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 |
|
A19 F57 I0 R1
|
85 |
36.1 |
800162 |
93.0% |
744150 |
140.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
CP000730 |
1,929,946 |
G→A |
39.2% |
intergenic (‑1029/‑139) |
USA300HOU_1794 ← / → USA300HOU_1796 |
hypothetical protein/hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | CP000730 | 1,929,946 | 0 | G | A | 39.2%
| 24.6
/ 29.9
| 38 | intergenic (‑1029/‑139) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (12/11); new base A (11/4); total (23/15) |
| Fisher's exact test for biased strand distribution p-value = 3.10e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.66e-01 |
ATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GT‑GATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCTAATTTTTCTTTTTGTAAAATA > CP000730/1929809‑1930085
|
ataatagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TT‑GCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTATTAAACGc > 2:159873/5‑141 (MQ=255)
ataGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GT‑GATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACg > 1:335014/1‑141 (MQ=255)
ataGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GT‑GATGCTTATTTTCCCTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACg > 1:290362/1‑141 (MQ=255)
taatagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TT‑GCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCa < 1:297687/138‑1 (MQ=255)
caatatagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TT‑GCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCa < 2:196202/135‑1 (MQ=255)
atagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GAGGAAGAGAGGAGGTGCATTAC‑T‑GT‑GCTAATCATTTTCGTTCGCATCATAGCACCAGTCATCAGTCGCTGTGCTGTGGCGTCTTATACTTATTGGCTTAGTCAACGCaac > 2:301096/2‑140 (MQ=255)
gTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GT‑GATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACaa < 1:24325/141‑1 (MQ=255)
gTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TT‑GCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacgaata > 1:12308/1‑135 (MQ=255)
gTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TT‑GCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaata > 2:286085/1‑135 (MQ=255)
tCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TT‑GCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataa > 2:314126/1‑134 (MQ=255)
gcctttccgtcAGGCTTCAATTTAAGCGCAGAGGGGAGGTGTA‑TAA‑G‑GT‑GATGCTTATGTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTGTTTCTTATTGGCTAAGTAGACGCAATACAAAAt < 2:77131/132‑1 (MQ=255)
gCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TT‑GCTAATCATTTTCGTTCACATCATAGCACCAATCATCAGTGGCTTTGCTGTTGCGTATCATACTTATTGGCTTAGTAAACGCaacaaatgatt > 2:102184/1‑132 (MQ=255)
gCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTA‑CTTT‑GCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataatt > 1:21717/1‑132 (MQ=255)
gCCTATCTCGCAGGCGTCAAGT‑‑GGCGAAGAGAGGAGGTGCATTAC‑T‑TT‑GCTAATCATTTGCGTTCACATCATAGCACCAGTCATCCGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataatt < 1:76933/141‑10 (MQ=255)
cTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TT‑GCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaa < 1:312343/141‑12 (MQ=255)
cTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TT‑GCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTCAATGGCTTAGTAAACGCaacaaataattaa > 1:187558/1‑130 (MQ=255)
tATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑TT‑GCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTAATTGGCTTAGTAAACGCaacaaataattaaa > 2:105831/1‑129 (MQ=255)
tATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGCAGGTGCA‑TTA‑C‑TTGGCTAATCATTTTCACTCACAACATAGCACAAGTCATGAGTGGCTGTGCTGATGCGTATTATACTTATTGGCTTAGTAAACGCaacaactaattaat > 2:149117/1‑129 (MQ=255)
tctctcAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTA‑CTTT‑GCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaatag > 2:295300/1‑127 (MQ=255)
tcAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GT‑GATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCCTTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATaacatacct > 2:278132/1‑133 (MQ=255)
tcAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GT‑GATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACat < 1:93331/141‑1 (MQ=255)
cAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GT‑GATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGc > 2:352045/1‑141 (MQ=255)
gaggTGTA‑TAA‑G‑GT‑GATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAGACAAAATAGGTGCCATATAGCCGCACCAATAAAAATcccccc > 2:28321/1‑139 (MQ=255)
cTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCCCACTACCGCAAATAGTGAg < 1:211986/141‑1 (MQ=255)
ttATATTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGACTAAGTAGACGCAATAAAAAATAGGTGAAATATAGCCGCACCAATAAAAATCACCTCACTACAGAAAATAATGAgg > 1:167631/1‑141 (MQ=255)
atAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTa > 1:102260/1‑141 (MQ=255)
catcaGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAACTAGTGAGGGGCTTGGTGTATAAGTAAATACTAAttt > 2:152766/1‑141 (MQ=255)
caGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGAGTGGTGTATAAGTAAACACTTATTTTCg > 2:156389/1‑141 (MQ=255)
cagtGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATta < 1:51878/138‑1 (MQ=255)
tttCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTCAATACTTATTTTCGTTGTCTTAATTATACTGCTAAtt < 2:44754/141‑1 (MQ=255)
tttCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCTAAtt < 1:160986/141‑1 (MQ=255)
tgtCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATAGAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCTAAtt < 2:177470/139‑1 (MQ=255)
ttttcttttcTAAGTCGAAGAAATACCAAATCGGTGACAGATAGCCGCACCAATAAAAATCCGCTCACTACCGAAAATAGTCAGGCGATTGGTGTATAAGTAAACACTTATTCTCAGCAGCTTACTTATACAGATAAtttt > 2:232616/10‑141 (MQ=255)
ggCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGGAAATACTTATTTTCGTTGTCTTAATTATACTTCTAATTTTTCttttt < 1:295689/141‑1 (MQ=255)
aGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCTAATTTTTCTTTTTGTaaa > 2:284509/1‑141 (MQ=255)
gTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCTAATTTTTCTTTTTGTaaaa < 1:323653/141‑1 (MQ=255)
tAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGAGTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCTATTTTTTCTTTTTGTaaact > 1:341922/1‑139 (MQ=255)
aGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCTAATTTTTCTTTTTGTAAAata < 1:233838/141‑1 (MQ=255)
|
ATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GT‑GATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCTAATTTTTCTTTTTGTAAAATA > CP000730/1929809‑1930085
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
