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 |
|
A21 F63 I0 R1
|
92 |
32.2 |
718920 |
92.2% |
662844 |
140.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
CP000730 |
1,929,941 |
A→T |
48.3% |
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 | 48.3%
| ‑2.3
/ 48.5
| 42 | intergenic (‑1024/‑144) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (9/12); new base T (10/10); total (20/22) |
| Fisher's exact test for biased strand distribution p-value = 7.58e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCTAATTTTTCTTTTTGTAA > CP000730/1929802‑1930081
|
tggtagaataagagagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCATTTGCGTTCACAGCATAGCACCAGTCATCAGGGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAg < 2:305221/129‑1 (MQ=255)
ggtataATAATAAAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTA‑CTT‑TGC‑TAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTGTACTTATTGGCTTAgg > 2:209550/3‑140 (MQ=255)
tataATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTa > 1:336584/1‑141 (MQ=255)
tataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTaa < 2:173789/141‑2 (MQ=255)
taaaataGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTATTTTCGTTCGCATCATAGCACCAGTCATCAGTGGCTGTGCCGTTGCGTTTTTTTCTTCATGGCTAAGTa > 2:24364/4‑141 (MQ=255)
ataataataGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑T‑TGC‑TAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTaaa < 2:56056/141‑3 (MQ=255)
ataataGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTGT‑C‑C‑TGT‑CAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGc < 1:82463/141‑1 (MQ=255)
ataGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATCGCGTTTTTTTGTTATTGGCTCCGTAGACg > 1:294474/1‑141 (MQ=255)
tagtagAGTCGCCTATCTCTCCGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGc < 2:282721/141‑1 (MQ=255)
tagtagAGTCGCCTATCTCTCAGGCGTCAATTTAGTCGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTTCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGc < 2:268317/141‑1 (MQ=255)
taatagAGTCGCCTATCTCTCAGGCGTCGATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCa < 1:249006/138‑1 (MQ=255)
aaagagagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCa < 1:37940/137‑1 (MQ=255)
agagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGGGTATTATACTTATTGGCTTAGTAAACGCaacaa > 1:159474/1‑138 (MQ=255)
agagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTA‑C‑TTTGC‑TAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTGTTATACTTATTGGCTTAGTGAACGCaacaa > 1:33425/1‑138 (MQ=255)
agagTCGCCTATCTCTCAGGCGTCAATT‑‑CACGAAGAGAGGAGGTGCA‑TTA‑C‑T‑TTACTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAAGGCaacaa > 1:231223/1‑138 (MQ=255)
agagTCGCCTAGCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑T‑TGC‑TAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaa < 1:63764/141‑4 (MQ=255)
gagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaa > 1:270385/1‑137 (MQ=255)
ccTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGATGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataatta > 1:172911/1‑131 (MQ=255)
ccTATCTCTCAGGCGTCAA‑‑TAGACGAAGGGAGGAGGTGCA‑TTA‑CTT‑TGC‑TAATCTTTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataatta > 1:232189/1‑131 (MQ=255)
tATCTCTCAGGCGGCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaat < 1:222125/141‑13 (MQ=255)
tATCTCTAAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaat < 2:94746/141‑13 (MQ=255)
ttctctcAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTATTTTCGTTCACATCATTGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGt < 2:313064/140‑1 (MQ=255)
aTCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaata > 1:221566/1‑128 (MQ=255)
aTCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaata > 1:32157/1‑128 (MQ=255)
aTCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGC‑TAATCATTTTCGTTCACATCATAGCACCAGTCAGCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaata < 1:346969/141‑14 (MQ=255)
tctcAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTCTTTTCTTATTCGCTAAGTGGACGCACT‑‑CCAC‑‑AATAGGCGAc > 2:230209/1‑141 (MQ=255)
cGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGTCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGc > 2:347322/1‑141 (MQ=255)
aaTTTAGACGCAGAAAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTATTTTCCTTCACATCAAAAAAAAAAAAAAAAGTGGCTGGGACAGTGCGTTTTTTTCTTACTGGCTACGTAGAAAAAAT‑‑ACAA‑‑AGCCGGTTTCA‑TAT‑Agaaaaa < 2:155225/141‑6 (MQ=255)
taA‑G‑G‑TGA‑TGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGc < 2:212254/141‑1 (MQ=255)
tATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAggg < 1:249357/141‑1 (MQ=255)
ttttCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGa < 1:171248/141‑1 (MQ=255)
ttttCGTTCACACCCTCGCACCAGTCATCAGTGGCTGTGCCATTGCGTTCTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGa < 1:24364/141‑1 (MQ=255)
catAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGt > 1:194722/1‑141 (MQ=255)
catAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGGGAGGGGGTTGGTGTATAAGt > 1:91724/1‑141 (MQ=255)
atAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCAACAAATAATTAATAGGCGACTTTATAAGCCAGCAACGA‑AAAAATCCCCACACTACTGC‑AATAGTGAGGGGATGGGTGcat > 2:125072/1‑141 (MQ=255)
cACCAGTCATCAGGGGCTGTGCCATTGCGTTTTTTTCTTAGTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATa < 2:241423/141‑1 (MQ=255)
gTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGtt > 2:309151/1‑141 (MQ=255)
cTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCt < 1:148616/141‑1 (MQ=255)
aTTGCGTTTTTTTCTTCTTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATCAGTCATTTCGTAGTTTCGTTGTCTTAATtat < 2:254164/141‑1 (MQ=255)
tttttCTTTTTTGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GAACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATCCTTATTTTCGTTGTCTTAAtttaccttctaa > 2:16784/1‑131 (MQ=255)
tttCGTATTGGCTAAGGAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCTAAtt < 2:336584/141‑1 (MQ=255)
aTTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCTAATTTTTCtt > 2:121646/1‑141 (MQ=255)
aaGTAGACCAAAT‑‑ACAA‑‑AATAGGTTACA‑AGT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAATTTGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGGCTTAATTATACTGCTAATTTTTCTTTTTGTaa < 2:351220/141‑1 (MQ=255)
|
TGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGA‑TGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACA‑TAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCTAATTTTTCTTTTTGTAA > CP000730/1929802‑1930081
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
