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 |
2,078,566:1 |
+T |
100% |
coding (253/681 nt) |
USA300HOU_RS10490 ← |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | USA300TCH1516_ALE | 2,078,566 | 1 | . | T | 91.3%
| 69.0
/ 0.7
| 23 | coding (253/681 nt) | USA300HOU_RS10490 | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base . (2/0); new base T (15/6); total (17/6) |
| 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 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. |
GATATGACAAATGCATATGCAGTTGAAAAATAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAAT‑T‑G‑‑TTTTTTTGACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGCATCTAAAATCCAAATAATCAATATTGTTGGACTTATAAAAGA > USA300TCH1516_ALE/2078427‑2078692
|
gATATGACAAATGCATATGCAGTTGAAAAATAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAAT‑T‑G‑‑t < 1:57126/141‑1 (MQ=255)
tatGACAAATGCATATGCAGTTGAAAAATAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAAT‑T‑G‑‑ttt > 2:92524/1‑141 (MQ=255)
tatGACAAATGCATATGCAGTTGAAAAATAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAAAATAGTTGACATTAAGCAAT‑T‑G‑‑ttt > 2:257927/1‑141 (MQ=255)
tatGACAAATGCATATGCAGTTGAAAAATAGATTGAATTTGGTTAACTCACATCTGCTTAGTAAGAATATAAAAAAATCACACGCGTTCCCATTAATGTTAAGACAATGAATGTAATATAGTTGGCATTAAGCAAT‑T‑G‑‑ttt > 2:77129/1‑141 (MQ=255)
gCATATGCAGTTGAAAAATAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAAT‑T‑G‑‑ttttttttgaacc > 2:31719/1‑135 (MQ=255)
cATATGCAGTTGAAAAATAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAAT‑T‑GT‑TTTTTTTGACACt > 1:249602/1‑141 (MQ=255)
tatGCAGTTGAAAAATAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAAT‑T‑GT‑TTTTTTTGACACTgg < 2:250935/141‑1 (MQ=255)
tGCAGTTGAAAAATAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAAT‑T‑GT‑TTTTTTTGACACTGGTa > 1:83674/1‑141 (MQ=255)
aGTTGAAAAATAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAAT‑T‑GT‑TTTTTTTGACACTGGTAAAc > 2:181770/1‑141 (MQ=255)
aaaaaTAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGAATTAAGCGATGT‑T‑‑TTTTTTTGACACTGGGaaagtaatt > 1:335009/1‑135 (MQ=255)
aaaaTAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAAT‑T‑GT‑TTTTTTTGACACTGTTAAAATCataa > 2:340619/1‑140 (MQ=255)
aaaaTAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAAT‑T‑GT‑TTTTTTTGACACTGGTAAACTCatat > 1:273559/1‑141 (MQ=255)
aaaaTAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAAT‑T‑GT‑TTTTTTTGACACTGGTAAACTCatat > 1:357153/1‑141 (MQ=255)
aaaaTAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAAT‑T‑GT‑TTTTTTTGAAACTGGTAAACTCatat > 1:148242/1‑141 (MQ=255)
aTTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAAT‑T‑GT‑TTTTTTTGACACTGGTAAACTCATATAAAAATAATATg > 1:156569/1‑141 (MQ=255)
gCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAAT‑T‑GT‑TTTTTTTGACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCt > 1:395702/1‑141 (MQ=255)
aTAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAAT‑T‑GT‑TTTTTTTGACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGAt > 1:253119/1‑141 (MQ=255)
atatAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAAT‑T‑GT‑TTTTTTTGACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTc < 1:18264/141‑1 (MQ=255)
atatAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAAT‑T‑GT‑TTTTTTTGACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTc < 2:389767/141‑1 (MQ=255)
aaaaaaaaTAATAAAAAGCATTCCAATTAAACTTAAAACAATGCATGTAATATAGTTAGCATTAAGCAAT‑T‑GT‑TTTTTTTGACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTc < 1:18563/137‑1 (MQ=255)
cAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAAT‑T‑GT‑TTTTTTTGACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCa < 1:232519/141‑1 (MQ=255)
gTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAAT‑T‑GT‑TTTTTTTGACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGCATc > 1:148010/1‑141 (MQ=255)
tGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAAT‑T‑GT‑TTTTTTTGACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGCATCTAAAATCCaaa > 1:351179/1‑141 (MQ=255)
ttAAAACAATGCATGTAATATAGTTGGCATTAAGCAAT‑T‑GT‑TTTTTTTGACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGCATCTAAAATCCAaata < 1:181770/141‑1 (MQ=255)
cATGTAATATAGTTGGCATTAAGCAAT‑T‑GT‑TTTTTTTGACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGCATCTAAAATCCAAATAATCAATAttgt > 1:8840/1‑141 (MQ=255)
aGTTGGCATTAAGCCAT‑TGG‑‑TTTTTTTGACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGCATCTAAAATCCAAATAATCAATATTGTTGGACTtata > 1:217773/1‑141 (MQ=255)
ggCATTAAGCAAT‑T‑GT‑TTTTTTTGACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGCATCTAAAATCCAAATAATCAATATTGTTGGACTTATAAAAg > 1:9146/1‑141 (MQ=255)
cATTAAGCAAT‑T‑GTTTTTTTTTGACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGCATCTAAAATCCAAATAATCAATATTGTTGGACTTATAAAAGa > 1:69530/1‑141 (MQ=255)
|
GATATGACAAATGCATATGCAGTTGAAAAATAGATTGAATTTGGTTCAATCACATCTGCTTCATAAGCATATAAACTAATAACAAGCGTTCCAATTAATGTTAAAACAATGCATGTAATATAGTTGGCATTAAGCAAT‑T‑G‑‑TTTTTTTGACACTGGTAAACTCATATAAAAATAATATGAATCATTACCACCTAATCTACGATTGAGTCTAAATAAGTGACCAGCATCTAAAATCCAAATAATCAATATTGTTGGACTTATAAAAGA > USA300TCH1516_ALE/2078427‑2078692
|
| 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
