Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	556,986	A→C	10.0%	K12T (AAG→ACG)	rpsN →	30S ribosomal protein S14

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	556,986	0	A	C	10.0%	139.4 / 7.4	50	K12T (AAG→ACG)	rpsN	30S ribosomal protein S14
Reads supporting (aligned to +/- strand):  ref base A (23/22);  new base C (3/2);  total (26/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.95e-01

ATGCTCTGCGCGGTTTGGACATCACCCTGACCACCACTGCTCGTTCGGACGACGAAGGCCGCGCTCTGCTGCGTGCTTTCAAGTTCCCGTTCCGCAACTGATTGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTGCTGAGCTGAAAGCGACCATCGTCAACCTGAACGCCTCTCCAGAAGAGCGTTTCGCTGCCGTTGTCGCTCTGCAGAAGCAGCCACGCGACGCTAGCGCCTCGCGCCTGC  >  NC_002947/556838‑557132                                                                                                                                                     |                                                                                                                                                     aTGCTCTGCGCGTTTTGGACATCACCCTGACCACCACTGCTCGTTCGGACGACGAAGGCCGCGCTCTGCTTCGTGCTTTCAAGTTCCCGTTCCGCAACTGATTGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGaa                                                                                                                                                      <  3:239601/149‑1 (MQ=255)  tGCTCTGCGCGGTTTGGACATCACCCTGACCACCACTGCTCGTTCGGACGACGAAGGCCGCGCTCTGCTGCGTGCTTTCAAGTTCCCGTTCCGCAACTGATTGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGAAg                                                                                                                                                     <  2:187920/149‑1 (MQ=255)     tctGCGCGGTTTGGACATCACCCTGACCACCACTGCTCGTTCGGACGACGAAGGCCGCGCTCTGCTGCGTGCTTTCAAGTTCCCGTTCCGCAACTGATTGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGAAGCGt                                                                                                                                                  >  2:36336/1‑149 (MQ=255)     tctGCGCGGTTTGGACATCACCCTGACCACCACTGCTCGTTCGGACGACGAAGGCCGCGCTCTGCTGCGTGCTTTCAAGTTCCCGTTCCGCAACTGATTGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGAAGCGt                                                                                                                                                  >  6:279851/1‑149 (MQ=255)         cgcgGTTTGGACATCACCCTGACCACCACTGCTCGTTCGGACGACGAAGGCCGCGCTCTGCTGCGTGCTTTCAAGTTCCCGTTCCGCAACTGATTGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGAAGCGTCa                                                                                                                                                <  1:292826/147‑1 (MQ=255)                  gACATCACCCTGACCACCACTGCTCGTTCGGACGACGAAGGCCGCGCTCTGCTGCGTGCTTTCAAGTTCCCGTTCCGCAACTGATTGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGACGCTTCAGCTCG‑Cg‑g                                                                                                                                      <  1:318079/146‑1 (MQ=255)                  gACATCACCCTGACCACCACTGCTCGTTCGGACGACGAAGGCCGCGCTCTGCTGCGTGCTTTCAAGTTCCCGTTCCGCAACTGATTGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGACGCTTCAGCTCG‑Cg‑g                                                                                                                                      >  2:318079/1‑146 (MQ=255)                              accaccACTGCTCGTTCGGACGACGAAGGCCGCGCTCTGCTGCGTGCTTTCAAGTTCCCGTTCCGCAACTGATTGGAGTAGGAGAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGc                                                                                                                         <  2:37275/147‑1 (MQ=255)                                  ccacTGCTCGTTCGGACGACGAAGGCCGCGCTCTGCTGCGTGCTTTCAAGTTCCCGTTCCGCAACTGATTGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTaagaa                                                                                                                   <  1:159944/149‑1 (MQ=255)                                   cacTGCTCGTTCGGACGACGAAGGCCGCGCTCTGCTGCGTGCTTTCAAGTTCCCGTTCCGCAACTGATTGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTaagaag                                                                                                                  >  8:51698/1‑149 (MQ=255)                                   cacTGCTCGTTCGGACGACGAAGGCCGCGCTCTGCTGCGTGCTTTCAAGTTCCCGTTCCGCAACTGATTGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGACCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTaag                                                                                                                     >  5:51657/1‑146 (MQ=255)                                        cTCGTTCGGACGACGAAGGCCGCGCTCTGCTGCGTGCTTTCAAGTTCCCGTTCCGCAACTGATTGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGc                                                                                                                         >  3:243052/1‑137 (MQ=255)                                        cTCGTTCGGACGACGAAGGCCGCGCTCTGCTGCGTGCTTTCAAGTTCCCGTTCCGCAACTGATTGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGc                                                                                                                         <  4:243052/137‑1 (MQ=255)                                           gTTCGGACGACGAAGGCCGCGCTCTGCTGCGTGCTTTCAAGTTCCCGTTCCGCAACTGATTGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CGTGTAGCAAAGTTCGCTAAGAAGCGTgc                                                                                                             <  1:171654/147‑1 (MQ=255)                                            ttCGGACGACGAAGGGCGCGCTCTGCTGCTTTCTTTCAAGTTCCCGTTCCGAAAGTTATTGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTgctga                                                                                                          <  7:114600/148‑1 (MQ=255)                                               ggACGACGAAGGCCGCGCTCTGCTGCGTGCTTTCAAGTTCCCGTTCCGCAACTGATTGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTgctgagct                                                                                                       >  8:69855/1‑148 (MQ=255)                                               ggACGACGAAGGCCGCGCTCTGCTGCGTGCTTTCAAGTTCCCGTACCGCAACTGATTGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGTGAGCTGACGCTTCAGCTCG‑CG‑Gtttttca                                                                                                                               <  6:183073/124‑7 (MQ=38)                                               ggACGACGAAGGCCGCGCTCTGCTGCGTGCTTTCAAGTTCCCGTACCGCAACTGATTGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGTGAGCTGACGCTTCAGCTCG‑CG‑Gtttttca                                                                                                                               >  5:183073/1‑118 (MQ=38)                                                  cgacgaAGGCCGCGCTCTGCTGCGTGCTTTCAAGTTCCCGTTCCGCAACTGATTGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTGCTGAGCTGaaa                                                                                                   <  1:36336/149‑1 (MQ=255)                                                      gaAGGCCGCGCTCTGCTGCGTGCTTTCAAGTTCCCGTTCCGCAACAGATTGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTGCTGAGCTGAAAGCGa                                                                                               >  1:50430/1‑149 (MQ=255)                                                        aGGCCGCGCTCTGCTGCGTGCTTTCAAGTTCCCGTTCCGCAACTGATTGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTGCTGAGCTGAAAGCGAc                                                                                              >  2:110523/1‑148 (MQ=255)                                                                   tgctgcGTGCTTTCAAGTTCCCGTTCCGCAACTGATTGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTGCTGAGCTGAAAGCGACCATCGTCAAc                                                                                    <  8:110697/147‑1 (MQ=255)                                                                      ggcGTGCTTTCAAGTTCCCCTTCCCCAACTGATTGCAGTAGGAAAATGGCCAAGACGACCAGGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTGCTGAGCTGAAAGCGACCATCGTCAACCTGaa                                                                               <  8:103253/148‑1 (MQ=255)                                                                         gTGCTTTCAAGTTCCCGTTCCGCAACTGATTGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTGCTGAGCTGAAAGCGACCATCGTCAACCTGAACGc                                                                            >  7:226090/1‑149 (MQ=255)                                                                             tttCAAGTTCCCGTTCCGCAACTGATTGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCaaa                                                                                                                               >  3:29062/1‑94 (MQ=255)                                                                             tttCAAGTTCCCGTTCCGCAACTGATTGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCaaa                                                                                                                               <  4:29062/94‑1 (MQ=255)                                                                                 aaGTTCCCGTTCCGCAACTGATTGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTGCTGAGCTGAAAGCGACCATCGTCAACCTGAACGCCtctc                                                                       >  1:138026/1‑146 (MQ=255)                                                                                   gTTCCCGTTCCGCAACTGATTGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTGCTGAGCTGAAAGCGACCATCGTCAACCTGAACGCCTCTCCagaa                                                                  <  7:51698/149‑1 (MQ=255)                                                                                     tCCCGTTCCGCAACTGATTGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTGCTGAGCTGAAAGCGACCATCGTCAACCTGAACGCCTCTCCagaa                                                                  >  1:107894/1‑147 (MQ=255)                                                                                     tCCCGTTCCGCAACTGATTGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTGCTGAGCTGAAAGCGACCATCGTCAACCTGAACGCCTCTCCagaa                                                                  >  8:175107/1‑147 (MQ=255)                                                                                          ttCCGCAACTGATTGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTGCTGAGCTGAAAGCGACCATCGTCAACCTGAACGCCTCTCCAGAAGAGCGtt                                                           >  6:103854/1‑149 (MQ=255)                                                                                              gCAACTGATTGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTGCTGAGCTGAAAGCGACCATCGTCAACCTGAACGCCTCTCCAGAAGAGCGTTTCGc                                                       >  1:317059/1‑149 (MQ=255)                                                                                                      ttGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTGCTGAGCTGAAAGCGACCATCGTCAACCTGAACGCCTCTCCAGAAGAGCGTTTCGCTGCCGTTg                                               <  7:69855/149‑1 (MQ=255)                                                                                                         gAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTGCTGAGCTGAAAGCGACCATCGTCAACCTGAACGCCTCTCCAGAAGAGCGTTTCGCTGCCGTTGTCg                                            <  5:279851/149‑1 (MQ=255)                                                                                                            tAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTGCTGAGCTGAAAGCGACCATCGTCAACCTGAACGCCTCTCCAGAAGAGCGTTTCGCTGCCGTTGTCGctc                                         >  1:148401/1‑149 (MQ=255)                                                                                                                aaaaTGGCCAAGAAGAGCATGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTGCTGAGCTGAAAGCGACCATCGTCAACCTGAACGCCTCTCCAGAAGAGCGTTTCGCTGCCGTTGTCGCTCTGCa                                     <  5:103854/149‑1 (MQ=255)                                                                                                                 aaaTGGCCAAGAAGAGCATGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTGCTGAGCTGAAAGCGACCATCGTCAACCTGAACGCCTCTCCAGAAGAGCGTTTCGCTGCCGTTGTCGCTCTGCa                                     <  2:148401/148‑1 (MQ=255)                                                                                                                      gCCAAGAAGAGCATGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTGCTGAGCTGAAAGCGACCATCGTCAACCTGAACGCCTCTCCAGAAGAGCGTTTCGCTGCCGTTGTCGCTCTGCAGAag                                 >  7:243785/1‑147 (MQ=255)                                                                                                                        cAATAAGAGCATGAAAAACCGCTAGCTGAAGCGTCAGCTCACCA‑CCAGCAAAGTTCGCTAAGAAGCGTGCTGAGCTGAAAGCGACCATCGTCAACCTGAACGCCTCTCCAGAAGAGCGTTTCGCTGCCGTTGTCGCTCTGCAGAagcag                              <  1:110523/149‑1 (MQ=255)                                                                                                                         aagaagAGCATGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTGCTGAGCTGAAAGCGACCATCGTCAACCTGAACGCCTCTCCAGAAGAGCGTTTCGCTGCCGTTGTCGCTCTGCAGAAGCAGcc                            <  2:50430/149‑1 (MQ=255)                                                                                                                           gaagaGCATGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTGCTGAGCTGAAAGCGACCATCGTCAACCTGAACGCCTCTCCAGAAGAGCGTTTCGCTGCCGTTGTCGCTCTGCAGAAGCAGCCAc                          <  2:317059/149‑1 (MQ=255)                                                                                                                           gaagaGCATGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTGCTGAGCTGAAAGCGACCATCGTCAACCTGAACGCCTCTCCAGAAGAGCGTTTCGCTGCCGTTGTCGCTCTGCAGAAGCAGCCAc                          >  2:263779/1‑149 (MQ=255)                                                                                                                                    gAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTGCTGAGCTGAAAGCGACCATCGTCAACCTGAACGCCTCTCCAGAAGAGCGTTTCGCTGCCGTTGTCGCTCTGc                                      <  2:56323/128‑1 (MQ=255)                                                                                                                                    gAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTGCTGAGCTGAAAGCGACCATCGTCAACCTGAACGCCTCTCCAGAAGAGCGTTTCGCTGCCGTTGTCGCTCTGc                                      >  1:56323/1‑128 (MQ=255)                                                                                                                                    gAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTGCTGAGCTGAAAGCGACCATCGTCAACCTGAACGCCTCTCCAGAAGAGCGTTTCGCTGCCGTTGTCGCTCTGCAGAAGCAGCCACGCGACGc                   >  4:124932/1‑147 (MQ=255)                                                                                                                                    gAAAAACCGCGAGCTGAAGCGACAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTGCAGAGCTGAAAGCGACCATCGTCAACCTGAACGCCTCTCCAGAAGACCGTTTCGCTGCCGTTGTCGCTCTTCAGAAGCAGCCACGCGACGcaa                 >  7:73509/1‑147 (MQ=255)                                                                                                                                     aaaaaCCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTGCTGAGCTGAAAGCGACCATCGTCAACCTGAACGCCTCTCCAGAAGAGCGTTTCGCTGCCGTTGTCGCTCTGCAGAAGCAGCCACGCGACGCTa                 <  2:107894/148‑1 (MQ=255)                                                                                                                                      aaaaCCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTGCTGAGCTGAAAGCGACCATCGTCAACCTGAACGCCTCTCCAGAAGAGCGTTTCGCTGCCGTTGTCGCTCTGCAGAAGCAGCCACGCGACGCTAgc               <  2:138026/149‑1 (MQ=255)                                                                                                                                       aaaCCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTGCTGAGCTGAAAGCGACCATCGTCAACCTGAACGCCTCTCCAGAAGAGCGTTTCGCTGCCGTTGTCGCTCTGCAGAAGCAGCCACGCGACGCTAgcg              >  1:210143/1‑149 (MQ=255)                                                                                                                                           cgtgAGCTGACGCTTCAGCTCG‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTGCTGAGCTGAAAGCGACCATCGTCAACCTGAACGCCTCTCCAGAAGAGCGTTTCGCTGCCGTTGTCGCTCTGCAGAAGCAGCCACGCGACGCTAGCGCCTc          >  1:282142/4‑149 (MQ=255)                                                                                                                                                   gAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTGCTGAGCTGAAAGCGACCATCGTCAACCTGAACGCCTCTCCAGAAGAGCGTTTCGCTGCCGTTGTCGCTCTGCAGAAGCAGCCACGCGACGCTAGCGCCTCGCGCCTgc  >  1:195314/1‑149 (MQ=255)                                                                                                                                                     |                                                                                                                                                     ATGCTCTGCGCGGTTTGGACATCACCCTGACCACCACTGCTCGTTCGGACGACGAAGGCCGCGCTCTGCTGCGTGCTTTCAAGTTCCCGTTCCGCAACTGATTGGAGTAGGAAAATGGCCAAGAAGAGCATGAAAAACCGCGAGCTGAAGCGTCAGCTCA‑CG‑GTAGCAAAGTTCGCTAAGAAGCGTGCTGAGCTGAAAGCGACCATCGTCAACCTGAACGCCTCTCCAGAAGAGCGTTTCGCTGCCGTTGTCGCTCTGCAGAAGCAGCCACGCGACGCTAGCGCCTCGCGCCTGC  >  NC_002947/556838‑557132

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑