Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP009273	3,433,439	C→A	R317L (CGC→CTC)	rpoA ←	RNA polymerase, alpha subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	3,433,439	0	C	A	100.0%	173.2 / NA	53	R317L (CGC→CTC)	rpoA	RNA polymerase, alpha subunit
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (30/23);  total (30/23)

AGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACC  >  CP009273/3433374‑3433503                                                                  |                                                                 aGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGgagc                                                                >  1:3559882/1‑68 (MQ=255)  gTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCa                                                               >  1:3378201/1‑68 (MQ=255)  gTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCa                                                               >  1:806601/1‑68 (MQ=255)    aaaaCCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATg                                                             >  1:3587276/1‑68 (MQ=255)    aaaaCCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATg                                                             >  1:1703929/1‑68 (MQ=255)      atccTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGcc                                                           <  1:2278427/66‑1 (MQ=255)      aaCCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGcc                                                           <  1:5425440/68‑1 (MQ=255)      aaCCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGcc                                                           <  1:4290933/68‑1 (MQ=255)      aaCCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGcc                                                           <  1:1834239/68‑1 (MQ=255)       aCCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGccc                                                          >  1:2986527/1‑68 (MQ=255)       aCCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGccc                                                          >  1:496874/1‑68 (MQ=255)         cTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCag                                                        >  1:2086614/1‑68 (MQ=255)         cTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCag                                                        >  1:3679714/1‑68 (MQ=255)          ttAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCaga                                                       <  1:5468983/68‑1 (MQ=255)           tAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCagag                                                      <  1:1893080/68‑1 (MQ=255)              ccTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACa                                                   >  1:3068150/1‑68 (MQ=255)              ccTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACa                                                   >  1:2345216/1‑68 (MQ=255)              ccTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACa                                                   >  1:5434526/1‑68 (MQ=255)              ccTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACa                                                   >  1:1381848/1‑68 (MQ=255)               cTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAg                                                  >  1:2010961/1‑68 (MQ=255)                tgtgATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGt                                                 <  1:2781138/68‑1 (MQ=255)                tgtgATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGt                                                 <  1:3905700/68‑1 (MQ=255)                tgtgATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGt                                                 <  1:5599162/68‑1 (MQ=255)                tgtgATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGt                                                 <  1:1291948/68‑1 (MQ=255)                tgggATCCGGTTACTCGTCAGCGATGCTTGCCGGGGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGt                                                 <  1:2871239/65‑1 (MQ=255)                ggtgATCCGTTTACTCGGCAGCGATGCGTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGt                                                 <  1:4668123/67‑1 (MQ=255)                     tCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACg                                            >  1:40836/1‑68 (MQ=255)                     tCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACg                                            >  1:4057907/1‑68 (MQ=255)                       cGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACggg                                          <  1:1947647/68‑1 (MQ=255)                       cGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACggg                                          <  1:1036339/68‑1 (MQ=255)                        ggTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGa                                         >  1:1804608/1‑68 (MQ=255)                          ttACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGatg                                       <  1:3331434/68‑3 (MQ=255)                           tACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCTGGAGCATGCCCAGAGACAGTCCACGGGAAGc                                      <  1:3579520/68‑1 (MQ=255)                           tACTCGTCAGCGATGCTTGCCGGTGGCCAATTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGc                                      >  1:5608003/1‑68 (MQ=255)                            aCTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGcc                                     >  1:5248819/1‑68 (MQ=255)                               cGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGc                                  >  1:4019759/1‑68 (MQ=255)                               cGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGc                                  >  1:5575410/1‑68 (MQ=255)                               cGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGc                                  >  1:2823644/1‑68 (MQ=255)                                    gCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCTGAGACAGTCCACGGGAAGCCAGCACGTc                             <  1:5656897/68‑1 (MQ=255)                                    gCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTc                             >  1:3981374/1‑68 (MQ=255)                                    gCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTc                             <  1:3006987/68‑1 (MQ=255)                                    gCGATGCTTGCCGGTGGCCAGATTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACgac                             >  1:2509528/1‑66 (MQ=255)                                      gATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCtt                           >  1:2579496/1‑68 (MQ=255)                                       aTGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCttt                          >  1:3542093/1‑68 (MQ=255)                                         gCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTaa                        <  1:2892557/68‑1 (MQ=255)                                              ccGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCa                   >  1:1405032/1‑68 (MQ=255)                                                ggTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGt                 <  1:2258379/68‑1 (MQ=255)                                                       aGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGAt          <  1:2471160/68‑1 (MQ=255)                                                       aGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGAt          <  1:961682/68‑1 (MQ=255)                                                        gTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGGACGTCTTTAATCTCAGTAAGAGAtt         >  1:1001386/1‑68 (MQ=255)                                                             ccAGGAGCATGCCCAGAGACAGTCGACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTa    >  1:1654625/1‑68 (MQ=255)                                                              cAGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTAc   <  1:3352511/68‑1 (MQ=255)                                                               aGGAGCATGCCCAGAGACAGTCCACGGGAAGCCGGCACGTCTTTAATCTCAGTAAGAGATTTTTTAcc  >  1:4084074/1‑68 (MQ=255)                                                               aGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTAcc  >  1:1444917/1‑68 (MQ=255)                                                                  |                                                                 AGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACC  >  CP009273/3433374‑3433503

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑