‑149 (MQ=255)
aatccgGTTAAAAAAAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCG‑TAAATTCAGCGCGAGCAGACTCATATTGCGCACCCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCAtt < 2:165180/145‑1 (MQ=255)
ggCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCG‑TCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCtgttg < 1:396966/149‑1 (MQ=255)
gCATCACGGTGGTTAATAATGCCGCTGTCGGCCAATCCGGACTAATCGCCG‑TCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCGGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCtgttgt < 1:493139/149‑1 (MQ=255)
cATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCG‑TCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTa > 2:203665/1‑149 (MQ=255)
aTCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCG‑TCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTaa < 1:251735/149‑1 (MQ=255)
aCGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCg < 1:515948/43‑1 (MQ=255)
aCGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCg > 2:515948/1‑43 (MQ=255)
gtggtgAATCATGCCGGTTTCGGCCAATCCGGCTTACTCCATGCTCCA‑TCAGCTCGAGTCGACTCAACTTTCGTTACTCCCCCAAAATGCCCCGACGTCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGcc < 1:122650/149‑1 (MQ=255)
gtggtgAATAATGCCGCTTTCGGTCAATCCGGATTAATCGCCG‑TCAATTCAGTGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGcc < 2:304783/149‑1 (MQ=255)
atGCCGCTTTCGGCCAATCCGGATTAATCGCCG‑TCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTCTAAATCGCCATTCAGCGac > 1:165320/1‑149 (MQ=255)
tGCCGCTTTCGGCCAATCCGGATTAATCGCCG‑TCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGaca > 1:214757/1‑149 (MQ=255)
gCTTTCGGCCAATCCGGATTAATCGCCG‑TCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGAcaacaa < 1:504380/149‑1 (MQ=255)
ggCCAATCCGGATTAATCGCCG‑TCAATTCAGCGCGAGCAGACTCATATTGCGTAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAGTCAgg > 1:359694/1‑149 (MQ=255)
|
TTTTATTAACAACGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCG‑TCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAGTCAGG > NC_000913_3_pae_tpiA/2679385‑2679667
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
