Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,836,534	(C)6→7	pseudogene (110/132 nt)	yicT →	pseudogene

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,836,528	1	.	C	100.0%	104.8 / NA	29	pseudogene (104/132 nt)	yicT	pseudogene
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (11/18);  total (11/18)

GCTCAATATTCAATCGGCTTCAGGAATACCTGGTCTAAGGTTTTGTGATGGACGATGAGCGGCTGAAGAATCCGCCTGTCGGTTCTTCTGTCCTCGAACGCATCCGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTG‑‑CCCCCCTGCTGACTCTCAGCCAACTGTATCGCCATTAAGGTGAAGATGTTGTTTTACTCGCCCCAGAACACCCTTTTTTATACGACTATTCTATTTCTTTAACCGCTGGCGAAAAAAACTG  >  NC_000913/3836378‑3836649                                                                                                                                                        |                                                                                                                           gCTCAATATTCAATCGGCTTCAGGAATACCTGGTCTAAGGTTTTGTGATGGACGATGAGCGGCTGAAGAATCCGCCTGTCGGTTCTTCTGTCCTCGAACGCATCCGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTg                                                                                                                             >  1:629869/1‑151 (MQ=255)      atatTCAATCGGCTTCAGGAATACCTGGTCTAAGGTTTTGTGATGGACGATGAGCGGCTGAAGAATCCGCCTGTCGGTTCTTCTGTCCTCGAACGCATCCGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTG‑‑ccccc                                                                                                                      >  1:418594/1‑151 (MQ=255)       tatTCAATCGGCTTCAGGAATACCTGGTCTAAGGTTTTGTGATGGACGATGAGCGGCTGAAGAATCCGCCTGTCGGTTCTTCTGTCCTCGAACGCATCCGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTG‑‑cccccc                                                                                                                     >  2:173781/1‑151 (MQ=255)          tCAATCGGCTTCAGGAATACCTGGTCTAAGGTTTTGTGATGGACGATGAGCGGCTGAAGAATCCGCCTGTCGGTTCTTCTGTCCTCGAACGCATCCGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTG‑‑ccccccctg                                                                                                                  >  2:373823/1‑148 (MQ=255)          tCAATCGGCTTCAGGAATACCTGGTCTAAGGTTTTGTGATGGACGATGAGCGGCTGAAGAATCCGCCTGTCGGTTCTTCTGTCCTCGAACGCATCCGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTG‑‑ccccccctg                                                                                                                  >  2:355558/1‑148 (MQ=255)            aaTCGGCTTCAGGAATACCTGGTCTAAGGTTTTGTGATGGACGATGAGCGGCTGAAGAATCCGCCTGTCGGCTCTTCTGTCCTCGAACGCATCCGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTG‑‑ccccccctgc                                                                                                                 >  2:137880/1‑146 (MQ=255)                ggCTTCAGGAATACCTGGTCTAAGGTTTTGTGATGGACGATGAGCGGCTGAAGAATCCGCCTGTCGGTTCTTCTGTCCTCGAACGCATCCGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTGC‑CCCCCCTGCTGAct                                                                                                             >  2:21160/1‑151 (MQ=255)                ggCTTCAGGAATACCTGGTCTAAGGTTTTGTGATGGACGATGAGCGGCTGAAGAATCCGCCTGTCGGTTCTTCTGTCCTCGAACGCATCCGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTGC‑CCCCCCTGCTGAct                                                                                                             >  2:159401/1‑151 (MQ=255)                       ggAATACCTGGTCTAAGGTTTTGTGATGGACGATGAGCGGCTGAAGAATCCGCCTGTCGGTTCTTCTGTCCTCGAACGCATCCGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTGC‑CCCCCCTGCTGACTCTCAGcc                                                                                                      <  2:594972/151‑1 (MQ=255)                         aaTACCTGGTCTAAGGTTTTGTGATGGACGATGAGCGGCTGAAGAATCCGCCTGTCGGTTCTTCTGTCCTCGAACGCATCCGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTGC‑CCCCCCTGCTGACTCTCAGCCa                                                                                                     >  1:245214/1‑150 (MQ=255)                               tGGTCTAAGGTTTTGTGATGGACGATGAGCGGCTGAAGAATCCGCCTGTCGGTTCTTCTGTCCTCGAACGCATCCGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTGC‑CCCCCCTGCTGACTCTCAGCCAACTGTAt                                                                                              >  2:447303/1‑151 (MQ=255)                                ggTCTAAGGTTTTGTGATGGACGATGAGCGGCTGAAGAATCCGCCTGTCGGTTCTTCTGTCCTCGAACGCATCCGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTGC‑CCCCCCTGCTGACTCTCAGCCAACTGTATc                                                                                             <  2:566780/151‑1 (MQ=255)                                     aaGGTTTTGTGATGGACGATGAGCGGCTGAAGAATCCGCCTGTCGGTTCTTCTGTCCTCGAACGCATCCGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTGC‑CCCCCCTGCTGACTCTCAGCCAACTGTATCGc                                                                                           <  1:110143/148‑1 (MQ=255)                                            tgtgATGGACGATGAGCGGCTGAAGAATCCGCCTGTCGGTTCTTCTGTCCTCGAACGCATCCGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTGCCCCCCCCTGCTGACTCTCAGCCAACTGTATCGCCATTAAGGt                                                                                  >  2:14086/1‑151 (MQ=255)                                                agggACGATGAGCGGCTGAAGAATCCGCCTGTCGGTTCTTCTGTCCTCGAACGCATCCGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTGC‑CCCCCCTGCTGACTCTCAGCCAACTGTATCGCCATTAAGGTg                                                                                 <  1:651473/145‑1 (MQ=255)                                                         gAGCGGCTGAAGAATCCGCCTGTCGGTTCTTCTGTCCTCGAACGCATCCGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTGC‑CCCCCCTGCTGACTCTCAGCCAACTGTATCGCCATTAAGGTGAAGATGTTGtttt                                                                    >  2:492544/1‑151 (MQ=255)                                                         gAGCGGCTGAAGAATCCGCCTGTCGGTTCTTCTGTCCTCGAACGCATCCGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTGC‑CCCCCCTGCTGACTCTCAGCCAACTGTATCGCCATTAAGGTGAAGATGTTGttt                                                                     <  2:489679/150‑1 (MQ=255)                                                         gAGCGGCTGAAGAATCCGCCTGTCGGTTCTTCTGTCCTCGAACGCATCCGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTGC‑CCCCCCTGCTGACTCTCAGCCAACTGTATCGCCATTAAGGTGAAGATGTTGttt                                                                     <  1:232036/150‑1 (MQ=255)                                                                 gaagaaTCCGCCTGTCGGTTCTTCTGTCCTCGAACGCATCCGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTGC‑CCCCCCTGCTGACTCTCAGCCAACTGTATCGCCATTAAGGTGAAGATGTTGTTTTACTCGccc                                                            <  2:315400/151‑1 (MQ=255)                                                                      aTCCGCCTGTCGGTTCTTCTGTCCTCGAACGCATCCGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTGC‑CCCCCCTGCTGACTCTCAGCCAACTGTATCGCCATTAAGGTGAAGATGTTGTTTTACTCGCCCCAGaa                                                       <  1:159398/151‑1 (MQ=255)                                                                      aTCCGCCTGTCGGTTCTTCTGTCCTCGAACGCATCCGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTGC‑CCCCCCTGCTGACTCTCAGCCAACTGTATCGCCATTAAGGTGAAGATGTTGTTTTACTCGCCCCAGa                                                        >  2:185757/1‑150 (MQ=255)                                                                          gCCTGTCGGTTCTTCTGTCCTCGAACGCATCCGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTGC‑CCCCCCTGCTGACTCTCAGCCAACTGTATCGCCATTAAGGTGAAGATGTTGTTTTACTCGCCCCAGAACAcc                                                   <  1:461855/151‑1 (MQ=255)                                                                           ccTGTCGGTTCTTCTGTCCTCGAACGCATCCGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTGC‑CCCCCCTGCTGACTCTCAGCCAACTGTATCGCCATTAAGGTGAAGATGTTGTTTTACTCGCCCCAGAACAccc                                                  <  1:257605/151‑1 (MQ=255)                                                                                cGGTTCTTCTGTCCTCGAACGCATCCGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTGC‑CCCCCCTGCTGACTCTCAGCCAACTGTATCGCCATTAAGGTGAAGATGTTGTTTTACTCGCCCCAGAACACCCtttt                                              <  2:228570/150‑1 (MQ=255)                                                                                 ggTTCTTCTGTCCTCGAACGCATCCGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTGC‑CCCCCCTGCTGACTCTCAGCCAACTGTATCGCCATTAAGGTGAAGATGTTGTTTTACTCGCCCCAGAACACCCtttttt                                            <  2:159866/151‑1 (MQ=255)                                                                                 ggTTCTTCTGTCCTCGAACGCATCCGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTGC‑CCCCCCTGCTGACTCTCAGCCAACTGTATCGCCATTAAGGTGAAGATGTTGTTTTACTCGCCCCAGAACACCCttttt                                             <  1:335051/150‑1 (MQ=255)                                                                                      ttctGTCCTCGAACGCATCCGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTGC‑CCCCCCTGCTGACTCTCAGCCAACTGTATCGCCATTAAGGTGAAGATGTTGTTTTACTCGCCCCAGAACACCCTTTTTTATACg                                       >  1:228314/1‑151 (MQ=255)                                                                                                 aaCGCATCCGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTGC‑CCCCCCTGCTGACTCTCAGCCAACTGTATCGCCATTAAGGTGAAGATGTTGTTTTACTCGCCCCAGAACACCCTTTTTTATACGActattctatt                            >  2:321001/1‑151 (MQ=255)                                                                                                   cGCATCCGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTGC‑CCCCCCTGCTGACTCTCAGCCAACTGTATCGCCATTAAGGTGAAGATGTTGTTTTACTCGCCCCAGAACACCCTTTTTTATACGACTATTCTATTTc                          <  2:350732/151‑1 (MQ=255)                                                                                                       tCCGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTGC‑CCCCCCTGCTGACTCTCAGCCAACTGTATCGCCATTAAGGTGAAGATGTTGTTTTACTCGCCCCAGAACACCCTTTTTTATACGACTATTCTATTTCttt                       <  1:492542/150‑1 (MQ=255)                                                                                                        ccGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTGC‑CCCCCCTGCTGACTCTCAGCCAACTGTATCGCCATTAAGGTGAAGATGTTGTTTTACTCGCCCCAGAACACCCTTTTTTATACGACTATTCTATTTCTTTa                      <  1:330652/150‑1 (MQ=255)                                                                                                             atatTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTGC‑CCCCCCTGCTGACTCTCAGCCAACTGTATCGCCATTAAGGTGAAGATGTTGTTTTACTCGCCCCAGAACACCCTTTTTTATACGACTATTCTATTTCTTTAACCGCt                <  1:379192/151‑1 (MQ=255)                                                                                                                 tCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTGC‑CCCCCCTGCTGACTCTCAGCCAACTGTATCGCCATTAAGGTGAAGATGTTGTTTTACTCGCCCCAGAACACCCTTTTTTATACGACTATTCTATTTCTTTAACCGCTGGc             <  2:245215/150‑1 (MQ=255)                                                                                                                   aCGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTGC‑CCCCCCTGCTGACTCTCAGCCAACTGTATCGCCATTAAGGTGAAGATGTTGTTTTACTCGCCCCAGAACACCCTTTTTTATACGACTATTCTATTTCTTTAACCGCTGGCGa           >  1:386433/1‑150 (MQ=255)                                                                                                                           aTGCGCCGTGTTTATTTGCAGGTGATTTGC‑CCCCCCTGCTGACTCTCAGCCAACTGTATCGCCATTAAGGTGAAGATGTTGTTTTACTCGCCCCAGAACACCCTTTTTTATACGACTATTCTATTTCTTTAACCGCTGGCGAAAAAAACTg  >  1:210655/1‑151 (MQ=255)                                                                                                                                                        |                                                                                                                           GCTCAATATTCAATCGGCTTCAGGAATACCTGGTCTAAGGTTTTGTGATGGACGATGAGCGGCTGAAGAATCCGCCTGTCGGTTCTTCTGTCCTCGAACGCATCCGCGATATTCACGCCAGTATGCGCCGTGTTTATTTGCAGGTGATTTG‑‑CCCCCCTGCTGACTCTCAGCCAACTGTATCGCCATTAAGGTGAAGATGTTGTTTTACTCGCCCCAGAACACCCTTTTTTATACGACTATTCTATTTCTTTAACCGCTGGCGAAAAAAACTG  >  NC_000913/3836378‑3836649

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑