Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,679,847 G→A 100% G111S (GGT→AGT)  USA300HOU_2536 → possible secretory antigen

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,679,8470GA91.7% 64.0 / ‑0.8 24G111S (GGT→AGT) USA300HOU_2536possible secretory antigen
Reads supporting (aligned to +/- strand):  ref base G (1/1);  new base A (7/15);  total (8/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.86e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTT  >  CP000730/2679713‑2679980
                                                                                                                                      |                                                                                                                                     
aTGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACAgtagta                                                                                                                                 >  1:116622/1‑141 (MQ=255)
     aaaaaTTGGGATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTaaa                                                                                                                            <  1:131622/141‑1 (MQ=255)
          ttGGTATTCAAATGCACGTAAATCAAAATAGGCGACTGGTCGTACACCAACAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTc                                                                                                                       <  1:96040/141‑1 (MQ=255)
            ggTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTCAg                                                                                                                     <  1:241970/141‑1 (MQ=255)
              tATTACAATGCACGTAAATCAAAATATGCGAATGGTCGTACACCAAGAAAATTTGATGTCATGCAATCAACTGCAGGATATTATGGCCATGTCGCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTCAGaa                                                                                                                   <  1:181230/141‑1 (MQ=255)
                    aaTGCTCGTAAATCAAAATATGCGACTGTTCGTACACCAAAAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTCAGAATACAAc                                                                                                             <  1:151879/141‑1 (MQ=255)
                     aTGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTCAGAATACAACt                                                                                                            <  1:120320/141‑1 (MQ=255)
                                     atatGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTaaa                                                                                            <  1:277019/141‑1 (MQ=255)
                                              tGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAaatacaatac                                                                                   <  2:164092/141‑1 (MQ=255)
                                                    tACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACgtgt                                                                             >  1:217984/1‑141 (MQ=255)
                                                           aGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACAGGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGc                                                                      <  2:266676/141‑1 (MQ=255)
                                                              aaaTTTGCGGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCaaa                                                                   <  1:179197/141‑1 (MQ=255)
                                                                aTTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCaaaaa                                                                 >  2:75194/1‑141 (MQ=255)
                                                                  ttGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAgg                                                               <  1:262741/141‑1 (MQ=255)
                                                                     cTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAAGACAATACACGTGTACTAAGCAAAAAGgcag                                                            >  2:210764/1‑141 (MQ=255)
                                                                            gCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTaa                                                     >  2:38628/1‑141 (MQ=255)
                                                                                   aCTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAAc                                              <  2:123025/141‑1 (MQ=255)
                                                                                   aCTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAAc                                              <  2:31212/141‑1 (MQ=255)
                                                                                               tatGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAATTACTATACTTTTGTAAAAATTCTTAAGGCAGCGCGTAACTTTAACTCGATTTACTaa                                  <  1:244315/141‑1 (MQ=255)
                                                                                                        gTCGCAGTTGTTGAACAAGTATATAAAAACAGTCGTATTAAAGTTTAAGAATACAACTTTTCTCGCCCATTAAAATCCAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAAc                         <  1:69769/141‑1 (MQ=255)
                                                                                                           gCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTc                      <  1:6312/141‑1 (MQ=255)
                                                                                                           gCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACAATATTTACTAATCAAAAAACTTc                      >  2:137466/1‑141 (MQ=255)
                                                                                                                     aaCAAGTATATAAAAACAGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAAc            >  1:89432/1‑141 (MQ=255)
                                                                                                                               taAAAACAGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAAttt  >  1:163786/1‑141 (MQ=255)
                                                                                                                                      |                                                                                                                                     
ATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTT  >  CP000730/2679713‑2679980

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: