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 |
|
A5 F58 I1 R1
|
12 |
20.5 |
473580 |
94.8% |
448953 |
140.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
USA300TCH1516_ALE |
2,373,698 |
+T |
coding (78/1335 nt) |
pbuG ← |
Guanine/hypoxanthine permease PbuG |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | USA300TCH1516_ALE | 2,373,697 | 1 | . | T | 95.2%
| 64.1
/ ‑3.3
| 21 | coding (79/1335 nt) | pbuG | Guanine/hypoxanthine permease PbuG |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base T (10/10); total (10/11) |
| 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 |
GCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAG‑GCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTAAAATACCTTAATAGTTTAATATCATTCTTAAT > USA300TCH1516_ALE/2373565‑2373828
|
gCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAG‑GCCATAGATTAAGaaa > 1:17780/1‑141 (MQ=255)
ctAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAG‑GCCATAGATTAAGAAAGTTGTGATACCGCCTAAg < 1:57495/141‑1 (MQ=255)
tagtGCAGTCGCTACAAAAATGGCACGTTGGTCCATTTGCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAACAGATGGTGGAGTTGT‑TAATAAAGTTGTGATACCGCCTAAGa < 2:131123/138‑1 (MQ=255)
aTGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAG‑GCCATAGATTAAGAAAGTTGTGATACCGCCTAAGAtt < 1:94933/141‑1 (MQ=255)
gCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAG‑GCCATAGATTAAGAAAGTTGTGATACCGCCTAAGATTTCTCtttt < 1:103057/141‑1 (MQ=255)
gCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAG‑GCCATAGATTAAGAAAGTTGTGATACCGACTAAGATTTCTCtttt > 1:135876/1‑141 (MQ=255)
aCAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAG‑GCCATAGATTAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTaaa > 2:209644/1‑141 (MQ=255)
cAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAG‑GCCATAGATTAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAg > 1:133650/1‑141 (MQ=255)
ccTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAG‑GCCATAGATTAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCata < 2:170850/141‑1 (MQ=255)
ttGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAG‑GCCATAGATTAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATAtt > 2:219064/1‑141 (MQ=255)
cATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAG‑GCCATAGATTAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGa < 2:683/141‑1 (MQ=255)
cATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAG‑GCCATAGATTAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGa > 1:189659/1‑141 (MQ=255)
tatCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAG‑GCCATAGATTAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGaaa < 1:80811/141‑1 (MQ=255)
ctGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAG‑GCCATAGATTAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGttt < 1:67224/141‑1 (MQ=255)
cgtttAACACACGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAG‑GCCATAGATTAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGaa < 1:105377/139‑1 (MQ=255)
cacCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAG‑GCCATAGATTAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGTTGc > 2:125881/1‑141 (MQ=255)
ttAAAACTTGCGGGTTAACTGCTAAAATATAG‑GCCATAGATTAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTaa > 1:28769/1‑141 (MQ=255)
aaaCTTGCGGGTTAACTGCTAAAATATAG‑GCCATAGATTAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTAAAAt < 1:131276/141‑1 (MQ=255)
cTTGCGGGTTAACTGCTAAAATATAG‑GCCATAGATTAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTAAAATAcc < 1:71805/141‑1 (MQ=255)
ataG‑GCCATAGATTAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGATTTACACGAATGGATGCTCCTTTTTTTAAATTCCCTTATTAGTTTCATATCATTCtt > 2:95977/1‑141 (MQ=255)
g‑gCCATAGATTAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACCGATGCTGACAAGGCATGAATGGATGCTCCTTTTTTTAAAATACCTTAATAGTTTAATATCATTCTtaat > 1:172769/1‑141 (MQ=255)
|
GCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAG‑GCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTAAAATACCTTAATAGTTTAATATCATTCTTAAT > USA300TCH1516_ALE/2373565‑2373828
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
