Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,440,683	G→A	T116I (ACC→ATC)	rpoA ←	RNA polymerase subunit alpha

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,440,683	0	G	A	100.0%	107.3 / NA	33	T116I (ACC→ATC)	rpoA	RNA polymerase subunit alpha
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (15/18);  total (15/18)

GAAGCCGGCACATAACCACGACCGCGCTGAACTTTGATACGCATGCTAATAGACGCGTTCTCATCGGTCAGGTGGCAGATCACGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGGTGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAGCCCTTTCAGGTTGAGCAGGATTTCCAGGATATCTTCCTGA  >  NC_000913/3440563‑3440808                                                                                                                         |                                                                                                                              gAAGCCGGCACATAACCACGACCGCGCTGAACTTTGATACGCATGCTAATAGACGCGTTCTCATCGGTCAGGTGGCAGATCACGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGATGATATCGGCTg                                                                                                                   >  2:47336/1‑133 (MQ=255)       ggCACATAACCACGACCGCGCTGAACTTTGATACGCATGCTAATAGACGCGTTCTCATCGGTCAGGTGGCAGATCACGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGATGATATCGGCTGCAGTca                                                                                                             <  2:134799/133‑1 (MQ=255)              aaCCACGACCGCGCTGAACTTTGATACGCATGCTAATAGACGCGTTCTCATCGGTCAGGTGGCAGATCACGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGATGATATCGGCTGCAGTCACAGGGcc                                                                                                      <  1:526791/133‑1 (MQ=255)              aaCCACGACCGCGCTGAACTTTGATACGCATGCTAATAGACGCGTTCTCATCGGTCAGGTGGCAGATCACGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGATGATATCGGCTGCAGTCACAGGGcc                                                                                                      <  2:368532/133‑1 (MQ=255)                       cgcgCTGAACTTTGATACGCATGCTAATAGACGCGTTCTCATCGGTCAGGTGGCAGATCACGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGATGATATCGGCTGCAGTCACAGGGCCAATGCCAGa                                                                                             <  2:437336/133‑1 (MQ=255)                          gcTGAACTTTGATACGCATGCTAATAGACGCGTTCTCATCGGTCAGGTGGCAGATCACGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGATGATATTGGCTGCAATCACAGCGCCAATACCAGAttt                                                                                          >  1:209050/1‑133 (MQ=255)                           cTGAACTTTGATACGCATGCTAATAGACGCGTTCTCATCGGTCAGGTGGCAGATCACGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGATGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTa                                                                                         >  2:5976/1‑133 (MQ=255)                             gAACTTTGATACGCATGCTAATAGACGCGTTCTCATCGGTCAGGTGGCAGATCACGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGATGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTAtt                                                                                       <  2:505307/133‑1 (MQ=255)                              aaCTTTGATACGCATGCTAATAGACGCGTTCTCATCGGTCAGGTGGCAGATCACGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGATGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTc                                                                                      <  2:105206/133‑1 (MQ=255)                                       aCGCATGCTAATAGACGCGTTCTCATCGGTCAGGTGGCAGATCACGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGATGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGa                                                                             <  2:7269/133‑1 (MQ=255)                                       aCGCATGCTAATAGACGCGTTCTCATCGGTCAGGTGGCAGATCACGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGATGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGa                                                                             <  2:6712/133‑1 (MQ=255)                                       aCGCATGCTAATAGACGCGTTCTCATCGGTCAGGTGGCAGATCACGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGATGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGa                                                                             <  2:60025/133‑1 (MQ=255)                                          cATGCTAATAGACGCGTTCTCATCGGTCAGGTGGCAGATCACGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGATGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATa                                                                          >  1:153173/1‑133 (MQ=255)                                                   aGACGCGTTCTCATCGGTCAGGTGGCAGATCACGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGATGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCt                                                                 >  1:401806/1‑133 (MQ=255)                                                       gcgTTCTCATCGGTCAGGTGGCAGATCACGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGATGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGc                                                             >  1:606342/1‑133 (MQ=255)                                                       gcgTTCTCATCGGTCAGGTGGCAGATCACGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGATGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGc                                                             >  2:541537/1‑133 (MQ=255)                                                       gcgTTCTCATCGGTCAGGTGGCAGATCACGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGATGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGc                                                             >  2:419530/1‑133 (MQ=255)                                                        cgTTCTCATCGGTCAGGTGGCAGATCACGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGATGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGcc                                                            >  1:26922/1‑133 (MQ=255)                                                        cgTTCTCATCGGTCAGGTGGCAGATCACGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGATGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGcc                                                            <  2:37659/133‑1 (MQ=255)                                                        cgTTCTCATCGGTCAGGTGGCAGATCACGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGATGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGcc                                                            <  1:47336/133‑1 (MQ=255)                                                          ttCTCATCGGTCAGGTGGCAGATCACGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGATGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCt                                                          >  1:373247/1‑133 (MQ=255)                                                           tctcATCGGTCAGGTGGCAGATCACGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGATGATATCGGCTGCAGTCACCGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTg                                                         >  2:602407/1‑133 (MQ=255)                                                             tcATCGGTCAGGTGGCAGATCACGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGATGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGaa                                                       <  2:153173/133‑1 (MQ=255)                                                               aTCGGTCAGGTGGCAGATCACGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGATGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAAct                                                     <  2:539372/133‑1 (MQ=255)                                                                         tGGCAGATCACGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGATGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCa                                           <  2:373247/133‑1 (MQ=255)                                                                          ggCAGATCACGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGATGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAg                                          <  2:52681/133‑1 (MQ=255)                                                                              gATCACGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGATGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGGAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAGCCCt                                      >  1:121062/1‑133 (MQ=255)                                                                                  aCGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGATGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTATGCCCTGGACTCTCACCGCCAGCCCTTTCa                                  >  1:304842/1‑133 (MQ=255)                                                                                             cTTGACGATTTCGACATCACCGTCGTGGATGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAGCCCTTTCAGGTTGAGCAgg                       <  2:401806/133‑1 (MQ=255)                                                                                                gACGATTTCGACATCCCGGTCGTGGATGATATCGGCTGCAGTCACGGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCCCCGCCAGCCCTTTCAGGTTGAGCAGGAtt                    <  1:602407/133‑1 (MQ=255)                                                                                                    aTTTCGACATCACCGTCGTGGATGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGAAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAGCCCTTTCAGGTTGAGCAGGATTTCCa                <  2:121062/133‑1 (MQ=255)                                                                                                                ccGTCGTGGATGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAGCCCTTTCAGGTTGAGCAGGATTTCCAGGATATCTTCCt    >  2:346397/1‑133 (MQ=255)                                                                                                                 cgtcgtGGATGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAGCCCTTTCAGGTTGAGCAGGATTTCCAGGATATCTTCCTg   >  1:527206/1‑133 (MQ=255)                                                                                                                  gtcgtGGATGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAGCCCTTTCAGGTTGAGCAGGATTTCCAGGATATCTTCCTGa  <  1:5976/133‑1 (MQ=255)                                                                                                                         |                                                                                                                              GAAGCCGGCACATAACCACGACCGCGCTGAACTTTGATACGCATGCTAATAGACGCGTTCTCATCGGTCAGGTGGCAGATCACGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGGTGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAGCCCTTTCAGGTTGAGCAGGATTTCCAGGATATCTTCCTGA  >  NC_000913/3440563‑3440808

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑