Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,712,693 T→A 11.1% Q70H (CAA→CAT)  isaA ← immunodominant antigen A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,712,6930TA11.1% 109.8 / 3.8 36Q70H (CAA→CAT) isaAimmunodominant antigen A
Reads supporting (aligned to +/- strand):  ref base T (12/20);  new base A (2/2);  total (14/22)
Fisher's exact test for biased strand distribution p-value = 6.34e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

GCTTACTGATTGTACATTTGAACCTTGGTTGTATGAAGTAGTGTAGTCTGCACCTGCAACGTTTGAGAAACCAGCAGTTTGACCATTAGCTGCTTCATAGCTCCATGACCATGTAGTACCATTTGAAGTGAAGTTATATTGGAAACCATCTTTTACAAAGTGGATGTCATATGCACCATCTTTGATTGGAGCTGCATTTAATTGATCTTGGTGATTATGCGCTAAGTCAACTAAGTGTGCTTGATCAACGTTTACTTCAGCAGCGTGTGCTTGATGTCCTGTACCT  >  CP000730/2712555‑2712840
                                                                                                                                          |                                                                                                                                                   
gCTTACTGATTGTACATTTGAACCTTGGTTGTATGAAGTAGTGTAGTCTGCACCTGCAACGTTTGAGAAACCAGCAGTTTGACCATTAGCTGCTTCATAGCTCCATGACCATGTAGTACCATTTGAAGTGAAGTTATATTGGAAACCAt                                                                                                                                           <  1:184816/149‑1 (MQ=255)
   tACTGATTGTACATTTGAACCTTGGTTGTATGAAGTAGTGTAGTCTGCACCTGCACCGTTTAAGAAAACAGACGTTCGAACATTAGCTGCTTCATCGCTCCATGACCATGTAGTACCATTTGAAGTGAAGTTATATTGGAAACCATCtt                                                                                                                                        <  1:181165/149‑1 (MQ=255)
     cTGATTGTACATTTGAACCTTGGTTGTATGAAGTAGTGTAGTCTGCACCTGCAACGTTTGAGAAACCAGCAGTTTGACCATTAGCTGCTTCATAGCTCCATGACCATGTAGTACCATTTGAAGTGAAGTTATAATGGAAACCATCtttt                                                                                                                                      >  1:271607/1‑149 (MQ=255)
     cTGATTGTACATTTGAACCTTGGTTGTATGAAGTAGTGTAGTCTGCACCTGCAACGTTTGAGAAACCAGCAGTTTGACCATTAGCTGCTTCATAGCTCCATGACCATGTAGTACCATTTGAAGTGAAGTTATAATGGAAACCATCtttt                                                                                                                                      >  1:68604/1‑149 (MQ=255)
       gATTGTACATTTGAACCTTGGTTGTATGAAGTAGTGTAGTCTGCACCTGCAACGTTTGAGAAACCAGCAGTTTGACCATTAGCTGCTTCATAGCTCCATGACCATGTAGTACCATTTGAAGTGAAGTTATATTGGAAACCATCTTTTAc                                                                                                                                    >  2:112265/1‑149 (MQ=255)
       gATTGTACATTTGAACCTTGGTTGTATGAAGTAGTGTAGTCTGCACCTGCAACGGTTGAGAAACCAGCAGTTTGACCATTAGCTGCTTCATAGCTCCATGACCATGTAGTACCATTTGAAGTGAAGTTATATTGGAAACCATCTTTTAc                                                                                                                                    >  2:112272/1‑149 (MQ=255)
                 ttGAACATTTGTTGTATGAAGTAGTGTAGTCTGCACCTGCAACGTTTAAGAGACCATCAGTTTGACCGTTGTCTGCTTCATAACTCCATGACCATCTAGTTCCATTTGTATTGACGTTATATTGGAATCCATCTTTTACAAAGTGGATg                                                                                                                          <  2:189045/149‑1 (MQ=255)
                    aaCCTTGGTTGTATGAAGTAGTGTAGTCTGCACCTGCAACGTTTGAGAAACCAGCAGTTTGACCATTAGCTGCTTCATAGCTCCATGACCATGTAGTACCATTTGAAGTGAAGTTATATTGGAAACCATCTTTTACAAAGTGGATGTCa                                                                                                                       >  2:71435/1‑149 (MQ=255)
                             tGTATGAAGTAGTGTAGTCTGCACCTGCAACGTTTGAGAAACCAGCAGTTTGACCATTAGCTGCTTCATAGCTCCATGACCATGTAGTACCATTTGAAGTGAAGTTATATTGGAAACCATCTTTTACAAAGTGGATGTCATATGCACCa                                                                                                              >  2:40243/1‑149 (MQ=255)
                                                         aaCGTTTGAGAAACCAGCAGTTTGACCATTAGCTGCTTCATAGCTCCATGACCATGTAGTACCATTTGAAGTGAAGTTATATTGGAAACCATCTTTTACAAAGTGGATGTCATATGCACCATCTTTGATTGGAGCTGCATTTAATTGAt                                                                                  <  2:140695/149‑1 (MQ=255)
                                                          aCGTTTGAGAAACCAGCAGTTTGACCATTAGCTGCTTCATAGCTCCATGACCATGTAGTACCATTTGAAGTGAAGTTATATTGGAAACCATCTTTTACAAAGTGGATGTCATATGCACCATCTTTGATTGGAGCTGCATTTAATTGATc                                                                                 >  2:5348/1‑149 (MQ=255)
                                                                gagaAACCAGCAGTTTGACCATTAGCTGCTTCATAGCTCCATGACCATGTAGTACCATTTGAAGTGAAGTTATATTGGAAACCATCTTTTACAAAGTGGATGTCATATGCACCATCTTTGATTGGAGCTGCATTTAATTGATCTTGGTg                                                                           >  2:255669/1‑149 (MQ=255)
                                                                 agaAACCAGCAGTTTGACCATTAGCTGCTTCATAGCTCCATGACCATGTAGTACCATTTGAAGTGAAGTTATATTGGAAACCATCTTTTACAAAGTGGATGTCATATGCACCATCTTTGATTGGAGCTGCATTTAATTGATCTTGGTGa                                                                          <  2:186386/149‑1 (MQ=255)
                                                                  gaAACCAGCAGTTTGACCATTAGCTGCTTCATAGCTCCATGACCATGTAGTACCATTTGAAGTGAAGTTATATTGGAAACCATCTTTTACAAAGTGGATGTCATATGCACCATCTTTGATTGGAGCTGCATTTAATTGATCTTGGTGAt                                                                         <  1:68935/149‑1 (MQ=255)
                                                                        agcagTTTGACCATTAGCTGCTTCATAGCTCCATGACCATGTAGTACCATTTGAAGTGAAGTTATATTGGAAACCATCTTTTACAAAGTGGATGTCATATGCACCATCTTTGATTGGAGCTGCATTTAATTGATCTTGGTGATTATgcg                                                                   <  2:188315/149‑1 (MQ=255)
                                                                                gACCATTAGCTGCTTCATAGCTCCATGACCATGTAGTACCATTTGAAGTGAAGTTATATTGGAAACCATCTTTTACAAAGTGGATGTCATATGCACCATCTTTGATTGGAGCTGCATTTAATTGATCTTGGTGATTATGCGCTAAGTCa                                                           <  2:167189/149‑1 (MQ=255)
                                                                                      tAGCTGCTTCATAGCTCCATGACCATGTAGTACCATTTGAAGTGAAGTTATATTGGAAACCATCTTTTACAAAGTGGATGTCATATGCACCATCTTTGATTGGAGCTGCATTTAATTGATCTTGGTGATTATGCGCTAAGTCAACTAAg                                                     <  1:88592/149‑1 (MQ=255)
                                                                                         ctgctTCATAGCTCCATGACCATGTAGTACCATTTGAAGTGAAGTTATATTGGAAACCATCTTTTACAAAGTGGATGTCATATGCACCATCTTTGATTGGAGCTGCATTTAATTGATCTTGGTGATTATGCGCTAAGTCAACTAAgtgt                                                  >  2:257698/1‑149 (MQ=255)
                                                                                                  aGCTCCATGACCATGTAGTACCATTTGAAGTGAAGTTATATTGGAAACCATCTTTTACAAAGTGGATGTCATATGCACCATCTTTGATTGGAGCTGCATTTAATTGATCTTGGTGATTATGCGCTAAGTCAACTAAGTGTGCTTGATCa                                         >  1:217792/1‑149 (MQ=255)
                                                                                                  aGCTCCATGACCATGTAGTACCATTTGAAGTGAAGTTATATTGGAAACCATCTTTTACAAAGTGGATGTCATATGCACCATCTTTGATTGGAGCTGCATTTAATTGATCTTGGTGATTATGCGCTAAGTCAACTAAGTGTGCTTGATCa                                         >  2:193863/1‑149 (MQ=255)
                                                                                                    cTCCATGACCATGTAGTACCATTTGAAGTGAAGTTATATTGGAAACCATCTTTTACAAAGTGGATGTCATATGCACCATCTTTGATTGGAGCTGCATTTAATTGATCTTGGTGATTATGCGCTAAGTCAACTAAGTGTGCTTGATCAAc                                       >  1:193173/1‑149 (MQ=255)
                                                                                                      ccATGACCATGTAGTACCATTTGAAGTGAAGTTATATTGGAAACCATCTTTTACAAAGTGGATGTCATATGCACCATCTTTGATTGGAGCTGCATTTAATTGATCTTGGTGATTATGCGCTAAGTCAACTAAGTGTGCTTGATCAACGt                                     >  2:259208/1‑149 (MQ=255)
                                                                                                             cATGTAGTACCATTTGAAGTGAAGTTATATTGGAAACCATCTTTTACAAAGTGGATGTCATATGCACCATCTTTGATTGGAGCTGCATTTAATTGATCTTGGTGATTATGCGCTAAGTCAACTAAGTGTGCTTGATCAACGTTTACTTc                              <  2:275252/149‑1 (MQ=255)
                                                                                                             cATGTAGTACCATTTGAAGTGAAGTTATATTGGAAACCATCTTTTACAAAGTGGATGTCATATGCACCATCTTTGATTGGAGCTGCATTTAATTGATCTTGGTGATTATGCGCTAAGTCAACTAAGTGTGCTTGATCAACGTTTACTTc                              <  1:178691/149‑1 (MQ=255)
                                                                                                             cATGTAGTACCATTTGAAGTGAAGTTATATTGGAAACCATCTTTTACAAAGTGGATGTCATATGCACCATCTTTGATTGGAGCTGCATTTAATTGATCTTGGTGATTATGCGCTAAGTCAACTAAGTGTGCTTGATCAACGTTTACTTc                              <  2:33783/149‑1 (MQ=255)
                                                                                                             cATGTAGTACCATTTGAAGTGAAGTTATATTGGAAACCATCTTTTACAAAGTGGATGTCATATGCACCATCTTTGATTGGAGCTGCATTTAATTGATCTTGGTGATTATGCGCTAAGTCAACTAAGTGTGCTTGATCAACGTTTACTTc                              <  1:276746/149‑1 (MQ=255)
                                                                                                                  agtaCCATTTGAAGTGAAGTTATATTGGAAACCATCTTTTACAAAGTGGATGTCATATGCACCATCTTTGATTGGAGCTGCATTTAATTGATCTTGGTGATTATGCGCTAAGTCAACTAAGTGTGCTTGATCAACGTTTACTTcagcag                         <  1:140650/149‑1 (MQ=255)
                                                                                                                  agtaCCATTTGAAGTGAAGTTATATTGGAAACCATCTTTTACAAAGTGGATGTCATATGCACCATCTTTGATTGGAGCTGCATTTAATTGATCTTGGTGATTATGCGCTAAGTCAACTAAGTGTGCTTGATCAACGTTTACTTcagcag                         <  1:189762/149‑1 (MQ=255)
                                                                                                                  agtaCCATTTGAAGTGAAGTTATATTGGAAACCATCTTTTACAAAGTGGATGTCATATGCACCATCTTTGATTGGAGCTGCATTTAATTGATCTTGGTGATTATGCGCTAAGTCAACTAAGTGTGCTTGATCAACGTTTACTTcagcag                         <  1:281827/149‑1 (MQ=255)
                                                                                                                     aCCATTTGAAGTGAAGTTATATTGGAAACCATCTTTTACAAAGTGGATGTCATATGCACCATCTTTGATTGGAGCTGCATTTAATTGATCTTGGTGATTATGCGCTAAGTCAACTAAGTGTGCTTGATCAACGTTTACTTCAGCAGCgt                      <  2:212964/149‑1 (MQ=255)
                                                                                                                       cATTTGAAGTGAAGTTATATTGGAAACCATCTTTTACAAAGTGGATGTCATATGCACCATCTTTGATTGGAGCTGCATTTAATTGATCTTGGTGATTATGCGCTAAGTCAACTAAGTGTGCTTGATCAACGTTTACTTCAGCAGCgtgt                    >  2:248164/1‑149 (MQ=255)
                                                                                                                        aTTTGAAGTGAAGTTATATTGGAAACCATCTTTTACAAAGTGGATGTCATATGCACCATCTTTGATTGGAGCTGCATTTAATTGATCTTGGTGATTATGCGCTAAGTCAACTAAGTGTGCTTGATCAACGTTTACTTCAGCAGCGtgtg                   <  1:184122/149‑1 (MQ=255)
                                                                                                                        aTTTGAAGTGAAGTTATATTGGAAACCATCTTTTACAAAGTGGATGTCATATGCACCATCTTTGATTGGAGCTGCATTTAATTGATCTTGGTGATTATGCGCTAAGTCAACTAAGTGTGCTTGATCAACGTTTACTTCAGCAGCGtgtg                   <  1:184125/149‑1 (MQ=255)
                                                                                                                                tgaagtTATATTGGAAACCATCTTTTACAAAGTGGATGTCATATGCACCATCTTTGATTGGAGCTGCATTTAAGTGATCTTGGTGATTATGCGCTAAGTCAACTAAGTGTGCTTGATCAACGTTTACTTCAGCAGCGTGTGCTTGATGt           <  1:59793/149‑1 (MQ=255)
                                                                                                                                 gaagtTATAATGGAAACCATCTTTTACAAAGTGGATGTCATATGCACCATCTTTGATTGGAGCTGCATTTAATTGATCTTGGTGATTATGCGCTAAGTCAACTAAGTGTGCTTGATCAACGTTTACTTCAGCAGCGTGTGCTTGATGTc          <  2:68604/149‑1 (MQ=255)
                                                                                                                                 gaagtTATAATGGAAACCATCTTTTACAAAGTGGATGTCATATGCACCATCTTTGATTGGAGCTGCATTTAATTGATCTTGGTGATTATGCGCTAAGTCAACTAAGTGTGATTGATCAACGTTTACTTCAGCAGCGTGTGCTTGATGTc          <  2:271607/149‑1 (MQ=255)
                                                                                                                                         atTGGAAACCATCTTTTACAAAGTGGATGTCATATGCACCATCTTTGATTGGAGCTGCATTTAATTGATCTTGGTGATTATGCGCTAAGTCAACTAAGTGTGCTTGATCAACGTTTACTTCAGCAGCGTGTGCTTGATGTCCTGTACct  >  1:296763/1‑149 (MQ=255)
                                                                                                                                          |                                                                                                                                                   
GCTTACTGATTGTACATTTGAACCTTGGTTGTATGAAGTAGTGTAGTCTGCACCTGCAACGTTTGAGAAACCAGCAGTTTGACCATTAGCTGCTTCATAGCTCCATGACCATGTAGTACCATTTGAAGTGAAGTTATATTGGAAACCATCTTTTACAAAGTGGATGTCATATGCACCATCTTTGATTGGAGCTGCATTTAATTGATCTTGGTGATTATGCGCTAAGTCAACTAAGTGTGCTTGATCAACGTTTACTTCAGCAGCGTGTGCTTGATGTCCTGTACCT  >  CP000730/2712555‑2712840

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑