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%	148.4 / NA	50	R317L (CGC→CTC)	rpoA	RNA polymerase, alpha subunit
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (27/23);  total (27/23)

AAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACC  >  CP009273/3433377‑3433503                                                               |                                                                 aaaaCCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATg                                                             <  1:818890/68‑1 (MQ=255)  aaaCCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGc                                                            <  1:3696249/68‑1 (MQ=255)   aaCCTTCACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGGGGCCAGTTTTCCAGGAGCATGcc                                                           <  1:161379/68‑1 (MQ=255)   aaCCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGcc                                                           <  1:3705072/68‑1 (MQ=255)   aaCCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGcc                                                           <  1:3032831/68‑1 (MQ=255)      cTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCag                                                        >  1:1776098/1‑68 (MQ=255)           ccTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACa                                                   >  1:5144213/1‑68 (MQ=255)           ccTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACa                                                   >  1:3306443/1‑68 (MQ=255)            cTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAg                                                  >  1:3335157/1‑68 (MQ=255)             tgtgATCCGGTTACTTGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGt                                                 <  1:3550438/68‑1 (MQ=255)             tgtgATCCGGTTACTCGTCAGCGATGCTTGCGGGTGGCCAGTTTTCCAGGAGCATGCCCAGTGACAGt                                                 <  1:4966250/68‑1 (MQ=255)             tgtgATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGt                                                 <  1:1869665/68‑1 (MQ=255)             tgtgATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGt                                                 <  1:4511747/68‑1 (MQ=255)                gATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTccc                                              >  1:5255707/1‑67 (MQ=255)                gATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCa                                              >  1:3395768/1‑68 (MQ=255)                gATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCa                                              >  1:4329870/1‑68 (MQ=255)                gATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCa                                              >  1:1904385/1‑68 (MQ=255)                  tCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACg                                            <  1:1773644/68‑1 (MQ=255)                  tCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACg                                            >  1:1905160/1‑68 (MQ=255)                  tCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACg                                            >  1:2001851/1‑68 (MQ=255)                    cGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACggg                                          >  1:4232419/1‑68 (MQ=255)                     ggTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGa                                         >  1:3350438/1‑68 (MQ=255)                     ggTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGa                                         >  1:878400/1‑68 (MQ=255)                     ggTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGa                                         >  1:3879276/1‑68 (MQ=255)                     ggTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGa                                         >  1:367505/1‑68 (MQ=255)                         aCTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGcc                                     >  1:2116277/1‑68 (MQ=255)                         aCTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGcc                                     >  1:904331/1‑68 (MQ=255)                           tCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAg                                   >  1:5945090/1‑68 (MQ=255)                            cGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAGGCCAGc                                  >  1:6185212/1‑68 (MQ=255)                            cGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGc                                  >  1:3614778/1‑68 (MQ=255)                            cGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGc                                  >  1:2551581/1‑68 (MQ=255)                            cGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGc                                  <  1:6195903/68‑1 (MQ=255)                             gTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGCa                                 <  1:2528595/68‑1 (MQ=255)                             gTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGCa                                 <  1:3540916/68‑1 (MQ=255)                                 gctaTGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTc                             <  1:5021319/65‑1 (MQ=255)                                 gCGATGCTTGCCGGTGGCCAGTTTTCGAGGAGCATGCCCAGCGCCAGTCCACGGGAAGCCAGCACGTc                             >  1:1348654/1‑68 (MQ=255)                                 gCGATGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTc                             >  1:4735526/1‑68 (MQ=255)                                 gCGATGCTTGCCGGTGGCCAGATTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTc                             <  1:2861510/68‑1 (MQ=255)                                 gCGATGCAAGCCGGGGGCCTGTGTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTc                             <  1:5587719/68‑1 (MQ=255)                                 gCGATGATTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGACCACGCGAAGCCAGCACGTc                             <  1:4240472/68‑1 (MQ=255)                                     tGCTTGCCGGTGGCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTa                         >  1:1533823/1‑68 (MQ=255)                                        ttGCCGGTGGCCAGTTTTCCGGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAAtc                      >  1:4591114/1‑68 (MQ=255)                                         tggcGGTGGCCAGTTTTCCAGCAGCATGCCCAGCGACAGTCCACGGGAACCCAGCACGTCTTTAAtct                     <  1:4987806/65‑1 (MQ=255)                                                ggCCAGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAag              <  1:812011/68‑1 (MQ=255)                                                    aGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGAt          <  1:5389976/68‑1 (MQ=255)                                                    aGTTTTCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGAt          <  1:997752/68‑1 (MQ=255)                                                       tttCCAGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGAtttt       >  1:2678277/1‑68 (MQ=255)                                                         tCCAGGACCATGCCCAGAGACAGTCCACGGGAACCCAGCACGTCTTTAATCTCAGTAAGAGAtttttt     <  1:4933341/68‑1 (MQ=255)                                                           cAGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTAc   <  1:5085222/68‑1 (MQ=255)                                                            aGGAGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTAcc  >  1:4317682/1‑68 (MQ=255)                                                               |                                                                 AAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACC  >  CP009273/3433377‑3433503

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑