Predicted mutation
evidence seq id position mutation annotation gene description
RA CP009273 3,208,093 T→C F563S (TTC→TCC)  rpoD → RNA polymerase, sigma 70 (sigma D) factor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0092733,208,0930TC100.0% 144.9 / NA 40F563S (TTC→TCC) rpoDRNA polymerase, sigma 70 (sigma D) factor
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (16/24);  total (16/24)

GGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCGTTCTGAAGTGCT  >  CP009273/3207962‑3208225
                                                                                                                                   |                                                                                                                                    
gggggATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATc                                                                                                                               <  1:2342340/139‑1 (MQ=255)
   ggATTCCATCGAGGATACCACCCTCGAGCAGCCGCTGGATGCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCCCGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGa                                                                                                                             <  1:1586556/138‑1 (MQ=255)
           tCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAacac                                                                                                                    <  1:1548759/139‑1 (MQ=255)
                   acccccCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACt                                                                                                               <  1:2445907/136‑1 (MQ=255)
                    ccaccCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTacac                                                                                                           <  1:2257191/139‑1 (MQ=255)
                     caccCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTacac                                                                                                           >  1:50739/1‑138 (MQ=255)
                           cGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGgaa                                                                                                    <  1:1044877/139‑1 (MQ=255)
                            gAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGgaag                                                                                                   >  1:1214370/1‑139 (MQ=255)
                             aGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGgaaga                                                                                                  >  1:1049713/1‑139 (MQ=255)
                             aGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGga                                                                                                     >  1:1022425/1‑136 (MQ=255)
                              gCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAGCGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGACCACCGACTACGCGCTGgaaga                                                                                                  <  1:2637016/138‑1 (MQ=255)
                              gCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGgaaga                                                                                                  <  1:2637516/138‑1 (MQ=255)
                              gCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGgaaga                                                                                                  <  1:1994346/138‑1 (MQ=255)
                              gCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGgaaga                                                                                                  <  1:684535/138‑1 (MQ=255)
                                tGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGaagaag                                                                                                <  1:2091458/138‑1 (MQ=255)
                                  ccGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTgg                                                                                             >  1:158649/1‑139 (MQ=255)
                                  ccGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTgg                                                                                             >  1:1213870/1‑139 (MQ=255)
                                   cGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCg                                                                                                                                    <  1:746610/99‑1 (MQ=255)
                                             tGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGatat                                                                                                                          >  1:2170551/1‑99 (MQ=255)
                                                    accGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGata                                                                                                                           <  1:1988022/91‑1 (MQ=255)
                                                             cTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGa                                                                    <  1:1165785/137‑1 (MQ=255)
                                                              tgcgtgcgGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGa                                                                                                                 >  1:563867/1‑91 (MQ=255)
                                                                          cGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGAt                                                     <  1:1031944/139‑1 (MQ=255)
                                                                          cGCACGACGTGCTGGCTGGCCTGACCGCGAGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGAt                                                     >  1:1313943/1‑139 (MQ=255)
                                                                           gCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACg                                                                              <  1:435428/113‑1 (MQ=255)
                                                                                    gctggctgGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATcgaagcgaag                                           >  1:1332263/1‑139 (MQ=255)
                                                                                     ctggctggCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGa                                                                    >  1:1859695/1‑113 (MQ=255)
                                                                                             ccTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGCACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTgcgc                                  >  1:1566933/1‑139 (MQ=255)
                                                                                             ccTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGtt                                                                                   <  1:2614399/90‑1 (MQ=255)
                                                                                                 aCCGCGCGGGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGTCGCTGCGCaa                                >  1:2675643/1‑137 (MQ=255)
                                                                                                       cgTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTAcc                                                                         >  1:1191219/1‑90 (MQ=255)
                                                                                                       cgTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTc                        >  1:1880554/1‑139 (MQ=255)
                                                                                                               aaaaGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAg                 <  1:2011060/138‑1 (MQ=255)
                                                                                                               aaaaGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACATATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAg                 <  1:652905/138‑1 (MQ=255)
                                                                                                                 aaGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGGGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCg              <  1:2755207/139‑1 (MQ=255)
                                                                                                                       tGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGgcgc                                       <  1:273330/108‑1 (MQ=255)
                                                                                                                          gTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCGTTCTGAAg      <  1:1475380/138‑1 (MQ=255)
                                                                                                                           tATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGaagaag                                                                                                <  1:2331066/47‑1 (MQ=255)
                                                                                                                              gCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCGTTCTGAAGtgct  >  1:1091760/1‑138 (MQ=255)
                                                                                                                               cGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGAt                                                     <  1:2405064/86‑1 (MQ=255)
                                                                                                                                   |                                                                                                                                    
GGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCGTTCTGAAGTGCT  >  CP009273/3207962‑3208225

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑