Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_pgi	3,440,243	T→C	T263A (ACT→GCT)	rpoA ←	RNA polymerase, alpha subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_pgi	3,440,243	0	T	C	100.0%	86.9 / NA	28	T263A (ACT→GCT)	rpoA	RNA polymerase, alpha subunit
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (15/13);  total (15/13)

TCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACGTACATCACGTAAGTCAACGAAAGCTTCCAGTTGTTCAGCCAGAATGGTTGCCGCACGACGAATC  >  NC_000913_3_pae_pgi/3440097‑3440382                                                                                                                                                   |                                                                                                                                            tCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATACTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGgccagcca                                                                                                                                           >  2:463985/1‑149 (MQ=255)          aGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGCCAATTCCAGAt                                                                                                                                  <  1:364883/149‑1 (MQ=255)                   gTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGCCAATTCCAGATCGTCAACAg                                                                                                                         >  1:352356/1‑149 (MQ=255)                      tttAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACGGCCAATTCCAGATCGTCAACAgggg                                                                                                                      >  1:137154/1‑148 (MQ=255)                      tttAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGCCAATTCCAGATCGTCAACAGGgc                                                                                                                      >  2:321821/1‑149 (MQ=255)                         aaTCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGCCAATTCCAGATCGTCAACAGGGCgca                                                                                                                   <  2:442431/149‑1 (MQ=255)                                 tAAGAGATTTTTTACCAAGGTTAGGGGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGCCAATTCCAGATCGTCAACAGGGCGCAGCAggatc                                                                                                           <  2:280557/149‑1 (MQ=255)                                    gagaTTTTTTACCAAGGTTAGACGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGAAGAGCGGACAGCCAATTCCAGATCGTCACCAGGGCGCAGCGggatcgga                                                                                                        >  2:227911/1‑149 (MQ=255)                                              aCCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGCCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTg                                                                                              >  1:352022/1‑149 (MQ=255)                                                cAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGTTACGTCGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGGTAGCAGAGCTGACAGCCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGt                                                                                            <  1:50570/149‑1 (MQ=255)                                                            ttttAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGCCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTc                                                                                >  2:224632/1‑149 (MQ=255)                                                                  ggAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGCCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCa                                                                          <  1:145454/149‑1 (MQ=255)                                                                      cTCAACCTCGGTACGCTGTACCAGATCACCGATAGAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGCCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCt                                                                      >  1:291539/1‑149 (MQ=255)                                                                            cTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGCCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACGTa                                                                >  1:338076/1‑149 (MQ=255)                                                                                    gCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGCCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACGTACATCACGt                                                        >  1:44297/1‑149 (MQ=255)                                                                                      tGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGCCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACGTACATCACGTaa                                                      <  1:129298/149‑1 (MQ=255)                                                                                        tACAAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGCCAATTCCAGCTCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACGTACATCACGTAAGt                                                    >  1:91368/1‑149 (MQ=255)                                                                                          ccAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGCCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACGTACATCACGTAAGTCa                                                  <  2:379402/149‑1 (MQ=255)                                                                                           cAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGCCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACGTACa                                                              >  2:175463/1‑136 (MQ=255)                                                                                           cAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGCCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACGTACa                                                              <  1:175463/136‑1 (MQ=255)                                                                                           cAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGCCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACGTACATCACGTAAGTCaa                                                 <  1:322307/149‑1 (MQ=255)                                                                                             gATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGCCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGGTTCTCTTCTTTCACTTCAGGCTGAGGTACCTCACGTAAGTCACCg                                               >  1:68875/1‑149 (MQ=255)                                                                                                 aCCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGCCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTTTCTTCTTTCACTTCAGGCTGACGTACATCACGTAAGTGAACGAAAg                                           >  1:414588/1‑149 (MQ=255)                                                                                                                       gCTTTAAGGCAGTGAGCAGAACGGACAGCCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGAGCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACGTACATCACGTAAGTCAACGAAAGCTTCCAGTTGTTCAGCCAGAAt                     <  2:141549/149‑1 (MQ=255)                                                                                                                           tAAGGCAGTTAGCAGAGCGGACAGCCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACGTACATCACGTAAGTCAACGAAAGCTTCCAGTTGTTCAGCCAGAATGGtt                 <  1:99270/149‑1 (MQ=255)                                                                                                                             aGGCAGTTAGCAGAGCGGACAGCCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACGTACATCACGTAAGTCAACGAAAGCTTCCAGTTGTTCAGCCCGACTGGttcc               >  2:169248/1‑147 (MQ=255)                                                                                                                             aGGCAGTTAGCAGAGCGGACAGCCAATTCCAGAGCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACTTACATCACGTAAGTCAACGAAAGCTTCCAGTTGTTCAGCCGGAATGGTTGc               <  1:234744/149‑1 (MQ=255)                                                                                                                                  gtgggCAGGGCGGACAGCTAAGTCCAGGTCGTCAATAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGTCTGACGTACATCACGTAAGTCAATGAAAGCTTCCATTTGTTCAGTCATAATGGTTGCCGTac          <  2:47157/145‑1 (MQ=255)                                                                                                                                          agCGGACAGCCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACGTACATCACGTAAGTCAACGAAAGCTTCCAGTTGTTCAGCCAGAATGGTTGCCGCACGACGAATc  >  1:63895/1‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                            TCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACGTACATCACGTAAGTCAACGAAAGCTTCCAGTTGTTCAGCCAGAATGGTTGCCGCACGACGAATC  >  NC_000913_3_pae_pgi/3440097‑3440382

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑