Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,338,233	T→C	T77A (ACC→GCC)	mlaD ←	intermembrane phospholipid transport system, substrate binding protein MlaD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,338,233	0	T	C	100.0%	86.9 / NA	25	T77A (ACC→GCC)	mlaD	intermembrane phospholipid transport system, substrate binding protein MlaD
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (13/12);  total (13/12)

TCCGGGTCTTCAAAACCGACGTTTAATGCCAGATATTGTTCCCCCAGCAGGCCGGAAGTACGAATGCTCAGCGAACTGGTATCTGGAATGTGGTTATAACGTTGTTCAATTTCCAGCGTTACGCGCGGCAGATAGGTTTTCGGGTCCAGCGTAATATCCGCCACCCGACCCACAACAACGCCACCAATACTGACCGGAGAGCGCGCTTTCAGGCCGCCAATGTTATCGAACGTCGCATAAAGCGTGTAGGTCGGTTCAGTACGTA  >  NC_000913/3338097‑3338361                                                                                                                                         |                                                                                                                                 tCCGGGTCTTCAAAACCGACGTTTAATGCCAGATATTGTTCCCCCAGCAGGCCGGAAGTACGAACGCTCAGCGAACTGGTATCTGGAATGTGGTTATAACGTTGTTCAATTTCCAGCGTTACGCGCGGCAGATAGGcttt                                                                                                                               <  2:430161/140‑1 (MQ=255)                          aTGCCAGATATTGTTCCCCCAGCAGGCCGGAAGTACGAATGCTCAGCGAACTGGTATCTGGAATGTGGTTATAACGTTGTTCAATTTCCAGCGTTACGCGCGGCAGATAGGCTTTCGGGTCCAGCGTAATATCCGCCAcc                                                                                                      <  1:462001/140‑1 (MQ=255)                             ccAGATATTGTTCCCCCAGCAGGCCGGAAGTACGAATGCTCAGCGAACTGGTATCTGGAATGTGGTTATAACGTTGTTCAATTTCCAGCGTTACGCGCGGCAGATAGGCTTTCGGGTCCAGCGTAATATCCGCCACCCGa                                                                                                   <  1:220649/140‑1 (MQ=255)                                 atatTGTTCCCCCAGCAGGCCGGAAGTACGAATGCTCAGCGAACTGGTATCTGGAATGTGGTTATAACGTTGTTCAATTTCCAGCGTTACGCGCGGCAGATAGGCTTTCGGGTCCAGCGTAATATCCGCCACCCGACCca                                                                                               >  2:432918/1‑140 (MQ=255)                                       ttCCCCCAGCAGGCCGGAAGTACGAATGCTCAGCGAACTGGTATCTGGAATGTGGTTATAACGTTGTTCAATTTCCAGCGTTACGCGCGGCAGATAGGCTTTCGGGTCCAGCGTAATATCCGCCACCCGACCCAcaacaa                                                                                         >  2:395422/1‑140 (MQ=255)                                          ccccAGCAGGCCGGAAGTACGAATGCTCAGCGAACTGGTATCTGGAATGTGGTTATAACGTTGTTCAATTTCCAGCGTTACGCGCGGCAGATAGGCTTTCGGGTCCAGCGTAATATCCGCCACCCGACCCACAACAACGc                                                                                      <  1:39985/140‑1 (MQ=255)                                                  ggCCGGAAGTACGAATGCTCAGCGAACTGGTATCTGGAATGTGGTTATAACGTTGTTCAATTTCCAGCGTTACGCGCGGCAGATAGGCTTTCGGGTCCAGCGTAATATCCGCCACCCGACCCACAACAACGCCACCAATa                                                                              >  1:73730/1‑140 (MQ=255)                                                    ccGGAAGTACGAATGCTCAGCGAACTGGTATCTGGAATGTGGTTATAACGTTGTTCAATTTCCAGCGTTACGCGCGGCAGATAGGCTTTCGGGTCCAGCGTAATATCCGCCACCCGACCCACAACAACGCCACCAATACt                                                                            <  1:395422/140‑1 (MQ=255)                                                                   cTCAGCGAACTGGTATCTGGAATGTGGTTATAACGTTGTTCAATTTCCAGCGTTACGCGCGGCAGATAGGCTTTCGGGTCCAGCGTAATATCCGCCACCCGACCCACAACAACGCCACCAATACTGACCGGAGAgcgcgc                                                             >  1:193347/1‑140 (MQ=255)                                                                      aGCGAACTGGTATCTGGAATGTGGTTATAACGTTGTTCAATTTCCAGCGTTACGCGCGGCAGATAGGCTTTCGGGTCCAGCGTAATATCCGCCACCCGACCCACAACAACGCCACCAATACTGACCGGAGAGCGCGCttt                                                          >  2:446789/1‑140 (MQ=255)                                                                              ggTATCTGGAATGTGGTTATAACGTTGTTCAATTTCCAGCGTTACGCGCGGCAGATAGGCTTTCGGGTCCAGCGTAATATCCGCCACCCGACCCACAACAACGCCACCAATACTGACCGGAGAGCGCGCTTTCAGgccgc                                                  >  2:407618/1‑140 (MQ=255)                                                                                         tgtgGTTATAACGTTGTTCAATTTCCAGCGTTACGCGCGGCAGATAGGCTTTCGGGTCCAGCGTAATATCCGCCACCCGACCCACAACAACGCCACCAATACTGACCGGAGAGCGCGCTTTCAGGCCGCCAATGTTATCg                                       >  2:318095/1‑140 (MQ=255)                                                                                                       tgttCAATTTCCAGCGTTACGCGCGGCAGATAGGCTTTCGGGTCCAGCGTAATATCCGCCACCCGACCCACAACAACGCCACCAATACTGACCGGAGAGCGCGCTTTCAGGCCGCCAATGTTATCGAACGTCGCATAAAg                         >  1:64399/1‑140 (MQ=255)                                                                                                        gttCAATTTCCAGCGTTACGCGCGGCAGATAGGCTTTCGGGTCCAGCGTAATATCCGCCACCCGACCCACAACAACGCCACCAATACTGACCGGAGAGCGCGCTTTCAGGCCGCCAATGTTATCGAACGTCGCAt                             <  1:132018/135‑1 (MQ=255)                                                                                                        gttCAATTTCCAGCGTTACGCGCGGCAGATAGGCTTTCGGGTCCAGCGTAATATCCGCCACCCGACCCACAACAACGCCACCAATACTGACCGGAGAGCGCGCTTTCAGGCCGCCAATGTTATCGAACGTCGCAt                             >  2:132018/1‑135 (MQ=255)                                                                                                           cAATTTCCAGCGTTACGCGCGGCAGATAGGCTTTCGGGTCCAGCGTAATATCCGCCACCCGACCCACAACAACGCCACCAATACTGACCGGAGAGCGCGCTTTCAGGCCGCCAATGTTATCGAACGTCGCATAAAGCgtg                     <  2:73730/140‑1 (MQ=255)                                                                                                           cAATTTCCAGCGTTACGCGCGGCAGATAGGCTTTCGGGTCCAGCGTAATATCCGCCACCCGACCCACAACAACGCCACCAATACTGACCGGAGAGCGCGCTTTCAGGCCGCCAATGTTATCGAACGTCGCATAAAGCgtg                     <  1:155873/140‑1 (MQ=255)                                                                                                              tttCCAGCGTTACGCGCGGCAGATAGGCTTTCGGGCCCAGCGTAATATCCGCCACCCGACCCACAACAACGCCACCAATACTGACCGGAGAGCGCGCTTTCAGGCCGCCAATGTTATCGAACGTCGCATAAAGCGTGTAg                  >  2:285961/1‑140 (MQ=255)                                                                                                                tCCAGCGTTACGCGCGGCAGATAGGCTTTCGGGTCCAGCGTAATATCCGCCACCCGACCCACAACAACGCCACCAATACTGACCGGAGAGCGCGCTTTCAGGCCGCCAATGTTATCGAACGTCGCATAAAGCGTGTAGGt                <  1:407618/140‑1 (MQ=255)                                                                                                                   aGCGTTACGCGCGGCAGATAGGCTTTCGGGTCCAGCGTAATATCCGCCACCCGACCCACAACAACGCCACCAATACTGACCGGAGAGCGCGCTTTCAGGCCGCCAATGTTATCGAACGTCGCATAAAGCgtg                     <  1:500535/132‑1 (MQ=255)                                                                                                                   aGCGTTACGCGCGGCAGATAGGCTTTCGGGTCCAGCGTAATATCCGCCACCCGACCCACAACAACGCCACCAATACTGACCGGAGAGCGCGCTTTCAGGCCGCCAATGTTATCGAACGTCGCATAAAGCgtg                     >  2:500535/1‑132 (MQ=255)                                                                                                                          cgcgcgGCAGATAGGCTTTCGTGTCCAGCGTAATATCCGCCACCCGACCCACAACAACGCCACCAATACTGACCGGAGAGCGCGCTTTCAGGCCGCCAATGTTATCGAACGTCGCATAAAGCGTGTAGGTCGGTTCAGTa      >  2:167248/1‑140 (MQ=255)                                                                                                                          cgcgcgGCAGATAGGCTTTCGGGTCCAGCGTAATATCCGCCACCCGACCCACAACAACGCCACCAATACTGACCGGAGAGCGCGCTTTCAGGCCGCCAATGTTATCGAACGTCGCATAAAGCGTGTAGGTCGGTTCAGt       >  2:208842/1‑139 (MQ=255)                                                                                                                          cgcgcgGCAGATAGGCTTTCGGGTCCAGCGTAATATCCGCCACCCGACCCACAACAACGCCACCAATACTGACCGGAGAGCGCGCTTTCAGGCCGCCAATGTTATCGAACGTCGCATAAAGCGTGTAGGTCGGTTCAGt       <  1:208842/139‑1 (MQ=255)                                                                                                                              gggCAGATAGGCTTTCGGGTCCAGCGTAATATCCGCCACCCGACCCACAACAACGCCACCAATACTGACCGGAGAGCGCGCTTTCAGGCCGCCAATGTTATCGAACGTCGCATAAAGCGTGTAGGTCGGTTCAGTACGTa  <  1:285961/139‑1 (MQ=255)                                                                                                                              cgGCAGATAGGCTTTCGTGTCCAGCGTAATATCCGCCACCCGACCCACAACAACGCCACCAATACTGACCGGAGAGCGCGCTTTCAGGCCGCCAATGTTATCGAACGTCGCATAAAGCGTGTAGGTCGGTTCAGTACGTa  <  1:167248/140‑1 (MQ=255)                                                                                                                                         |                                                                                                                                 TCCGGGTCTTCAAAACCGACGTTTAATGCCAGATATTGTTCCCCCAGCAGGCCGGAAGTACGAATGCTCAGCGAACTGGTATCTGGAATGTGGTTATAACGTTGTTCAATTTCCAGCGTTACGCGCGGCAGATAGGTTTTCGGGTCCAGCGTAATATCCGCCACCCGACCCACAACAACGCCACCAATACTGACCGGAGAGCGCGCTTTCAGGCCGCCAATGTTATCGAACGTCGCATAAAGCGTGTAGGTCGGTTCAGTACGTA  >  NC_000913/3338097‑3338361

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑