Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP009273	4,173,770	T→G	D866E (GAT→GAG)	rpoB →	RNA polymerase, beta subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	4,173,770	0	T	G	100.0%	224.3 / NA	58	D866E (GAT→GAG)	rpoB	RNA polymerase, beta subunit
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (30/28);  total (30/28)

TGTTGTTCAGGAAGACCGTTTCACCACCATCCACATTCAGGAACTGGCGTGTGTGTCCCGTGACACCAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGATGAATCCGGTATCGTTTACATTGGTGCGGAAGTGACCGGTGGCGACATTCTGGTTGGTAAGGTAACGCCGAAAGGTGAAACTCAGCTGACCCCAGAAGAAAAACTGCTGCGTGCGATCTTCGGTGAGAA  >  CP009273/4173635‑4173898                                                                                                                                        |                                                                                                                                 tgttgtTCAGGAAGACCGTTTCACCACCATCCACATTCAGGAACTGGCGTGTGTGTCCCGTGACACCAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGaa                                                                                                                               >  1:1941278/1‑139 (MQ=255)    tgttCAGGAAGACCGTTTCACCACCATCCACATTCAGGAACTGGCGTGTGTGTCCCGTGACACCAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATcc                                                                                                                            >  1:3964271/1‑139 (MQ=255)       tCAGGAAGACCGTTTCACCACCATCCACATTCAGGAACTGGCGTGTGTGTCCCGTGACACCAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGt                                                                                                                         <  1:1967768/139‑1 (MQ=255)       tCAGGAAGACCGTTTCACCACCATCCACATTCAGGAACTGGCGTGTGTGTCCCGTGACACCAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGt                                                                                                                         <  1:1586999/139‑1 (MQ=255)        cAGGAAGACCGTTTCACCACCATCCACATTCAGGAACTGGCGTGTGTGTCCCGTGACACCAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAAACCGGTa                                                                                                                        >  1:3888919/1‑139 (MQ=255)         aGGAAGACCGTTTCACCACCATCCACCTTCAGGAACTGGCGTGTGTGTCCCGTGACACCAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTa                                                                                                                        >  1:3864380/1‑138 (MQ=255)         aGGAAGACCGTTTCACCACCATCCACATTCAGGAACTGGCGTGTGTGTCCCGTGACACCAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTa                                                                                                                        <  1:2049430/138‑1 (MQ=255)         aGGAAGACCGTCTCACCACCATCCACATTCAGGAACTGGCGTGGGTGTCCCGGGACACCAAGCTGGGTCCGGAAGAGAGCACCGCGGACATCCCGTACGTGGGTGAAGCTGCGCTCTCCAAAATGGAGGACTCCggga                                                                                                                        >  1:2349320/1‑136 (MQ=255)           gAAGACCGTTTCACCACCATCCACATTCAGGAACTGGCGTGTGTGTCCCGTGACACCAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCg                                                                                                                     >  1:1257829/1‑139 (MQ=255)              gACCGTTTCACCACCATCCACATTCAGGAACTGGCGTGTGTGTCCCGTTACACCAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGtt                                                                                                                   >  1:2537797/1‑138 (MQ=255)                ccGTTTCACCACCATCCACATTCAGGAACTGGCGTGTGTGTCCCGTGACACCAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTa                                                                                                                 <  1:2561127/138‑1 (MQ=255)                  gTTTCACCACCATCCACATTCAGGAACTGGCGTGTGTGTCCCGTGACACCAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACAt                                                                                                              <  1:4113464/139‑1 (MQ=255)                  gTTTCACCACCATCCACATTCAGGAACTGGCGTGTGTGTCCCGTGACACCAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACAt                                                                                                              <  1:2384378/139‑1 (MQ=255)                   tttCACCACCATCCACATTCAGGAACTGGCGTGTGTGTCCCGTGACACCAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACAtt                                                                                                             >  1:2834796/1‑139 (MQ=255)                   tttCACCACCATCCACATTCAGGAACTGGCGTGTGTGTCCCGTGACACCAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACAtt                                                                                                             >  1:1728376/1‑139 (MQ=255)                   tttCACCACCATCCACATTCAGGAACTGGCGTGTGTGTCCCGTGACACCAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACAt                                                                                                              >  1:4219165/1‑138 (MQ=255)                    ttCACCACCATCCACATTCAGGAACTGGCGTGTGTGTCCCGTGACACCAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATc                                                                                                                             <  1:1280199/122‑1 (MQ=255)                       accaccATCCACATTCGGGAACTGGCGTGTGTGTCCCGTGACACCAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACATTGGTg                                                                                                         <  1:84119/139‑1 (MQ=255)                            caTCCACATTCAGGAACTGGCGTGTGTGTCCCGTGACACCAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGt                                                                                                                         <  1:1720091/118‑1 (MQ=255)                              tCCACATTCAGGAACTGGCGTGTGTGTCCCGTGACACCAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGtt                                                                                                                   >  1:3451519/1‑122 (MQ=255)                              tCCACATTCAGGAACTGGCGTGTGTGTCCCGTGACACCAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGt                                                                                                  >  1:3200124/1‑139 (MQ=255)                              tCCACATTCAGGAACTGGCGTGTGTGTCCCGTGACACCAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGt                                                                                                  >  1:1648897/1‑139 (MQ=255)                                   aTTCAGGAACTGGCGTGTGTGTCCCGTGACACCAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGTGAc                                                                                               <  1:574024/137‑1 (MQ=255)                                   aTTCAGGAACTGGCGTGTGTGTCCCGTGACACCAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGTGACCg                                                                                             >  1:660680/1‑139 (MQ=255)                                      cAGGAACTGGCGTGTGTGTCCCGTGACACCAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACa                                                                                                               >  1:3890501/1‑118 (MQ=255)                                       aGGAACTGGCGTGTGTGTCCCGTGACACCAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTa                                                                                                                        >  1:3078525/1‑108 (MQ=255)                                         gAACTGGTGATTGTGTCCCGCGGCACCAAGCTGGGTTCGGACGAGATCGCCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGTGACCGGTGGCg                                                                                       >  1:3151449/1‑139 (MQ=255)                                             tGGCGTGTGTGTCCCGTGACACCAAGCTGGGTACGGAAGAGATCACCGCTGACATCCCGCACGTGGGTGCAGCTGCGTTCTCCAAACTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGTGACCGGGGGCGACac                                                                                   >  1:2746516/1‑138 (MQ=255)                                                 gtgtgtgtCCCGTGACACCAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGTGACCGGTGGCGACATTCtt                                                                               <  1:2738050/139‑2 (MQ=255)                                                   gtgtgtCCCGTGACACCAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGTGACCGGTGGCGACATTCtggt                                                                             <  1:2833014/139‑1 (MQ=255)                                                      tgtCCCGTGACACCAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGTGACCGGTGGCGACATTCtggttgg                                                                          >  1:1216692/1‑139 (MQ=255)                                                              gACACCAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGTGACCGGTGGCGACATTCTGGTTggtaaggta                                                                   <  1:1028328/138‑1 (MQ=255)                                                              gACACCAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGTGACCGGTGGCGACATTCTGGTTggtaaggta                                                                   >  1:3522710/1‑138 (MQ=255)                                                                   cAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGTGACCGGTGGCGACATTCTGGTTGGTAAGGTAACGCCg                                                             <  1:1895284/139‑1 (MQ=255)                                                                     aGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGTGACCGGTGGCGACATTCTGGTTGGTAAGGTAACGCCGaa                                                           >  1:4065353/1‑139 (MQ=255)                                                                      gCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGt                                                                                                                    <  1:2490872/81‑1 (MQ=255)                                                                           gTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGTGACCGGTGGCGACATTCTGGTTGGTAAGGTAACGCCGAAAGGTg                                                      <  1:662463/138‑1 (MQ=255)                                                                                gAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACATTGGt                                                                                                          >  1:318011/1‑81 (MQ=255)                                                                                  agagATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGTGACAGGTGGCGACATTCTGGTTGGTAAGGTAACGCCGAAAGGTGAAACTCAg                                              <  1:1332087/139‑1 (MQ=255)                                                                                     gaTCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGTGACCGGTGGCGACATTCTGGTTGGTAAGGTAACGCCGAAAGGTGAAACTCAGCt                                            <  1:1868232/138‑1 (MQ=255)                                                                                         aCCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGTGACAGGTGGCGACATTCTGGTTGGTAAGGTAACGCCGAAAGGTGAAACTCAGCTGAcc                                        >  1:3503330/1‑138 (MQ=255)                                                                                          ccGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGTGACCGGTGGCGACATTCTGGTTGGTAAGGTAACGCCGAAAGGTGAAACTCAGCTGAcccc                                      <  1:1718506/139‑1 (MQ=255)                                                                                          ccGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGTGACCGGTGGCGACATTCTGGTTGGTAAGGTAACGCCGAAAGGTGAAACTCAGCTGAcccc                                      <  1:1693915/139‑1 (MQ=255)                                                                                           cGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGTGACCGGTGGCGACATTCTGGTTggta                                                                        >  1:1523229/1‑104 (MQ=255)                                                                                              tGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGTGACCGGTGGCGACATTCTGGTTGGTAAGGTAACGCCGAAAGGTGAAACTCAGCTGACCCCaga                                   <  1:3201654/138‑1 (MQ=255)                                                                                                aCATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGTGACCGGTGGCGACATTCTGGTTGGTAAGGTAACGCCGaa                                                           <  1:3555980/112‑1 (MQ=255)                                                                                                    cccGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGTGACCGGTGGCGACATTCTGGTTGGTAAGGTAACGCCGAAAGGTg                                                      <  1:43210/113‑1 (MQ=255)                                                                                                         aCGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGTGACCGGTGGCGACATTCTGGTTGGTAAGGTAACGCCGAAAGGTGAAACTCAGCTGACCCCAGAAGAAAAActgct                       <  1:908453/139‑1 (MQ=255)                                                                                                          cGTGGGTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGTGACCGGTGGCGACATTCTGGTTGGTAAGGTAACGCCGAAAGGTGAAACt                                                 >  1:1384855/1‑112 (MQ=255)                                                                                                              ggTGAAGCTGCGCTCTCCAAACTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGTGACCGGTGGCGACATTCTGGTTGGTAAGGTAACGCCGAAAGGTGAAACTCAGCt                                            >  1:2216484/1‑113 (MQ=255)                                                                                                                       gcgcTCTCCAAACTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGTGACCGGTGGCGACATTCTGGTTGGTAAGGTAACGCCGAAAGGTGAAACTCAGCTGACCCCAGAAGAAAAACTGCTGCGTGCGATCTTCg         <  1:2386539/139‑1 (MQ=255)                                                                                                                        cgcTCTCCAAACTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGTGACCGGTGGCGACATTCTGGTTGGTAAGGTAACGCCGAAAGGTGAAACTCAGCTGACCCCAGAAGAAAAACTGCTGCGTGCGATCTTCgg        >  1:2071419/1‑139 (MQ=255)                                                                                                                         gcTCTCCAAACTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGTGACCGGTGGCGACATTCTGGTTGGTAAGGTAACGCCGAAAGGTGAAACTCAGCTGACCCCAGAAGAAAAACTGCTGCGTGCGATCTTCGGt       >  1:213526/1‑139 (MQ=255)                                                                                                                             tcCAAACTGGAGGAATCCGGTATCGTTTAGATTGGTGCGGAAGTGACCGGTGGCGACATTCTGGTTGGTAAGGTAACGCCGAAAGGGGAAACTCAGGTGACCCCAGAAGAAAAACTGCTGCGTGCGATCTTCGGTgaga   >  1:3175503/1‑139 (MQ=255)                                                                                                                             tcCAAACTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGTGAc                                                                                               <  1:198739/47‑1 (MQ=255)                                                                                                                              ccAAACTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGTGACCGGTGGCGACATTCTGGTTGGTAAGGTAACGCCGAAAGGTGAAACTCAGCTGACCCCAGAAGAAAAACTGCTGCGTGCGATCTTCGGTGAGaa  >  1:4176029/1‑139 (MQ=255)                                                                                                                              ccAAACTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGTGACCGGTGGCGACATTCTGGTTGGTAAGGTAACGCCGAAAGGTGAAACTCAGCTGACCCCAGAAGAAAAACTGCTGCGTGCGATCTTCGGTGAGaa  <  1:2006222/139‑1 (MQ=255)                                                                                                                                  aCTGGAGGAATCCGGTATCGTTTACATTGGTGCGGAAGTGACCGGTGGCGACATTCTGGTTGGTAAGGTAACGCCGAAAGGTGAAACTCAGCTGACCCCa                                     <  1:1940693/100‑1 (MQ=255)                                                                                                                                        |                                                                                                                                 TGTTGTTCAGGAAGACCGTTTCACCACCATCCACATTCAGGAACTGGCGTGTGTGTCCCGTGACACCAAGCTGGGTCCGGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGATGAATCCGGTATCGTTTACATTGGTGCGGAAGTGACCGGTGGCGACATTCTGGTTGGTAAGGTAACGCCGAAAGGTGAAACTCAGCTGACCCCAGAAGAAAAACTGCTGCGTGCGATCTTCGGTGAGAA  >  CP009273/4173635‑4173898

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑