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 |
|
A9 F22 I0 R2
|
95 |
29.9 |
669916 |
92.3% |
618332 |
139.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
CP000730 |
1,929,917 |
C→T |
38.7% |
intergenic (‑1000/‑168) |
USA300HOU_1794 ← / → USA300HOU_1796 |
hypothetical protein/hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | CP000730 | 1,929,917 | 0 | C | T | 38.7%
| 32.9
/ 45.1
| 47 | intergenic (‑1000/‑168) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base C (14/14); new base T (5/13); total (20/27) |
| Fisher's exact test for biased strand distribution p-value = 2.20e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.59e-01 |
ACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAAT > CP000730/1929780‑1930055
|
aCTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCAtt > 2:222136/1‑141 (MQ=255)
aCTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCAtt > 1:22891/1‑141 (MQ=255)
aCTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCAtt < 2:95373/141‑1 (MQ=255)
cTGTGCGTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTg < 2:78453/141‑1 (MQ=255)
tgtgCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCATGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGc < 2:321466/141‑1 (MQ=255)
tgtgCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGc < 1:298140/141‑1 (MQ=255)
atgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCGTAGCACCAGTCATCAGTGGCTGTGCTGTTGCGt > 1:31670/2‑141 (MQ=255)
cTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtatt > 1:15080/1‑141 (MQ=255)
cacagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTg > 2:173140/5‑141 (MQ=255)
ccGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTgg > 1:60036/1‑141 (MQ=255)
cagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGc < 2:215288/139‑1 (MQ=255)
agatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCt < 2:316340/140‑1 (MQ=255)
tggtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCttag < 2:115722/138‑4 (MQ=255)
tgatATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTaa > 2:99658/1‑141 (MQ=255)
tataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTaa < 1:280839/141‑2 (MQ=255)
aataatAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACg > 1:93037/1‑141 (MQ=255)
ataatagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGc < 2:36173/137‑1 (MQ=255)
ataatagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGc < 2:301488/137‑1 (MQ=255)
ataatagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGc < 1:158128/137‑1 (MQ=255)
ataatagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTA‑C‑TT‑‑TGCTAATCATTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCa < 2:283603/137‑1 (MQ=255)
taatagTGTCGCCTATCTTTAAGGCGTCAATT‑‑GAAGAAGAGAGGAGGTGCATTAC‑T‑ATGCTAATCAT‑‑TTTCGTTCAAATCATAGCCCCAGTCATCAGTGGCTGTGCTATTGCGTATTATACTTATTGGCTTAGTAAACGCa < 2:44104/138‑1 (MQ=255)
tagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaaca < 1:304971/141‑3 (MQ=255)
tagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaaca < 1:204486/141‑3 (MQ=255)
gagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaa > 2:263415/1‑137 (MQ=255)
gagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTA‑CTTTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaa < 1:232403/141‑5 (MQ=255)
agTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCGGTGGCTGTGCTGTTGCAAATTATGCTTATTGGCTTCGTAAACGCaacaaat < 2:52958/141‑6 (MQ=255)
gTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGTCTAAGTAGACGCAATACaa > 2:170569/1‑141 (MQ=255)
gTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACaa > 2:170563/1‑141 (MQ=255)
cGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCAATTGCGTTTTTTTCTTATTGGCTAAGTACACGCAATACaaaa > 1:302135/1‑141 (MQ=255)
gagagataGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGt > 2:242800/8‑141 (MQ=255)
gCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAg > 2:214335/1‑141 (MQ=255)
tCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCg < 1:305019/141‑1 (MQ=255)
aaTTTAGTCGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCa < 1:300793/141‑1 (MQ=255)
cGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATaaa < 1:245639/141‑1 (MQ=255)
gCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATaaaa > 2:47681/1‑141 (MQ=255)
ggTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCAc < 1:9449/141‑1 (MQ=255)
gTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTatttgcggt < 2:196222/141‑9 (MQ=255)
ttCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGgtg > 1:118140/1‑141 (MQ=255)
tCACATCATAGCGAGACTGCTCAGTGGCTGCGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCGCTACCGCAAATAGTGAGGGGAtttttat < 1:268926/141‑6 (MQ=255)
cacaTCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGta < 2:145325/141‑1 (MQ=255)
catcatAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGtata < 2:71282/141‑1 (MQ=255)
atcatAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATCGTGAgggattttttattggt > 2:268926/1‑128 (MQ=255)
gCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAAt > 1:152156/1‑141 (MQ=255)
gTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTAt < 1:57165/141‑1 (MQ=255)
aGTGGCTGTGCCATTGCGTTTTTTTTTTTTTTGCTAAGTAGACGCAATACAAAATAGTTGGCATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGt > 2:7309/1‑141 (MQ=255)
gCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATTGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTc < 2:69516/141‑1 (MQ=255)
gCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAAt > 1:188161/1‑141 (MQ=255)
|
ACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAAT > CP000730/1929780‑1930055
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
