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 |
1,929,941 |
A→T |
32.3% |
intergenic (‑1024/‑144) |
USA300HOU_1794 ← / → USA300HOU_1796 |
hypothetical protein/hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | CP000730 | 1,929,941 | 0 | A | T | 32.3%
| 37.2
/ 31.7
| 37 | intergenic (‑1024/‑144) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (12/13); new base T (2/10); total (14/23) |
| Fisher's exact test for biased strand distribution p-value = 8.36e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.32e-01 |
TGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAAG‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCTAATTTTT > CP000730/1929802‑1930071
|
tgatATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAAG‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTaa > 2:99658/1‑141 (MQ=255)
tataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACT‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTaa < 1:280839/141‑2 (MQ=255)
aataatAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACT‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACg > 1:93037/1‑141 (MQ=255)
ataatagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACT‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGc < 2:301488/137‑1 (MQ=255)
ataatagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACT‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGc < 1:158128/137‑1 (MQ=255)
ataatagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACT‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGc < 2:36173/137‑1 (MQ=255)
ataatagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTAC‑TT‑‑TGCTAATCATTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCa < 2:283603/137‑1 (MQ=255)
taatagTGTCGCCTATCTTTAAGGCGTCAATT‑‑GAAGAAGAGAGGAGGTGCATTACT‑ATGCTAATCAT‑‑TTTCGTTCAAATCATAGCCCCAGTCATCAGTGGCTGTGCTATTGCGTATTATACTTATTGGCTTAGTAAACGCa < 2:44104/138‑1 (MQ=255)
tagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACT‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaaca < 1:204486/141‑3 (MQ=255)
tagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACT‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaaca < 1:304971/141‑3 (MQ=255)
gagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACT‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaa > 2:263415/1‑137 (MQ=255)
gagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACTTTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaa < 1:232403/141‑5 (MQ=255)
agTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACT‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCGGTGGCTGTGCTGTTGCAAATTATGCTTATTGGCTTCGTAAACGCaacaaat < 2:52958/141‑6 (MQ=255)
gTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAAG‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGTCTAAGTAGACGCAATACaa > 2:170569/1‑141 (MQ=255)
gTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAAG‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACaa > 2:170563/1‑141 (MQ=255)
cGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAAG‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCAATTGCGTTTTTTTCTTATTGGCTAAGTACACGCAATACaaaa > 1:302135/1‑141 (MQ=255)
gagagataGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAAG‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGt > 2:242800/8‑141 (MQ=255)
gCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAAG‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAg > 2:214335/1‑141 (MQ=255)
tCAATTTAGACGCAGAGAGGAGGTGTA‑TAAG‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCg < 1:305019/141‑1 (MQ=255)
aaTTTAGTCGCAGAGAGGAGGTGTA‑TAAG‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCa < 1:300793/141‑1 (MQ=255)
cGCAGAGAGGAGGTGTA‑TAAG‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATaaa < 1:245639/141‑1 (MQ=255)
gCAGAGAGGAGGTGTA‑TAAG‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATaaaa > 2:47681/1‑141 (MQ=255)
ggTGTA‑TAAG‑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)
tttttttCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCt < 1:254328/141‑1 (MQ=255)
tttttttCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCt > 2:228964/1‑141 (MQ=255)
tttCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCTAAtt < 1:99658/141‑1 (MQ=255)
cTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCTAAttttt < 2:39688/141‑1 (MQ=255)
|
TGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAAG‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCTAATTTTT > CP000730/1929802‑1930071
|
| 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
