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 |
2,018,612 |
G→A |
100% |
R103* (CGA→TGA) |
mgt ← |
Monofunctional glycosyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | USA300TCH1516_ALE | 2,018,612 | 0 | G | A | 97.5%
| 116.4
/ ‑5.2
| 37 | R103* (CGA→TGA) | mgt | Monofunctional glycosyltransferase |
| Reads supporting (aligned to +/- strand): ref base G (0/1); new base A (20/16); total (20/17) |
| Fisher's exact test for biased strand distribution p-value = 4.59e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-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. |
ATTATCATAAAAATAATTTTTGACAACTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCGTTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGATAAAAAATACA > USA300TCH1516_ALE/2018481‑2018737
|
aTTATCATAAAAATAATTTTTGACAACTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTc < 2:2762/141‑1 (MQ=255)
aTTATCATAAAAATAATTTTTGACAACTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGGAGAATCATTCATCTTc < 1:234736/141‑1 (MQ=255)
ttATCATAAAAATAATTTTTGACAACTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTAATCTTcc > 2:237207/1‑141 (MQ=255)
aTCATAAAAATAATTTTTGACAACTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATGATTCATCTTCCAt > 2:284267/1‑141 (MQ=255)
aTCATAAAAATAATTTTTGACAACTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCAt < 2:30963/141‑1 (MQ=255)
ataatTTTTGACAACTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTTCATTGAAATaaa > 1:246561/1‑141 (MQ=255)
ataatTTTTGACAACTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATaaa > 2:22183/1‑141 (MQ=255)
aatTTTTGACAACTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAgg < 1:123306/141‑1 (MQ=255)
atTTTTGACAACTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAACTAAAGGc > 1:194479/1‑141 (MQ=255)
atTTTTGACAACTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGc > 1:43106/1‑141 (MQ=255)
atTTTTGACAACTTGCTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGc > 1:292994/1‑141 (MQ=255)
tttttGACAACTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGATGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAATGCa > 2:42243/1‑141 (MQ=255)
aCTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACa > 1:207707/1‑141 (MQ=255)
cTTGTTGTGTAATGGTACTGCCACCTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACAt > 1:295523/1‑141 (MQ=255)
ggTACTACCACCTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATGCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGtt > 1:73611/1‑141 (MQ=255)
tactacCACCTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTAt < 1:232272/141‑1 (MQ=255)
ccaccTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCt > 1:270453/1‑141 (MQ=255)
ccaccTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCt < 1:173096/141‑1 (MQ=255)
ccTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGac > 1:208416/1‑141 (MQ=255)
caTCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAac < 1:157487/141‑1 (MQ=255)
tctcTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAacta > 2:34090/1‑141 (MQ=255)
tctcTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAacta > 1:85693/1‑141 (MQ=255)
ttGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTCCTTTTTTTTTCAAttt > 2:329410/1‑141 (MQ=255)
caaaaTAACGCTCTATTTGTCCCTTTCAACTCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACACTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAAttttt < 2:255419/140‑1 (MQ=255)
tAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAg < 1:389331/141‑1 (MQ=255)
tAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAg < 1:343727/141‑1 (MQ=255)
aaGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAGtt > 1:198771/1‑141 (MQ=255)
aaGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTATATTTTCAATTTTTCTTAGtt > 1:221677/1‑141 (MQ=255)
ttGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAGTTCATCCACAt < 2:112872/141‑1 (MQ=255)
ttGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAGTTCATCCACAt < 2:367141/141‑1 (MQ=255)
ctGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAGTTCATCCACAt < 2:235057/140‑1 (MQ=255)
ttCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAGCTACTTTTATTTTCAATTTTTCTTAGTTCATCCACATTATCGCgt > 1:131815/1‑141 (MQ=255)
aTCGTATACTTGATTATTGTCGAAGCGTGCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGa < 2:295523/141‑1 (MQ=255)
tCGAATCCATGATGATTGTAGAATCATTCATCTTCCAGTGAAATATCGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGAt < 1:89723/141‑1 (MQ=255)
atgatgATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCCCCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGATAAAAAATa < 1:378946/141‑1 (MQ=255)
tgatgaTTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGATAAAAAATAc > 1:179646/1‑141 (MQ=255)
tatgatTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATTCTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGATAAAAAATACa < 2:317323/140‑1 (MQ=255)
|
ATTATCATAAAAATAATTTTTGACAACTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCGTTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGATAAAAAATACA > USA300TCH1516_ALE/2018481‑2018737
|
| 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
