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 F68 I1 R1
|
13 |
30.2 |
709236 |
94.0% |
666681 |
140.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
USA300TCH1516_ALE |
1,744,428 |
T→C |
K82E (AAA→GAA) |
apt ← |
Adenine phosphoribosyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | USA300TCH1516_ALE | 1,744,428 | 0 | T | C | 96.0%
| 73.2
/ NA
| 25 | K82E (AAA→GAA) | apt | Adenine phosphoribosyltransferase |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (12/12); total (12/13) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01 |
ACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATC > USA300TCH1516_ALE/1744300‑1744560
|
accaGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTATGTCATACTCATAACGAATGACTTCACGAGGTAATTCCCCTTCTTTTCt > 2:100729/1‑141 (MQ=255)
gCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATAACTTCACGAGGTAATTCCCCTTCTTTTCTAACAGGt > 2:204069/1‑141 (MQ=255)
tcatcTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTCCCCTTCTTTTCTAACAGGTGCAAAGCCa > 1:162388/1‑141 (MQ=255)
tcatcTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTCCCCTTCTTTTCTAACAGGTGCAAAGCCa < 2:99521/141‑1 (MQ=255)
aaTCAACATATGTTGATCTGGTTTAATTGTATTTTTGTGCATTGTTAAAACATTTGTACCATATTCTATGTCATACTCATATCGACTGACTTCACGTGGTACGTCCTCTTCTTTTTTAACAGGTGCAAAGCCAATCCCCAt < 2:232581/141‑1 (MQ=255)
ttAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTCCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTg < 1:68844/141‑1 (MQ=255)
acacGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTCCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATaa > 1:60533/1‑141 (MQ=255)
tggACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTCCCCTTCTTTTCTAACAGGTGCAGAGACAAACCCCATCGACTAGGCAAc > 2:595/3‑141 (MQ=255)
gACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTCCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAg < 1:207352/141‑1 (MQ=255)
gtgCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTCCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCAcg < 1:78334/141‑1 (MQ=255)
aaaaCATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTCCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGCTAAAGCCCCGCGCTTCAGGt > 2:202547/1‑141 (MQ=255)
aCATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTCCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGCACAGCCAATGATAAAGCCACGCGCTTCAGGTCCt > 1:97740/1‑141 (MQ=255)
aCCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTCCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCCGGTCCTACACCGat > 1:2698/1‑141 (MQ=255)
ggTCATACTCATAACGAATGACTTCACGAGGTAATTCCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACAtctc > 2:293420/1‑141 (MQ=255)
gTCATACTCATAACGAATGACTTCACGAGGTAATTCGGCTTCTTTTCTAATAGGTGTTAAGCTTGTGCTTGTTGATTGCGCTACAGGACAGAAAATTATAATTGTTGGTGCTTCTGGTGCTACAATGATATCAACATctct < 2:236470/141‑1 (MQ=255)
tCATACTCATAACGAATGACTTCACGAGGTAATTCCCCTTCTTTGCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTg < 2:346465/141‑1 (MQ=255)
tCATACTCATAACGAATGACTTCACGAGGTAATTCCCCTTCGTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTg < 2:122513/141‑1 (MQ=255)
tCATACTCAGAACGAATGACTCCACGAGGTAATTCCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTg < 2:298533/141‑1 (MQ=255)
cTCATAACGAGTGACTTCACGAGGTAATTCCCCTTCTTCTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGCACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCttt < 2:295021/141‑1 (MQ=255)
gAATGACTTCACGAGGTAATTCCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTAtt > 2:315882/1‑141 (MQ=255)
cTTCACGAGGTAATTCCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACaa < 1:327948/141‑1 (MQ=255)
cTTCACGAGGTAATTCCCCTTCTTCTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACaa < 1:124699/141‑1 (MQ=255)
cggcttAATGTCCCTTCGGTGCTAACAGGTGCAAAGCCAATCCCCATTGAAGAAGCTACAGGACAGCCAAAGATAAGGGGTGGTTGTGCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTa < 2:216546/136‑1 (MQ=255)
aGGTAATTCCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTAtt > 1:240188/1‑140 (MQ=255)
aGGTAATTCCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATc > 1:331342/1‑141 (MQ=255)
|
ACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATC > USA300TCH1516_ALE/1744300‑1744560
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
