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 |
1,744,362 |
G→A |
100% |
H104Y (CAC→TAC) |
apt ← |
Adenine phosphoribosyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | USA300TCH1516_ALE | 1,744,362 | 0 | G | A | 95.7%
| 64.0
/ ‑5.0
| 22 | H104Y (CAC→TAC) | apt | Adenine phosphoribosyltransferase |
| Reads supporting (aligned to +/- strand): ref base G (0/1); new base A (13/8); total (13/9) |
| Fisher's exact test for biased strand distribution p-value = 4.09e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-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. |
TACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATT‑G‑TTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCAC > USA300TCH1516_ALE/1744242‑1744499
|
tACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATT‑G‑TTAAAACATTTGTAc < 1:108576/141‑1 (MQ=255)
aCCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATT‑G‑TTAAAACATTTGTAcc > 2:38285/1‑141 (MQ=255)
aCCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATT‑G‑TTAAAACATTTGTACCATATTCTAGGTc > 2:124448/1‑141 (MQ=255)
ccTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATT‑G‑TTAAAACATTTGTACCATATTCTAGGTCATAc > 1:163859/1‑141 (MQ=255)
tATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTACTTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATT‑G‑TTAAAACATTTGTACCATATTCTAGGTAATACTGATAACGAATGACTTCACg > 1:356675/1‑141 (MQ=255)
gctgctTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATT‑G‑TTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGCCTTCACGAGGt > 2:160449/1‑141 (MQ=255)
gctgctTCAATCGTACAACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATT‑G‑TTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGt > 1:234957/1‑141 (MQ=255)
ctgctTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATT‑G‑TTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTa > 2:121720/1‑141 (MQ=255)
gTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATT‑G‑TTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCcttct > 2:23360/1‑141 (MQ=255)
tACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATT‑G‑TTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCcttctt < 1:38285/141‑1 (MQ=255)
accaccAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATT‑G‑TTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCttt > 1:361443/1‑141 (MQ=255)
gCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATT‑G‑TTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGt > 2:348193/1‑141 (MQ=255)
aaaTCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATT‑G‑TTAAAACATTTGTACCATATTCTAGGTTATACTTATAACGAATGACTTCACGAGGTAATTTCCCTGCTTTTCTAACAGGTGCAAAg < 1:241345/141‑1 (MQ=255)
atcatcTGTTATTAACACCCGTCGACCTGGTTGAATAGAAAAAT‑‑TGCATTAGATTTAAACATTTGTCCCATATTCTAGGGCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGcc < 1:89384/141‑1 (MQ=255)
tcatcTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATT‑G‑TTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCa < 2:98809/141‑1 (MQ=255)
catcTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATT‑G‑TTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCaa > 1:63240/1‑141 (MQ=255)
gTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATT‑G‑TTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATcccc < 1:121720/141‑1 (MQ=255)
aaCACACGTTGACCTGGTTTAATTGCATCTTTGTACATT‑G‑TTAAAACATTGGTACCATATTCTAGGGCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGaa < 1:103798/141‑1 (MQ=255)
ttGACCTGGTTTAATTGCATCTTTGTACATT‑G‑TTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCTTTGAATAGGCTAc > 1:101212/1‑141 (MQ=255)
tttAATTGCATCTTTGTACATT‑G‑TTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGcc < 1:380256/141‑1 (MQ=255)
tGCATCTTTGTACATT‑G‑TTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGAt > 1:396411/1‑141 (MQ=255)
cTTTGTACATT‑G‑TTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGc < 1:250323/141‑1 (MQ=255)
tgtaCATT‑G‑TTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCAc < 2:35025/141‑1 (MQ=255)
|
TACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATT‑G‑TTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCAC > USA300TCH1516_ALE/1744242‑1744499
|
| 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
