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 F178 I0 R1
|
39 |
50.1 |
1100758 |
94.0% |
1034712 |
140.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
CP000730 |
1,233,504 |
T→A |
100% |
V470D (GTT→GAT) |
USA300HOU_1157 → |
non‑specific serine/threonine protein kinase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | CP000730 | 1,233,504 | 0 | T | A | 95.8%
| 71.6
/ ‑2.9
| 24 | V470D (GTT→GAT) | USA300HOU_1157 | non‑specific serine/threonine protein kinase |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base A (6/17); total (6/18) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.46e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
GTGAACGTGTTGAACGTGGTGACAGTGT‑TGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGTTACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCTTTAGGCATTAAGC > CP000730/1233369‑1233632
|
gTGAACGTGTTGAACGTGGTGACA‑TGTGTGATGTGGTGATATCAAAGGGTCCTTGAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACg < 2:292569/140‑1 (MQ=255)
aCGTGTTGAACGTGGTGACAGTGT‑TGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTg < 2:295910/140‑1 (MQ=255)
cGTGTTGAACGTGGTGACAGTGT‑TGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGa > 1:441160/1‑140 (MQ=255)
gtgtTGAACGTGGTGACAGTGT‑TGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGaa < 1:419613/140‑1 (MQ=255)
gtgtTGAACGTGGTGACAGTGT‑TGATGTTGTTATATCAAAGGACCCTGAAAAGGTTAAAATGCCAAAAGACAATGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGaa > 1:17829/1‑140 (MQ=255)
taaCGTAGTGACAGTGT‑TGATTTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGt < 2:8813/139‑1 (MQ=255)
gAACGTGGTTACAGTGT‑TGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGt < 1:529085/140‑1 (MQ=255)
gtgACAGTGT‑TGATGTTGTTATATCAAAGGGCCCTGAAGGGGTTGAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGTTACGATTGAAAAAGTATataat < 2:193278/140‑1 (MQ=255)
t‑tGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAgcg < 1:245328/140‑1 (MQ=255)
gATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAACGTATATAATAATCAAGCGcc > 1:441763/1‑140 (MQ=255)
gATGTTGTTATAACAAAGGGCCCTGAAAAAGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGcc < 1:160633/140‑1 (MQ=255)
aTGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCa < 2:444134/140‑1 (MQ=255)
gggCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCaa < 1:450342/140‑1 (MQ=255)
gAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAg < 2:458748/140‑1 (MQ=255)
gAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGAAAGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAg < 2:440870/140‑1 (MQ=255)
aaaaGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAgt < 2:17829/140‑1 (MQ=255)
ccAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATAc < 1:310190/140‑1 (MQ=255)
ccAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATAc < 1:310207/140‑1 (MQ=255)
aaaTGTCAGTGGTTTACCTAAGGAGGAAGCCTTGCATAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATGATCAAGCGCCAAAAGGATACATTGTGGATCAAAGTGTAACCGCAAATACTg < 2:390341/140‑1 (MQ=255)
cATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCg > 1:121306/1‑140 (MQ=255)
aggaAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCAAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAat < 1:33299/140‑1 (MQ=255)
ttAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATc > 1:549611/1‑140 (MQ=255)
gTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCTTTAGGCATTAAg > 1:298725/1‑140 (MQ=255)
tCTTAAAGATTATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCTTTAGGCATTAAGc < 1:313554/140‑1 (MQ=255)
|
GTGAACGTGTTGAACGTGGTGACAGTGT‑TGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGTTACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCTTTAGGCATTAAGC > CP000730/1233369‑1233632
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
