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 |
1,613,762 |
T→C |
100% |
intergenic (‑31/‑37) |
scpA ← / → USA300HOU_RS08000 |
Segregation and condensation protein A/hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | USA300TCH1516_ALE | 1,613,762 | 0 | T | C | 99.0%
| 81.6
/ ‑6.6
| 25 | intergenic (‑31/‑37) | scpA/USA300HOU_RS08000 | Segregation and condensation protein A/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (13/11); minor base G (1/0); total (14/11) |
| 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: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
TAAATATCTATTTCAAATTTTTGGATAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCATGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACATTTTAGAAGATGCATGGAAAGCTGAA > USA300TCH1516_ALE/1613625‑1613894
|
tAAATATCTATTTCAAATTTTTGGATAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGaa > 1:136899/1‑141 (MQ=255)
aaaTATCTATTTCAAATTTCTGGATAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGaaa > 1:237104/1‑141 (MQ=255)
ttttGGATAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAAt > 2:233111/1‑141 (MQ=255)
gATAAGATGCAGCAATCAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATCATATCTACTTCGGATTGCGTCATATGTGCATAATTCTCTCAAAAATTATAGCAGGAAAATAACTTACTTTTAAATTgggg > 2:134960/1‑141 (MQ=255)
aTGAAGCAATAAAACTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCCCCCAAATATTATATCACTAAAATAACTTACTTTTAAATTGGGGTGATaa < 1:233111/141‑1 (MQ=255)
tGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAAc < 2:388561/141‑1 (MQ=255)
gcagcaATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACa < 2:209275/141‑1 (MQ=255)
gcagcaATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACa < 2:201834/141‑1 (MQ=255)
gaaaTAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACaaaa < 1:176214/139‑1 (MQ=255)
aTACATCTAATGGCCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGc < 2:258962/141‑1 (MQ=255)
aTAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGc > 1:314706/1‑141 (MQ=255)
ccATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATa > 2:257317/1‑141 (MQ=255)
ttCATCCATAAGATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATAc < 1:16756/141‑1 (MQ=255)
cTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCt < 1:40440/141‑1 (MQ=255)
tGCGTCATATGTGCATGAGTCTCTAAGATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACCTTATTTCCTATGTCAt < 2:97829/141‑1 (MQ=255)
gCGTAATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATg > 1:269112/1‑141 (MQ=255)
gTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGAc < 1:39860/141‑1 (MQ=255)
tCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACa > 1:327048/1‑141 (MQ=255)
atGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACAtttt < 2:314706/141‑1 (MQ=255)
cATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACATTTTagaag > 1:184379/1‑141 (MQ=255)
tctAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACATTTTAGAAGATGCATgg > 2:33714/1‑141 (MQ=255)
aaTATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACATTTTAGAAGATGCATGGAAAGc > 2:147027/1‑141 (MQ=255)
ttatAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACATTTTAGTAGATGCATGGAAAGCTGaa > 1:314914/1‑141 (MQ=255)
ttatAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACATTTTAGAAGATGCATGGAAAGCTGaa > 1:36927/1‑141 (MQ=255)
ttatAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACATTTTAGAAGATGCATGGAAAGCTGaa > 2:308012/1‑141 (MQ=255)
|
TAAATATCTATTTCAAATTTTTGGATAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCATGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACATTTTAGAAGATGCATGGAAAGCTGAA > USA300TCH1516_ALE/1613625‑1613894
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
