Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	508,601	(C)6→7	coding (570/1293 nt)	ybaT →	APC family permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	508,595	1	.	C	97.5%	125.3 / ‑2.8	40	coding (564/1293 nt)	ybaT	APC family permease
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base C (21/18);  total (21/19)
Fisher's exact test for biased strand distribution p-value = 4.75e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01

ATCCTCGTCGGCATTAAAATGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCG‑CCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTGGCATGATGGCGAACGCGGC  >  NZ_CP009273/508506‑508678                                                                                           |                                                                                    aTCCTCGTCGGCATTAAAATGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTgcg                                                                                      >  2:98156/1‑90 (MQ=255)   ccTCGTCGGCATTAAAATGATGATCCTGTTATTGCTGCTTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCG‑cc                                                                                   <  2:648085/90‑1 (MQ=255)   ccTCGTCGGCATTAAAATGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCG‑cc                                                                                   <  2:578006/90‑1 (MQ=255)    cTCGTCGGCATTAAAATGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCG‑ccc                                                                                  >  2:1391488/1‑90 (MQ=255)      cgtcgGCATTAAAATGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCG‑ccccc                                                                                >  1:160630/1‑90 (MQ=255)        tcgGCATTAAAATGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCG‑ccccccc                                                                              <  2:637211/90‑2 (MQ=255)           gCATTAAAATGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCG‑cccccccagc                                                                           >  1:1297277/1‑86 (MQ=255)           gCATTAAAATGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCG‑cccccccagc                                                                           >  1:1374789/1‑86 (MQ=255)             aTTAAAATGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTc                                                                          <  1:98156/90‑1 (MQ=255)                aaaaTGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCgg                                                                       <  2:1421296/90‑1 (MQ=255)                   atgatgATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGc                                                                    <  2:696255/90‑1 (MQ=255)                     gatgatCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGt                                                                  >  1:1562016/1‑90 (MQ=255)                     gatgatCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGt                                                                  >  2:40520/1‑90 (MQ=255)                     gatgatCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCG‑cc                                                                                   >  2:698660/1‑72 (MQ=255)                     gatgatCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCG‑cc                                                                                   <  1:698660/72‑1 (MQ=255)                        gatCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGttct                                                               >  2:1429428/1‑90 (MQ=255)                         atCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCG‑CCCCCCAGCTCCGGTGCGttcttc                                                             <  2:1086076/90‑1 (MQ=255)                          tCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGttcttc                                                             >  2:599661/1‑90 (MQ=255)                             tGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTcc                                                          <  1:311885/90‑1 (MQ=255)                              gTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCt                                                         >  2:904146/1‑90 (MQ=255)                                tATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGt                                                       >  1:620094/1‑90 (MQ=255)                                  ttGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTGTTCTCCTGTAt                                                     <  1:594484/90‑1 (MQ=255)                                   tGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCt                                                         >  2:266946/1‑85 (MQ=255)                                   tGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCt                                                         <  1:266946/85‑1 (MQ=255)                                   tGCTCATTATTGCCGGTGTCTGGTCGCGGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTAtt                                                    <  1:1038072/90‑1 (MQ=255)                                      tGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTggg                                                 >  1:1002552/1‑90 (MQ=255)                                       gATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGa                                                >  1:820296/1‑90 (MQ=255)                                        attattGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGAt                                               >  2:306106/1‑90 (MQ=255)                                          tattGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATaa                                             <  1:904146/90‑1 (MQ=255)                                           attGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAAc                                            <  1:682450/90‑1 (MQ=255)                                           attGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAAc                                            <  2:920980/90‑1 (MQ=255)                                           attGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAAc                                            <  2:773664/90‑1 (MQ=255)                                           attGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAAc                                            <  1:1278996/90‑1 (MQ=255)                                              gCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACttt                                         >  1:245535/1‑90 (MQ=255)                                                 ggTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCt                                      <  2:1297277/90‑1 (MQ=255)                                                 ggTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCt                                      >  1:171396/1‑90 (MQ=255)                                                 ggTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCt                                      >  1:1551853/1‑90 (MQ=255)                                                   tgtCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGttct                                                               >  2:1390331/1‑63 (MQ=255)                                                   tgtCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGttct                                                               <  1:1390331/63‑1 (MQ=255)                                                    gtCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGc                                   <  2:1123857/90‑1 (MQ=255)                                                        ggTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTAt                               >  1:27951/1‑90 (MQ=255)                                                            gCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCgg                           >  2:501023/1‑90 (MQ=255)                                                            gCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCgg                           >  2:930807/1‑90 (MQ=255)                                                             cTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCggg                          >  2:94669/1‑90 (MQ=255)                                                              tGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGc                         >  2:1006384/1‑90 (MQ=255)                                                                   ccGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTgg                    <  1:532634/90‑1 (MQ=255)                                                                     ggCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTGGCa                  >  1:1292394/1‑90 (MQ=255)                                                                      gcgcATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTGGCat                 <  2:160630/90‑1 (MQ=255)                                                                                ccGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTGGCATGATGGCGAAc       >  1:1112109/1‑90 (MQ=255)                                                                                     tctGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTGGCATGATGGCGAACgcggc  <  2:124242/90‑1 (MQ=255)                                                                                           |                                                                                    ATCCTCGTCGGCATTAAAATGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCG‑CCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTGGCATGATGGCGAACGCGGC  >  NZ_CP009273/508506‑508678

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑