Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,440,085 G→T 100% intergenic (‑45/‑891) cspA ← / → xpaC cold shock protein CspA/5‑bromo‑4‑chloroindolyl phosphate hydrolysis protein XpaC

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,440,0850GT100.0% 131.7 / NA 47intergenic (‑45/‑891)cspA/xpaCcold shock protein CspA/5‑bromo‑4‑chloroindolyl phosphate hydrolysis protein XpaC
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (14/33);  total (14/33)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAATTAT  >  CP000730/1439948‑1440222
                                                                                                                                         |                                                                                                                                         
tGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCat                                                                                                                                        >  2:182656/1‑141 (MQ=255)
tGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCat                                                                                                                                        >  2:538693/1‑141 (MQ=255)
tGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCat                                                                                                                                        >  2:451957/1‑141 (MQ=255)
 gAAAAATGTACGAATACGTCCTTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCata                                                                                                                                       <  2:622128/141‑1 (MQ=255)
 gAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCata                                                                                                                                       <  1:409457/141‑1 (MQ=255)
     aaTGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAc                                                                                                                                   <  1:203572/141‑1 (MQ=255)
                     aTTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCaaa                                                                                                                   >  1:237125/1‑141 (MQ=255)
                      ttttCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGTAAAt                                                                                                                  >  1:391927/1‑141 (MQ=255)
                      ttttCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAAt                                                                                                                  >  1:96067/1‑141 (MQ=255)
                      ttttCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAAt                                                                                                                  >  1:391216/1‑141 (MQ=255)
                       tttCTCCTTCAACTTCGGTAAAGTCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACACAAAATACATGCAAAtt                                                                                                                 <  1:331437/141‑1 (MQ=255)
                           tcCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTCCAAAAAATACATGCAAATTTCAc                                                                                                             >  1:351704/1‑141 (MQ=255)
                               tCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAATATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCaa                                                                                                         <  1:141350/141‑1 (MQ=255)
                               tCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCATTCaa                                                                                                         <  1:453186/141‑1 (MQ=255)
                               tCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCaa                                                                                                         <  1:93226/141‑1 (MQ=255)
                                cAACTTCGATAAACCCGAATCCTTTTTCACCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCaaa                                                                                                        <  2:312697/141‑1 (MQ=255)
                                      cGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCt                                                                                                  <  1:86315/141‑1 (MQ=255)
                                             accGAATTCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACAAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAat                                                                                           <  2:323263/140‑1 (MQ=255)
                                                 aaaccTTTTTCCGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCCCCAAGACTACCATTCAATCAATATGCTTAATCTCATATTATAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATgg                                                                                       <  1:294912/138‑1 (MQ=255)
                                                  tgccTTTTTCAGCCTTAAACCATTTATCTGTATCTTGATTGATAATCTGAATCATAAAAGAATAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAGTTTCACTTAAATAATCTCTGCAATATGGa                                                                                      <  2:208656/139‑1 (MQ=255)
                                                   accTTTTTCACCGTTAAACCATTTAACTGTACCTTGTTTCATATTCTGAAACCTCCAATACTAAAATTCATTCAATTTGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaa                                                                                     <  2:229222/140‑1 (MQ=255)
                                                          tCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGATTAatcat                                                                              <  2:243295/141‑1 (MQ=255)
                                                          tCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAatcat                                                                              <  2:318006/141‑1 (MQ=255)
                                                          tCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATGCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAatcat                                                                              <  2:476851/141‑1 (MQ=255)
                                                            aGCGTTAGACCAATTAGCTGTACCTTGTTTCATAATCTGAAACCTCCAAGGCTAAAATTCATTCAATATGCTTATTCTCATATTACCAAAAATACATGCTAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCt                                                                            <  2:598799/141‑1 (MQ=255)
                                                             gCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTg                                                                           <  1:445646/141‑1 (MQ=255)
                                                             gCGTTAAACCATTTAACTGTACCTTGTTTCAGAATCTGAAACCTCCAACACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTg                                                                           <  1:76019/141‑1 (MQ=255)
                                                              tgTTAAACTATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTTCAATATGGAATAATAATCttc                                                                          >  2:517830/2‑139 (MQ=255)
                                                                      cATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTg                                                                  <  1:288227/141‑1 (MQ=255)
                                                                      cATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTg                                                                  <  1:536514/141‑1 (MQ=255)
                                                                             ttGTCCCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAACATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATtata                                                           <  1:521928/140‑1 (MQ=255)
                                                                                tACCTTGTGGCATAATCTGAAACCTCCAAGACTAAAATTCATGCAATATGCTTATTCTCATATTACAAAAAATACAGGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTg                                                        <  2:151352/141‑1 (MQ=255)
                                                                                 cccTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGc                                                       <  1:175586/140‑1 (MQ=255)
                                                                                         tCATAATCTGAAACCACCAAGACTAAAACTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGttatta                                               <  2:354196/141‑1 (MQ=255)
                                                                                                 tGAAACCTCCGATACGAAAATTCATTGAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAAttt                                       >  2:558071/1‑140 (MQ=255)
                                                                                                     aCCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcaat                                   >  1:648760/1‑141 (MQ=255)
                                                                                                             aaCTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACaataat                           <  1:643059/140‑1 (MQ=255)
                                                                                                              aCTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAataata                          <  1:111859/141‑1 (MQ=255)
                                                                                                                 aaaaTTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATaaaa                       >  2:35984/1‑141 (MQ=255)
                                                                                                                 aaaaTTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATaaaa                       >  2:545293/1‑141 (MQ=255)
                                                                                                                  acattcattcAATATCCTTATTCTCATATTACAAAAAATACATGCAAATTTCTCTCTATTATTCTTTGTAATATGGAATAATCATCTGATTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATaaaaa                      <  2:55626/139‑1 (MQ=255)
                                                                                                                      tctgtcaATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAatat                  <  2:411447/137‑1 (MQ=255)
                                                                                                                      tcattcaATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACATTAATAAAAAatat                  >  1:46372/1‑141 (MQ=255)
                                                                                                                                ttcTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATc        <  2:337735/139‑1 (MQ=255)
                                                                                                                                 gCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCa       <  2:551231/141‑1 (MQ=255)
                                                                                                                                  cTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCaa      <  2:515660/141‑1 (MQ=255)
                                                                                                                                      ttCTCATATTACAAAAAAGACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAattat  <  2:33555/141‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                         
TGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAATTAT  >  CP000730/1439948‑1440222

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: