Predicted mutation
evidence seq id position mutation annotation gene description
RA CP000730 1,672,590 G→T L135I (CTT→ATT)  rpoD ← DNA‑directed RNA polymerase sigma subunit RpoD

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,672,5900GT93.2% 170.6 / 7.0 59L135I (CTT→ATT) rpoDDNA‑directed RNA polymerase sigma subunit RpoD
Reads supporting (aligned to +/- strand):  ref base G (4/0);  new base T (23/32);  total (27/32)
Fisher's exact test for biased strand distribution p-value = 3.86e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.32e-01

ATCCTTTGTTAAAGTCAAATTTTTCAACAGCTTTAATAAGACCCATATTACCTTCTTGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAAGTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCAATTTCTTTAAGGTACATACGAACTGGGTCATTTATTTTAACACCTGGAGGG  >  CP000730/1672452‑1672726
                                                                                                                                          |                                                                                                                                        
aTCCTTTGTTAAAGTCAAATTTTTCAACAGCTTTAATAAGACCCATATTACCTTCTTGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTc                                                                                                                                        >  1:682314/1‑141 (MQ=255)
     ttGTTAAAGTCAAATTTTTCAACAGCTTTAATAAGACCCATATTACCTTCTTGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAAGTCTTGAt                                                                                                                                   >  1:730579/1‑141 (MQ=255)
                 aaTTTTTCAACAGCTTTAATAAGACCCATATTACCTTCTTGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTtca                                                                                                                       >  2:916505/1‑141 (MQ=255)
                 aaTTTTTCAACAGCTTTAATAAGACCCATATTACCTTCTTGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACCtca                                                                                                                       >  2:975936/1‑141 (MQ=255)
                  aTTTTTCAACAGCTTTAATAAGACCCATATTACCTTCTTGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTtcat                                                                                                                      <  2:413299/141‑1 (MQ=255)
                   ttttgCAACAGCTTTTATAAGGCCCATATTACCTTCTTGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTGGAACTTTGCGTTAGTTCGCTTCTGCGATTCTTGATTTGGCTACTtcatc                                                                                                                     <  2:208318/141‑1 (MQ=255)
                       tCAACAGCTTTAATAAGACCCATATTACCTTCTTGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCt                                                                                                                 >  1:862129/1‑141 (MQ=255)
                       tCAACAGCTTTAATAAGACCCATATTACCTTCTTGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAAGTCTTGATTTTGCTACTTCATCACCt                                                                                                                 >  1:626163/1‑141 (MQ=255)
                         tttttttttAATAAGACAAATATTACATTCTTGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTg                                                                                                               >  2:347604/7‑141 (MQ=255)
                         aaCAGCTTTAATAAGACCCATATTACCTTCTTGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCt                                                                                                                                       >  2:290714/1‑117 (MQ=255)
                         aaCAGCTTTAATAAGACCCATATTACCTTCTTGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCt                                                                                                                                       <  1:290714/117‑1 (MQ=255)
                           cAGCTTTAATAAGACCCATATTACCTTCTTGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGtt                                                                                                             >  1:57223/1‑141 (MQ=255)
                            aGCTTTAATAAGACCCATATTACCTTCTTGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTc                                                                                                            <  1:662399/141‑1 (MQ=255)
                                    taaGACCCATATTACCTTCTTGGATTAAATCAAGGAAGAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAGCGTAAGTTCGGTTGTGCAATGCTTGATTGTGCAACTTCaccaccaggggcagtacgtt                                                                                                    <  2:429923/141‑15 (MQ=255)
                                         cccATATTACCTTCTTGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACCTCATCACCTTGTTCAATACGTTTGGcc                                                                                               <  1:975936/141‑2 (MQ=255)
                                          ccATATTACCTTCTTGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCATTACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTa                                                                                              <  2:220622/141‑1 (MQ=255)
                                              atTACCTTCTTGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTc                                                                                          <  1:792677/141‑1 (MQ=255)
                                                tACCTTCTTGGATTAAATCAAGGAATAACATACCTCGACCTACGTATCTTTTAGCAATACTTACGACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGa                                                                                        <  1:482942/141‑1 (MQ=255)
                                                tACCTTCTTGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGa                                                                                        <  2:1005036/141‑1 (MQ=255)
                                                tACCTTCTTGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGa                                                                                        <  2:440658/141‑1 (MQ=255)
                                                  ccTTCTTGGATTAAATCAAGGAATAGCATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGAtt                                                                                      <  1:687806/141‑1 (MQ=255)
                                                   cttcttGGATTAAATCAAGGCATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGAttt                                                                                     >  2:513371/1‑141 (MQ=255)
                                                   cttcttGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAAGTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGAttt                                                                                     >  1:76817/1‑141 (MQ=255)
                                                     tcttGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATttct                                                                                   <  1:347604/141‑1 (MQ=255)
                                                     tcttGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGAAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTTGCTAATTCGATttct                                                                                   >  1:867080/1‑141 (MQ=255)
                                                            ttAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTtgtg                                                                            <  2:357937/141‑1 (MQ=255)
                                                                    aGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTtaat                                                                    >  2:754926/1‑141 (MQ=255)
                                                                     ggAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTtaata                                                                   >  2:953897/1‑141 (MQ=255)
                                                                          aaCATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAAGTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTa                                                              >  1:142615/1‑141 (MQ=255)
                                                                                 cACGACCTACGTATCTTTTATCAATACTTACAACTAAACTTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGcc                                                       <  1:978356/141‑1 (MQ=255)
                                                                                 aaCGACATAAGTATCTTTTAGAAATACTTATAACTACTTATAATTTTGCTTCTTCAATTCTTGATTTTTCTACTTCATCGTCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGcc                                                       <  2:89861/140‑1 (MQ=255)
                                                                                  aCGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGccc                                                      <  1:102790/141‑1 (MQ=255)
                                                                                    gACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCaa                                                    >  1:185231/1‑141 (MQ=255)
                                                                                     aCCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACt                                                                                                                          <  1:17909/70‑1 (MQ=255)
                                                                                     aCCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACt                                                                                                                          >  2:17909/1‑70 (MQ=255)
                                                                                     aCCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCAAt                                                   <  1:78681/141‑1 (MQ=255)
                                                                                          cGTATCTTTTAGCAATGCTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGCTTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAactaacgcatcagtat                                              >  1:645717/1‑127 (MQ=255)
                                                                                             aTCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCAATTTCTTTaa                                           <  1:730831/141‑1 (MQ=255)
                                                                                                    aGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCATGTTCCATACGTTTGGCCAATAAGATTTCTACTTGTGCACTTAATAAGTTAACACGCCCACTTTCTTTAAGGTACAt                                    <  1:923254/141‑1 (MQ=255)
                                                                                                     gCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCAc                                                                         >  1:597754/1‑103 (MQ=255)
                                                                                                     gCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCAc                                                                         <  2:597754/103‑1 (MQ=255)
                                                                                                      cAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCAATTTCTTTAAGGTACATAc                                  >  1:209669/1‑141 (MQ=255)
                                                                                                       aaTACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCAATTTCTTTAAGGTACATACg                                 <  2:154917/141‑1 (MQ=255)
                                                                                                             tACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCAATTTCTTTAAGGTACATACGAACTgg                           >  2:123294/1‑141 (MQ=255)
                                                                                                               cAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCAATTTCTTTAAGGTACATACGAACTGGGt                         >  2:417558/1‑141 (MQ=255)
                                                                                                                aaCTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCAATTTCTTTAAGGTACATACGAACTGGGTc                        <  2:380399/141‑1 (MQ=255)
                                                                                                                   tAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCAATTTCTTTAAGGTACATACGAACTGGGTCatt                     <  1:92252/141‑1 (MQ=255)
                                                                                                                     aaCGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCAATTTCTTTAAGGTACATACGAACTGGGTCattta                   >  1:856933/1‑141 (MQ=255)
                                                                                                                     aaCGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCAATTTCTTTAAGGTACATACGAACTGGGTCattta                   >  2:704215/1‑141 (MQ=255)
                                                                                                                     aaCGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCAATTTCTTTAAGGTACATACGAACTGGGTCattta                   <  2:74365/141‑1 (MQ=255)
                                                                                                                       cGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCAATTTCTTTAAGGTACATACGAACTGGGTCatttatt                 <  2:57223/141‑1 (MQ=255)
                                                                                                                           aGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCAATTTCTTTAAGGTACATACGAACTGGGTCATTTATTTTaa             >  2:254726/1‑141 (MQ=255)
                                                                                                                            gTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCAATTTCTTTAAGGTACATACGAACTGGGTCATTTATTTTAac            <  1:534337/141‑1 (MQ=255)
                                                                                                                             ttCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCAATTTCTTTAAGGTACATACGAACTGGGTCATTTATTTTAaca           <  1:587091/141‑1 (MQ=255)
                                                                                                                              tCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCAATTTCTTTAAGGTACATACGAACTGGGTCATTTATTTTAacac          <  2:137228/141‑1 (MQ=255)
                                                                                                                                gCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCAATTTCTTTAAGGTACATACGAACTGGGTCATTTATTTTAACACCt        >  2:843528/1‑141 (MQ=255)
                                                                                                                                 cTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCAATTTCTTTAAGGTACATACGAACTGGGTCATTTATTTTAACACCTg       <  1:22610/141‑1 (MQ=255)
                                                                                                                                  ttCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCAATTTCTTTAAGGTACATACGAACTGGGTCATTTATTTTAACACCTgg      <  1:466033/141‑1 (MQ=255)
                                                                                                                                      gCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCAATTTCTTTAAGGTACATACGAACTGGGTCATTTATTTTAACACCTGGAggg  >  2:749568/1‑141 (MQ=255)
                                                                                                                                          |                                                                                                                                        
ATCCTTTGTTAAAGTCAAATTTTTCAACAGCTTTAATAAGACCCATATTACCTTCTTGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAAGTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCAATTTCTTTAAGGTACATACGAACTGGGTCATTTATTTTAACACCTGGAGGG  >  CP000730/1672452‑1672726

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑