Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 190,047 G→T 11.9% G14C (GGT→TGT)  dxr → 1‑deoxy‑D‑xylulose 5‑phosphate reductoisomerase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP009273190,0470GT11.9% 115.7 / 6.7 49G14C (GGT→TGT) dxr1‑deoxy‑D‑xylulose 5‑phosphate reductoisomerase
Reads supporting (aligned to +/- strand):  ref base G (24/19);  new base T (3/3);  total (27/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.42e-01

TGATGCAGTTCTGATTTCTTGAACGACAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTGGCAGGCAAAAATGTCACTCGCATGGTAGAACAGTGCCTGGAATTCTCTCCCCGCTATGCCGTAATGGACGATGAAGCGAGTGCG  >  CP009273/189903‑190193
                                                                                                                                                |                                                                                                                                                  
tGATGCAGTTCTGATTTCTTGAACGACAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTg                                                                                                                                                >  1:797548/1‑149 (MQ=255)
   tGCAGTTCTGATTTCTTGAACGACAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTTGTTgcag                                                                                                                                             >  1:388110/1‑149 (MQ=255)
   tGCAGTTCTGATTTCTTGAACGACAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCT‑GATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTTGTTgcagc                                                                                                                                            >  1:667933/1‑149 (MQ=255)
   tGCAGTTCTGATTTCTTGAACGACAAAAACGCCGCGCAGTATATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTTGTTgcag                                                                                                                                             >  1:209780/1‑149 (MQ=255)
     cAGTTCTGATTTCTTGAACGACAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTgcagca                                                                                                                                           <  1:712738/149‑1 (MQ=255)
                gcgtGAACGGCAAAAACCCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTGTTGCTTTTTATTCTGTCGCAACCCTGGATGTTTCATGAAGCAGCTCACCACTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACgtg                                                                                                                                <  1:9736/146‑1 (MQ=255)
                 cctGAACGACAAAAACGCCGCTCAGGAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACgtgg                                                                                                                               <  1:260395/147‑1 (MQ=255)
                   tGAACGACAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACgtggtg                                                                                                                             >  1:29955/1‑149 (MQ=255)
                       cGACAAAAACGCCGCTCAGTAGATACTTGCGGAGCGGCTGGGGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGcc                                                                                                                         <  2:546484/149‑1 (MQ=255)
                        gACAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCa                                                                                                                        >  1:345681/1‑149 (MQ=255)
                         aCAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCAt                                                                                                                       <  1:61303/149‑1 (MQ=255)
                           aaacaCACCGCACAATAAAACCTAGCCGATGGGATGGCGGCATGGTGCTTGTGATGCGGTCTCGTCGCTGGGTGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTTGACGTGGTGCGCCATaa                                                                                                                     >  1:639792/1‑149 (MQ=255)
                              aaCGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCTTTCTGGGCTCTACCGGGTCGGTTGGTTGCAGCCCGGTGGAAGTGGTGCGCGATAAttc                                                                                                                  >  1:240721/1‑147 (MQ=255)
                              aaCGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCGCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATcc                                                                                                                  >  1:595871/1‑149 (MQ=255)
                                 gccgcTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGa                                                                                                               >  2:96175/1‑149 (MQ=255)
                                    gcTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCCCGCTGGACGTCGGGCGCCAACATCCCCAaca                                                                                                            >  1:698397/1‑149 (MQ=255)
                                             aTCCTTGCGGATCGGCTGGCGGGGTTTTGCTTTTTATTCTGTCTCAACTCTGGGTGTTTCATGAAGCAACGCACCATTCTGGGCTCGACCGGCTCGGTTGTTTGCAGCACGCTGGACGTGGTACACCATATTACCGGCCACTTCCGCGt                                                                                                   >  1:150733/1‑149 (MQ=255)
                                              tCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTGTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCAGGGTGGACGTGGTGCGGCATGAGCCCGAACACTTCGGGGTa                                                                                                  >  1:261390/1‑149 (MQ=255)
                                                cTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGt                                                                                                >  2:489786/1‑149 (MQ=255)
                                                               gcggcgTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCAGGCGGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTggcagg                                                                                 <  2:676945/149‑1 (MQ=255)
                                                                          cTTTTTTTTCTCTCTCAACTCTGGGTGTGTCATGAAGCACCCCACCCTTCTCGGCTCGACCGGCCCGATTGGTTTCAGCACGCTGGACGTGGTGCGCCATAATCCCCAACACTTCCGCCTAGTTGCGCTTGTGGCAGGCAAAAATGTCa                                                                      <  1:40943/149‑1 (MQ=255)
                                                                             tttATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGGCGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTGGCAGGCAAAAATGTCACTc                                                                   >  1:648877/1‑149 (MQ=255)
                                                                                      tctcAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATGCCGAACCCTTCCGGGTAGTTGCGCGGGTGGCGGGCAAAAATGTCACTCGCATGGTAg                                                          >  1:801141/1‑149 (MQ=255)
                                                                                       ctcAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTGGCAGGCAAAAATGTCACTCGCATGGTAGa                                                         <  2:797548/149‑1 (MQ=255)
                                                                                          aaCTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTTCGCTGGTGGCCGGCAAAAATGTCACTCGCATGGTAGAACa                                                      >  2:823081/1‑149 (MQ=255)
                                                                                             tctGGATGTTTCATGCAGCAACTCACCATTCTGGGCTCGACCGGCGCGGTTGGTTGCAGCACGCTGGACGTGGTGCGCCATAGTGCCGAACACTTCCGCGTCGGTGGGCTGGTGGCCGGCAAAACTGTCACTCGCATGGCAggaaggtg                                                   >  1:813481/1‑142 (MQ=255)
                                                                                                    gTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTGGCAGGCAAAAATGTCACTCGCATGGTAGAACAGTGCCTggta                                            <  1:489786/149‑3 (MQ=255)
                                                                                                      ttCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTGGTTGCGCTGGTGGCAGGCAAAAATGTCACTCGCCTGGTAGAACAGGGCCTGGAAtt                                          >  1:689490/1‑149 (MQ=255)
                                                                                                      ttCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTGGCAGGCAAAAATGTCACTCGCATGGTAGAACAGTGCCTGGAAtt                                          <  2:698397/149‑1 (MQ=255)
                                                                                                        caggAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTTGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTGGCAGGCAAAAATGTCACTCGCATGGTAGAACAGTGCCTGGAATtct                                        <  2:667933/146‑1 (MQ=255)
                                                                                                        cATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTTGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTGGCAGGCCCAGAACTCACTCGCATGGTAGAACAGTGCCTGGAATtct                                        <  2:209780/149‑1 (MQ=255)
                                                                                                        cATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTTGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTGGCAGGCAAAAATGTCACTCGCATGGTAGAACAGTGCCTGGAATtct                                        <  2:388110/149‑1 (MQ=255)
                                                                                                        cATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGTACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTGGCAGGCAAAAATGTCACTCGCATGGTAGAACAGTGCCTGGAATtct                                        <  2:258094/149‑1 (MQ=255)
                                                                                                               cAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTGGCAGGCAAAAATGTCACTCGCATGGTAGAACAGTGCCTGGAATTCTCTCCCCg                                 >  2:60743/1‑149 (MQ=255)
                                                                                                                  cTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTGGCAGGCAAAAATGTCACTCGCATGGTAGAACAGTGCCTGGAATTCTCTCCCCGCTa                              <  2:345681/149‑1 (MQ=255)
                                                                                                                     aCCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTGGCAGGCAAAAATGTCACTCGCATGGTAGAACAGTGCCTGGAATTCTCTCCCCGCTATGc                           <  2:271978/149‑1 (MQ=255)
                                                                                                                       cATTCTGGGCTCGCCCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTGGCAGGCAAAAATGTCACTCGCATGGTAGAACAGTGCCTGGAATTCTCTCCCCGCTATGCCg                         <  1:543487/149‑1 (MQ=255)
                                                                                                                       cATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTGGCAGGCAAAAATGTCACTCGCATGGTAGAACCGTGCCTGGAATTCTCTCCCCGCTGTGCCg                         >  2:832674/1‑149 (MQ=255)
                                                                                                                       cATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTGGCAGGCAAAAATGTCACTCGCATGGTAGAACAGTGCCTGGAATTCTCTCCCCGCTATGCCg                         <  2:29955/149‑1 (MQ=255)
                                                                                                                         ttCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTGGCAGGCAAAAATGTCACTCGCATGGTAGAACAGTGCCTCGAATTCTCTCCCCGCTATGCCGTa                       >  2:866029/1‑149 (MQ=255)
                                                                                                                                cTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTGGCAGGCAAAAATGTCCCTCGCATGGTAGAACAGTGCCTGGCATTCTCTCCCCGCTATGCCGTAATGGACg                >  1:715655/1‑149 (MQ=255)
                                                                                                                                cTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTGGCAGGCAAAAATGTCACTCGCATGGTAGAACAGTGCCTGGAATTCTCTCCCCGCTATGCCGTAATGGACg                >  2:671882/1‑149 (MQ=255)
                                                                                                                                cTCGACCGGCTCGATTGGTTGCAGCACACTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTGGCAGGCACAAATGTCACTCGCATGGTAGAACAGTGCCTGGAATTCTCTCCCCGCTATGCCGGAATggtgg                >  2:275774/1‑146 (MQ=255)
                                                                                                                                  cGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTGGCAGGCAAAAATGTCACTCGCATGGTAGAACAGTGCCTGGAATTCTCTCCCCGCTATGCCGTAATGGACGAt              >  2:434451/1‑149 (MQ=255)
                                                                                                                                       cgCTCGACTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTGGCAGGCAAAAATGTCACTCGCATGGTAGAACAGTGCCTGGAATTCTCTTCCCGCTATGCCGTAATGGACGATGAAGc         <  2:479527/148‑1 (MQ=255)
                                                                                                                                           cGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTGGCAGGCAAAAATGTCACTCGCATGGTAGAACAGTGCCTGGAATTCTCTCCCCGCTATGCCGTAATGGACGATGAAGCGAGt     >  1:786736/1‑149 (MQ=255)
                                                                                                                                            gATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTGGCAGGCAAAAATGTCACTCGCATGGTAGAACAGTGCCTGGAATTCTCTCCCCGCTATGCCGTAATGGACGATGAAGCGAGTg    <  2:265263/149‑1 (MQ=255)
                                                                                                                                              ttGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTGGCAGGCAAAAATGTCACTCGCATGGTAGAACAGTGCCTGGAATTCTCTCCCCGCTATGCCGTAATGGACGATGAAGCGAGTGCg  <  2:662772/149‑1 (MQ=255)
                                                                                                                                              ttGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTGGCAGGCAAAAATGTCACTCGCATGGTAGAACAGTGCCTGGAATTCTCTCCCCGCTATGCCGTAATGGACGATGAAGCGAGTGCg  <  2:806149/149‑1 (MQ=255)
                                                                                                                                                |                                                                                                                                                  
TGATGCAGTTCTGATTTCTTGAACGACAAAAACGCCGCTCAGTAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATGTTTCATGAAGCAACTCACCATTCTGGGCTCGACCGGCTCGATTGGTTGCAGCACGCTGGACGTGGTGCGCCATAATCCCGAACACTTCCGCGTAGTTGCGCTGGTGGCAGGCAAAAATGTCACTCGCATGGTAGAACAGTGCCTGGAATTCTCTCCCCGCTATGCCGTAATGGACGATGAAGCGAGTGCG  >  CP009273/189903‑190193

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑