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 |
|
A13 F40 I0 R1
|
17 |
35.0 |
784744 |
95.0% |
745506 |
140.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
USA300TCH1516_ALE |
1,744,472 |
G→A |
73.6% |
A67V (GCT→GTT) |
apt ← |
Adenine phosphoribosyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | USA300TCH1516_ALE | 1,744,472 | 0 | G | A | 73.6%
| 22.8
/ 10.0
| 25 | A67V (GCT→GTT) | apt | Adenine phosphoribosyltransferase |
| Reads supporting (aligned to +/- strand): ref base G (2/4); new base A (10/8); total (12/13) |
| Fisher's exact test for biased strand distribution p-value = 6.40e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.68e-01 |
TGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCT > USA300TCH1516_ALE/1744342‑1744610
|
tGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAACTACAGGACa < 1:277360/141‑1 (MQ=255)
gTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGc > 2:337810/1‑141 (MQ=255)
tttAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGcc < 1:337810/141‑1 (MQ=255)
tttAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAACTACAGGACAGcc < 1:311658/141‑1 (MQ=255)
tttAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATGCTAGGTCATACTCATAACGAATTACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAACTACAGGACAGcc < 2:76996/141‑1 (MQ=255)
ttGCATCTTTGTGCATTGTTAAAACATTTGTCCCATATTCTAGGTCATACTCATCACGAATGGCTTCACGAGGTAATTTCCCTTCTTTTCTAACAGACACAAACACAATCCCCAATGAATAAACTACAAGACCGCCAAtca > 2:138507/1‑139 (MQ=255)
ttGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACAAGGTAATTTCCCTTCTTTTCTAACATGTGCAAAGCCAATACCCATTGAATAAACTCCATGAAAGCCAATGa > 2:388860/1‑141 (MQ=255)
cATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAACTACAGGACAGCCAATGATAAAGCCACgcgc > 1:196244/1‑141 (MQ=255)
aaaaCATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAACTACAGGACAGCCAATGATAAAGCCACGCGCTTCCGGt > 1:191514/1‑141 (MQ=255)
aCCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAACTACTGTACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGat > 1:47790/1‑141 (MQ=255)
gTCCTACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATctct < 1:40065/141‑1 (MQ=255)
tCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCACTCCCCATTTAATAAACTACAGGACAACCAAAGAGAAAACCACGCGCTTACAGTCCTACAAACAGATCAAGAtactct > 2:213662/1‑136 (MQ=255)
tACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAACTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGATCCTACAACGATATCAACATCTCTGTCt > 2:110869/1‑141 (MQ=255)
cTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAACTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCttt < 1:192072/141‑1 (MQ=255)
cTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAACTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTATCttt > 1:240125/1‑141 (MQ=255)
aCGAATGCCTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAACTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTa < 1:226946/141‑1 (MQ=255)
gAATGACTTCACGAGGTAATTTCCCTGTTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTAtt < 2:314604/141‑1 (MQ=255)
tAATGTCCCTTCTTTTCTAACATGTGCAAAGCCAAGCCCCATTGAATAAACTACAGGACCGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGt < 2:45488/141‑1 (MQ=255)
tggcgttcttTTGTATCAGGGTCAAGGGCAATCCCCTTTTAATATTCTTCATGACAGCATGTTATATAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCa < 2:4921/136‑1 (MQ=255)
cTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACATTTTTATCTGTTGCATAGCCATATGCt > 1:259841/1‑141 (MQ=255)
aGGTGCAAAGCCAATCCCCATTGAATAAACTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTTTTGCATATCCATATGCTTCAcc > 2:134736/1‑141 (MQ=255)
aaaGCCAATCCCCATTGAATAAACTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATc > 1:237085/1‑141 (MQ=255)
ccccCTTGACTAAACTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTgt < 1:15035/141‑1 (MQ=255)
cccATTGAATAAACTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTgta < 1:242009/141‑1 (MQ=255)
aaGCCAGAGAACAGCCAATGATGAAGTCACGCGCGTCAGGTCCTACAACGATATCAACATCTCCGTGTGTGTGGTATCGTACATGTGTATCTGTTGCATAGCCATATGCTTCACCATTAGCCATAATTGTAGTAATATCCt < 2:160075/141‑1 (MQ=255)
|
TGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCT > USA300TCH1516_ALE/1744342‑1744610
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
