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 |
|
A15 F177 I0 R1
|
51 |
26.9 |
575130 |
96.6% |
555575 |
140.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
CP000730 |
2,679,650 |
G→A |
100% |
C45Y (TGT→TAT) |
USA300HOU_2536 → |
possible secretory antigen |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | CP000730 | 2,679,650 | 0 | G | A | 93.4%
| 69.0
/ ‑3.1
| 27 | C45Y (TGT→TAT) | USA300HOU_2536 | possible secretory antigen |
| Reads supporting (aligned to +/- strand): ref base G (0/2); new base A (16/9); total (16/11) |
| Fisher's exact test for biased strand distribution p-value = 1.57e-01 |
| 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: Variant not supported by required number of reads on each strand. |
AAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTCAGCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTC > CP000730/2679515‑2679786
|
aaaTGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTCAGCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTTATTATTATAGTAAAAACCAATAGACAt > 1:102689/1‑141 (MQ=255)
aaaTGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTCAGCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACAt > 1:102685/1‑141 (MQ=255)
aTGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTCAGCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACAtgg > 1:220446/1‑141 (MQ=255)
aaaGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTCAGCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCAtttga > 1:43821/1‑139 (MQ=255)
attaATTGCTTTTGCAGTACTTTTCTCAGCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCgg < 1:250969/141‑1 (MQ=255)
ttaATTGCTTTTGCAGTACTTTTCTCAGCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGt < 2:25568/141‑1 (MQ=255)
tgtttttGCATTACTTTTCTCAGCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAAcc < 2:101664/138‑1 (MQ=255)
tttCCCCGCAGATTTCACTTATCACTTCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATg < 1:64676/141‑1 (MQ=255)
ttCTCAGCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGAtag > 2:65414/1‑139 (MQ=255)
tctcAGCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATggg < 1:156716/141‑1 (MQ=255)
tctcAGCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAAACTGTTTATAATAGATggg > 2:261289/1‑141 (MQ=255)
ctcAGCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATgggg > 1:58183/1‑141 (MQ=255)
cagcagATTTCACTTATCAATCCGTAGAACAAAAGCAACAATCGCATGCCGCAGTTAATTATTATAATAAAAACCAAAATACATGGTAGGCAATTAAACTTCAAGAACAAATCAGTAAACCAAATTCTaaaacataaggca > 2:20526/1‑130 (MQ=255)
cagATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATg < 2:13674/141‑1 (MQ=255)
cACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTaaaaa < 1:265125/141‑1 (MQ=255)
aTCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACACGTCGGTAAACCTGTTTCTAATAAATGGGGCAATGCTAAAAATTGGTAttt > 2:87879/1‑140 (MQ=255)
cGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACaa > 1:223501/1‑141 (MQ=255)
gaactaaccagtccaTCGCATGGCGCAATTAAGTACTATAGTAAAAACCAATGTACAGTGTGGGCATTTAAACGTCGCGCACAACTCGGTAAACCTGTTTCTAAAAGATGGGGCAATGCTACAAATTGGTATTACAATGCa < 2:244516/127‑1 (MQ=255)
aCAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACg < 2:162651/141‑1 (MQ=255)
tCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTAGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAAGGCTAAAAAGTGGTATTACAATGCACATGAATCaaa > 1:120939/1‑141 (MQ=255)
aTGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTACACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGa > 2:7559/1‑141 (MQ=255)
aTGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGGTGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAAACAAAATATgaga > 2:7539/1‑141 (MQ=255)
tGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGAc > 1:153037/1‑141 (MQ=255)
tGCCGAAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGAc < 2:38875/141‑1 (MQ=255)
cGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTgg > 1:170889/1‑141 (MQ=255)
ataGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGaa < 1:116274/141‑1 (MQ=255)
cAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAAAAAACTTGCTGTc > 2:248699/1‑141 (MQ=255)
|
AAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTCAGCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTC > CP000730/2679515‑2679786
|
| 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
