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 |
|
A1 F169 I0 R1
|
75 |
34.0 |
794130 |
95.7% |
759982 |
140.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
USA300TCH1516_ALE |
1,932,853 |
T→C |
100% |
I799V (ATT→GTT) |
USA300HOU_RS09605 ← |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | USA300TCH1516_ALE | 1,932,853 | 0 | T | C | 97.0%
| 80.8
/ ‑5.5
| 28 | I799V (ATT→GTT) | USA300HOU_RS09605 | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (13/14); minor base A (0/1); total (13/15) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.09e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CTTTTGATAAACTAATATATTCAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAATGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAACCAATAATTTTAGTTGGAAATGTTTTGAATAATTTTA > USA300TCH1516_ALE/1932724‑1932978
|
cTTTTGATAAACTAATATATTCAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAATCGTCGATTCGaa > 1:344347/1‑141 (MQ=255)
aTAAACTAATATATTCAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACACAAGTCGATCCGAAGTGTCg < 2:199467/141‑1 (MQ=255)
aCTAATATATTCAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGcccc < 1:115533/141‑1 (MQ=255)
aCTAATATATTCAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCCCTATCTGTTTACGCCAAACGTCGATTCGAACTGTCGcccc < 1:290751/141‑1 (MQ=255)
ctatTCATTTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAAc < 2:80436/140‑1 (MQ=255)
atatTCAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAAc < 2:387245/141‑1 (MQ=255)
atatTCAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAAc < 1:193432/141‑1 (MQ=255)
cAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTCTATATATATCTCAATCTTCGATTCGAAGTGTCGCCCCTAAAACAGAAg > 1:205089/1‑141 (MQ=255)
cAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGaaa > 2:302138/1‑140 (MQ=255)
cAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAg > 1:227842/1‑141 (MQ=255)
aTTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGACGTGTCGCCCCTAAAACAGAATCa > 2:233431/1‑141 (MQ=255)
gTTTGCCGAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCatat < 1:242339/141‑1 (MQ=255)
tttGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCAtata < 2:91730/141‑1 (MQ=255)
tGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTATTCATAAATATAATTAGCAATCTCTATATGTATTTCAACAACGTCGATTCGAAGTGTGGCACCTAAAACAGAAACATATAAt > 2:8097/1‑141 (MQ=255)
gCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATc < 1:365386/141‑1 (MQ=255)
gCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATc < 1:328927/141‑1 (MQ=255)
ccTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATCAATATAATTAGCAATCTCCATATGTATTTCCCAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAATCATATAATCt > 2:119180/1‑141 (MQ=255)
tctcATTAAAATATGAGTATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACtatata < 2:147683/141‑1 (MQ=255)
tctcATTAAAATATGAGTATATACCAGTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACtatata < 2:147680/141‑1 (MQ=255)
aaTATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCAtt > 2:111161/1‑141 (MQ=255)
tATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTtaata > 1:4016/1‑141 (MQ=255)
aaTATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTTACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAACCa < 1:31172/141‑1 (MQ=255)
cttcATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAACCAATAAttt > 1:137284/1‑141 (MQ=255)
ttcATAAATATAATTAGCAAGCTCTATAGGTATTTCACAAACGTCGATTCGAAGAGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAACCAATAAtttt > 1:256431/1‑141 (MQ=255)
aaTCTCTATATGTATTTCACAAACGTCGATTCGATGTGTCTTCCCTAAATTAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTTATATAATTTTATTAAACTAATAATTTTAGTTGGATATGTTTTGat > 2:94006/1‑140 (MQ=255)
tctATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAACCAATAATTTTAGTTGGAAATGTTTTGaataat > 1:65671/1‑141 (MQ=255)
tataTGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAACCAATAATTTTAGTTGGAAATGTTTTGAATAAttt < 1:381165/141‑1 (MQ=255)
aatGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAACCAATAATTTTAGTTGGAAATGTTTTGAATAATTTTa < 1:8203/140‑1 (MQ=255)
|
CTTTTGATAAACTAATATATTCAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAATGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAACCAATAATTTTAGTTGGAAATGTTTTGAATAATTTTA > USA300TCH1516_ALE/1932724‑1932978
|
| 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
