Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,513,930 A→T 100% L413F (TTA→TTT USA300HOU_1379 → hypothetical membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,513,9300AT100.0% 148.2 / ‑6.5 49L413F (TTA→TTTUSA300HOU_1379hypothetical membrane protein
Reads supporting (aligned to +/- strand):  ref base A (1/0);  major base T (19/27);  minor base G (1/1);  total (21/28)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AATTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTAC  >  CP000730/1513793‑1514064
                                                                                                                                         |                                                                                                                                      
aattaattTGTATTTATCGCTTTATTAGTAGCGATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCAAAACAAGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTAtt                                                                                                                                     <  2:420407/141‑1 (MQ=255)
aaTTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTAtt                                                                                                                                     <  1:97324/141‑1 (MQ=255)
   ttatttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCCCATCGCGTAAAAAAACCAGCATCTATACCACTCATAATATGCTTTATTGtc                                                                                                                                  >  1:605458/1‑140 (MQ=255)
     atttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTAtt                                                                                                                                <  1:45770/141‑1 (MQ=255)
       ttgtcggtatCGCTTTATTAGTAGCCAGTGGAATGGGGCTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTAGCACATCGCGTAAAAAAACCGGCATCTATATCACTCATAATATGTTTTATTGTATTAg                                                                                                                              <  1:386867/135‑1 (MQ=255)
                  gCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATg                                                                                                                   <  1:635785/141‑1 (MQ=255)
                      tattaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATTTATATCACTCATAATATGTTTTTTTGTATTTGGGTTATTTATGCTat                                                                                                               >  1:514970/1‑141 (MQ=255)
                       attaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAGTAAAAGTACCACATAGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATGGTATTAGGATTATTAATGcattt                                                                                                              >  2:435673/1‑137 (MQ=255)
                       attaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCatt                                                                                                              >  1:400491/1‑141 (MQ=255)
                       attaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGATTGATTGTATTAGGATTATTAATGCCatt                                                                                                              >  2:43256/1‑141 (MQ=255)
                          agtagCCATTGGCATTGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCattatt                                                                                                           <  1:590591/141‑1 (MQ=255)
                          agtagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCattatt                                                                                                           <  1:19814/141‑1 (MQ=255)
                          agtagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCattatt                                                                                                           <  1:359876/141‑1 (MQ=255)
                            tagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTg                                                                                                         <  2:452434/141‑1 (MQ=255)
                            tagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTg                                                                                                         <  1:97956/141‑1 (MQ=255)
                                  ttGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTAt                                                                                                   <  1:297864/141‑1 (MQ=255)
                                      cattgagTTTGTCTCTTGTACAAACCGTACAAAAAATACTGCACTAAAAGTACCACACCTCGTAAAAAAACCAGCATCTATATCACTCATTATATGTTTTATTGTGTTAGGGGTAGTAATGCCATTATTTTGATTATCACt                                                                                               <  2:276593/135‑1 (MQ=255)
                                          gggTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATc                                                                                           <  2:641213/141‑1 (MQ=255)
                                           ggTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCTCTTATcc                                                                                          >  2:568198/1‑141 (MQ=255)
                                           ggTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATcc                                                                                          >  2:596179/1‑141 (MQ=255)
                                           ggTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATcc                                                                                          >  2:624961/1‑141 (MQ=255)
                                            gTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCt                                                                                         >  2:661136/1‑141 (MQ=255)
                                            gTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATctt                                                                                         >  2:364032/1‑139 (MQ=255)
                                               tGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATAACTTTTCCTTGt                                                                                      >  1:9299/1‑141 (MQ=255)
                                                 tctcTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAGCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTAt                                                                                    <  2:439660/141‑1 (MQ=255)
                                                 tctcTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTAt                                                                                    <  2:549609/141‑1 (MQ=255)
                                                 tctcTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTAt                                                                                    <  2:378703/141‑1 (MQ=255)
                                                    ctTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTCGTATTta                                                                                 <  2:75756/141‑1 (MQ=255)
                                                       ggATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATaa                                                                              <  1:390276/141‑1 (MQ=255)
                                                       ggATAAAGCGTACAAAAAATACTGCAAGAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATaa                                                                              <  2:53081/141‑1 (MQ=255)
                                                                              gCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTaaa                                                       >  1:332462/1‑141 (MQ=255)
                                                                               cAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAg                                                      <  2:54325/141‑1 (MQ=255)
                                                                                aaTAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGa                                                     <  1:458250/141‑1 (MQ=255)
                                                                                 aTAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGAt                                                    >  1:2771/1‑141 (MQ=255)
                                                                                                 gcgTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACaat                                    >  2:479593/1‑141 (MQ=255)
                                                                                                   gTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGGTAAACaataa                                  >  1:563794/1‑141 (MQ=255)
                                                                                                    tAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACaataat                                 >  1:241784/1‑141 (MQ=255)
                                                                                                       aaaaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCa                              <  2:467560/141‑1 (MQ=255)
                                                                                                       aaaaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCa                              <  2:332462/141‑1 (MQ=255)
                                                                                                         aaactcgtaTCTATATCTCTCACAATATGTTTGATTGTATTAGGAATATTAATGCCATTATTTGGACTATCACTTATCCGTGTATCTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACt                            <  2:426069/133‑1 (MQ=255)
                                                                                                          aaCCAGCATCTATATCACTGCTATGTTGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACtt                           >  1:160259/1‑141 (MQ=255)
                                                                                                           aCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTa                          <  2:2771/141‑1 (MQ=255)
                                                                                                            ccAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTaa                         <  1:112453/141‑1 (MQ=255)
                                                                                                                      tatCACTCATAATATGTTTTCTTGTATTAGGATTATTCATGCCATTATTTGGTTTATCACTTAGCCTTGTATTTATAATGGAATTAATATTATGTATTAGAGATCGTCGTGCTACACAATAATGCACTTAACGTTTTGTAc               >  2:251770/1‑141 (MQ=255)
                                                                                                                         ctcTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGa            <  1:665298/139‑1 (MQ=255)
                                                                                                                           cTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACg          <  1:41151/141‑1 (MQ=255)
                                                                                                                               taataTGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAAt      >  1:344214/1‑141 (MQ=255)
                                                                                                                                 atatGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTATTATAACTTGAGAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAAttt    >  1:154321/1‑141 (MQ=255)
                                                                                                                                   atGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTAc  >  1:21710/1‑141 (MQ=255)
                                                                                                                                         |                                                                                                                                      
AATTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTAC  >  CP000730/1513793‑1514064

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: