Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,616,809	C→A	P239Q (CCG→CAG)	bepA →	beta‑barrel assembly‑enhancing protease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,616,809	0	C	A	100.0%	114.5 / NA	34	P239Q (CCG→CAG)	bepA	beta‑barrel assembly‑enhancing protease
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (16/18);  total (16/18)

TCACCCAGCAAAATGAACAGGAAGCGGACCGCATTGGTATTCAGGTGCTGCAACGCTCGGGATTCGATCCGCAGGCGATGCCAACCTTCCTCGAAAAATTACTCGATCAGGCGCGTTACTCCTCGCGCCCGCCGGAAATTTTATTGACTCACCCGTTGCCGGAAAGTCGTCTGGCAGATGCCCGCAACCGTGCTAATCAGATGCGCCCGATGGTGGTGCAGTCGTCGGAAGATTTCTATCTGGCGAAAGCGCGCACACTGGGG  >  NC_000913/2616680‑2616942                                                                                                                                  |                                                                                                                                      tCACCCAGCAAAATGAACAGGAAGCGGACCGCATTGGTATTCAGGTGCTGCAACGCTCGGGATTCGATCCGCAGGCGATGCCAACCTTCCTCGAAAAATTACTCGATCAGGCGCGTTACTCCTCGCGCCAGCCGGAAAtt                                                                                                                             >  2:444773/1‑140 (MQ=255)    cccAGCAAAATGAACAGGAAGCGGACCGCATTGGTATTCAGGTGCTGCAACGCTCGGGATTCGATCCGCAGGCGATGCCAACCTTCCTCGAAAAATTACTCGATCAGGCGCGTTACTCCTCGCGCCAGCCGGAAATTTTa                                                                                                                          >  1:554808/1‑140 (MQ=255)    cccAGCAAAATGAACAGGAAGCGGACCGCATTGGTATTCAGGTGCTGCAACGCTCGGGATTCGATCCGCAGGCGATGCCAACCTTCCTCGAAAAATTACTCGATCAGGCGCGTTACTCCTCGCGCCAGCCGGAAATTTTa                                                                                                                          <  2:333838/140‑1 (MQ=255)    cccAGCAAAATGAACAGGAAGCGGACCGCATTGGTATTCAGGTGCTGCAACGCTCGGGATTCGATCCGCAGGCGATGCCAACCTTCCTCGAAAAATTACTCGATCAGGCGCGTTACTCCTCGCGCCAGCCGGAAATTTTa                                                                                                                          >  1:708476/1‑140 (MQ=255)     ccAGCAAAATGAACAGGAAGCGGACCGCATTGGTATTCAGGTGCTGCAACGCTCGGGATTCGATCCGCAGGCGATGCCAACCTTCCTCGAAAAATTACTCGATCAGGCGCGTTACTCCTCGCGCCAGCCGGAAATTTTAt                                                                                                                         <  1:361618/140‑1 (MQ=255)     ccAGCAAAATGAACAGGAAGCGGACCGCATTGGTATTCAGGTGCTGCAACGCTCGGGATTCGATCCGCAGGCGATGCCAACCTTCCTCGAAAAATTACTCGATCAGGCGCGTTACTCCTCGCGCCAGCCGGAAATTTTAt                                                                                                                         <  2:659507/140‑1 (MQ=255)         cAAAATGAACAGGAAGCGGACCGCATTGGTATTCAGGTGCTGCAACGCTCGGGATTCGATCCGCAGGCGATGCCAACCTTCCTCGAAAAATTACTCGATCAGGCGCGTTACTCCTCGCGCCAGCCGGAAATTTTATTGAc                                                                                                                     >  1:443681/1‑140 (MQ=255)          aaaaTGAACAGGAAGCGGACCGCATTGGTATTCAGGTGCTGCAACGCTCGGGATTCGATCCGCAGGCGATGCCAACCTTCCTCGAAAAATTACTCGATCAGGCGCGTTACTCCTCGCGCCAGCCGGAAATTTTATTGACt                                                                                                                    <  2:29936/140‑1 (MQ=255)          aaaaTGAACAGGAAGCGGACCGCATTGGTATTCAGGTGCTGCAACGCTCGGGATTCGATCCGCAGGCGATGCCAACCTTCCTCGAAAAATTACTCGATCAGGCGCGTTACTCCTCGCGCCAGCCGGAAATTTTATTGACt                                                                                                                    <  1:444773/140‑1 (MQ=255)             aTGAACAGGAAGCGGACCGCATTGGTATTCAGGTGCTGCAACGCTCGGGATTCGATCCGCAGGCGATGCCAACCTTCCTCGAAAAATTACTCGATCAGGCGCGTTACTCCTCGCGCCAGCCGGAAATTTTATTGACTCAc                                                                                                                 >  2:488386/1‑140 (MQ=255)                          ggACCGCATTGGTATTCAGGTGCTGCAACGCTCGGGATTCGATCCGCAGGCGATGCCAACCTTCCTCGAAAAATTACTCGATCAGGCGCGTTACTCCTCGCGCCAGCCGGAAATTTTATTGACTCACCCGTTGCCGGaaa                                                                                                    >  1:488269/1‑140 (MQ=255)                                    ggTATTCAGGTGCTGCAACGCTCGGGATTCGATCCGCAGGCGATGCCAACCTTCCTCGAAAAATTACTCGATCAGGCGCGTTACTCCTCGCGCCAGCCGGAAATTTTATTGACTCACCCGTTGCCGGAAAGTCGTCTGGc                                                                                          <  1:488386/140‑1 (MQ=255)                                      tATTCAGGTGCTGCAACGCTCGGGATTCGATCCGCAGGCGATGCCAACCTTCCTCGAAAAATTACTCGATCAGGCGCGTTACTCCTCGCGCCAGCCGGAAATTTTATTGACTCACCCGTTGCCGGAAAGTCGTCTGGCAg                                                                                        <  1:343553/140‑1 (MQ=255)                                        ttCAGGTGCTGCAACGCTCGGGATTCGATCCGCAGGCGATGCCAACCTTCCTCGAAAAATTACTCGATCAGGCGCGTTACTCCTCGCGCCAGCCGGAAATTTTATTGACTCACCCGTTGCCGGAAAGTCGTCTGGCAGAt                                                                                      >  2:170821/1‑140 (MQ=255)                                           aGGTGCTGCAACGCTCGGGATTCGATCCGCAGGCGATGCCAACCTTCCTCGAAAAATTACTCGATCAGGCGCGTTACTCCTCGCGCCAGCCGGAAATTTTATTGACTCACCCGTTGCCGGAAAGTCGTCTGGCAGATGcc                                                                                   >  1:341373/1‑140 (MQ=255)                                               gctgcAACGCTCGGGATTCGATCCGCAGGCGATGCCAACCTTCCTCGAAAAATTACTCGATCAGGCGCGTTACTCCTCGCGCCAGCCGGAAATTTTATTGACTCACCCGTTGCCGGAAAGTCGTCTGGCAGATGCCCGCa                                                                               >  2:667849/1‑140 (MQ=255)                                                ctgcAACGCTCGGGATTCGATCCGCAGGCGATGCCAACCTTCCTCGAAAAATTACTCGATCAGGCGCGTTACTCCTCGCGCCAGCCGGAAATTTTATTGACTCACCCGTTGCCGGAAAGTCGTCTGGCAGATGCCCGCaa                                                                              <  1:860433/140‑1 (MQ=255)                                                ctgcAACGCTCGGGATTCGATCCGCAGGCGATGCCAACCTTCCTCGAAAAATTACTCGATCAGGCGCGTTACTCCTCGCGCCAGCCGGAAATTTTATTGACTCACCCGTTGCCGGAAAGTCGTCTGGCAGATGCCCGCaa                                                                              >  2:323993/1‑140 (MQ=255)                                                              aTTCGATCCGCAGGCGATGCCAACCTTCCTCGAAAAATTACTCGATCAGGCGCGTTACTCCTCGCGCCAGCCGGAAATTTTATTGACTCACCCGTTGCCGGAAAGTCGTCTGGCAGATGCCCGCAACCGTGCTAATCAGa                                                                <  2:708476/140‑1 (MQ=255)                                                                     ccGCAGGCGATGCCAACCTTCCTCGAAAAATTACTCGATCAGGCGCGTTACTCCTCGCGCCAGCCGGAAATTTTATTGACTCACCCGTTGCCGGAAAGTCGTCTGGCAGATGCCCGCAACCGTGCTAATCAGAt                                                               >  1:310270/1‑134 (MQ=255)                                                                     ccGCAGGCGATGCCAACCTTCCTCGAAAAATTACTCGATCAGGCGCGTTACTCCTCGCGCCAGCCGGAAATTTTATTGACTCACCCGTTGCCGGAAAGTCGTCTGGCAGATGCCCGCAACCGTGCTAATCAGAt                                                               <  2:310270/134‑1 (MQ=255)                                                                       gCAGGCGATGCCAACCTTCCTCGAAAAATTACTCGATCAGGCGCGTTACTCCTCGCGCCAGCCGGAAATTTTATTGACTCACCCGTTGCCGGAAAGTCGTCTGGCAGATGCCCGCAACCGTGCTAATCAGATGCGCCCGa                                                       >  1:87142/1‑140 (MQ=255)                                                                                gCCAACCTTCCTCGAAAAATTACTCGATCAGGCGCGTTACTCCTCGCGCCAGCCGGAAATTTTATTGACTCACCCGTTGCCGGAAAGTCGTCTGGCAGATGCCCGCAACCGTGCTAATCAGATGCGCCCGATGGTGGTGc                                              >  1:850328/1‑140 (MQ=255)                                                                                gCCAACCTTCCTCGAAAAATTACTCGATCAGGCGCGTTACTCCTCGCGCCAGCCGGAAATTTTATTGACTCACCCGTTGCCGGAAAGTCGTCTGGCAGATGCCCGCAACCGTGCTAATCAGATGCGCCCGATGGTGGTGc                                              >  2:857781/1‑140 (MQ=255)                                                                                 ccAACCTTCCTCGAAAAATTACTCGATCAGGCGCGTTACTCCTCGCGCCAGCCGGAAATTTTATTGACTCACCCGTTGCCGGAAAGTCGTCTGGCAGATGCCCGCAACCGTGCTAATCAGATGCGCCCGATGGTGGTGCa                                             <  2:341373/140‑1 (MQ=255)                                                                                                     aCTCGATCAGGCGCGTTACTCCTCGCGCCAGCCGGAAATTTTATTGACTCACCCGTTGCCGGAAAGTCGTCTGGCAGATGCCCGCAACCGTGCTAATCAGATGCGCCCGATGGTGGTGCAGTCGTCGGAAGATTTCTATc                         >  1:85124/1‑140 (MQ=255)                                                                                                                  cgTTACTCCTCGCGCCAGCCGGAAATTTTATTGACTCACCCGTTGCCGGAAAGTCGTCTGGCAGATGCCCGCAACCGTGCTAATCAGATGCGCCCGATGGTGGTGCAGTCGTCGGAAGATTTCTATCTGGCGAAAgcgcg            <  2:554808/140‑1 (MQ=255)                                                                                                                  cgTTACTCCTCGCGCCAGCCGGAAATTTTATTGACTCACCCGTTGCCGGAAAGTCGTCTGGCAGATGCCCGCAACCGTGCTAATCAGATGCGCCCGATGGTGGTGCAGTCGTCGGAAGATTTCTATCTGGCGAAAgcgcg            <  1:644011/140‑1 (MQ=255)                                                                                                                  cgTTACTCCTCGCGCCAGCCGGAAATTTTATTGACTCACCCGTTGCCGGAAAGTCGTCTGGCAGATGCCCGCAACCGTGCTAATCAGATGCGCCCGATGGTGGTGCAGTCGTCGGAAGATTTCTATCTGGCGAAAgcgcg            <  2:85124/140‑1 (MQ=255)                                                                                                                    ttACTCCTCGCGCCAGCCGGAAATTTTATTGACTCACCCGTTGCCGGAAAGTCGTCTGGCAGATGCCCGCAACCGTGCTAATCAGATGCGCCCGATGGTGGTGCAGTCGTCGGAAGATTTCTATCTGGCGAAAGCGCGca          <  1:66706/140‑1 (MQ=255)                                                                                                                      aCTCCTCGCGCCAGCCGGAAATTTTATTGACTCACCCGTTGCCGGAAAGTCGTCTGGCAGATGCCCGCAACCGTGCTAATCAGATGCGCCCGATGGTGGTGCAGTCGTCGGAAGATTTCTATCTGGCGAAAGCGCGcaca        <  1:857781/140‑1 (MQ=255)                                                                                                                      aCTCCTCGCGCCAGCCGGAAATTTTATTGACTCACCCGTTGCCGGAAAGTCGTCTGGCAGATGCCCGCAACCGTGCTAATCAGATGCGCCCGATGGTGGTGCAGTCGTCGGAAGATTTCTATCTGGCGAAAGCGCGcaca        <  2:64397/140‑1 (MQ=255)                                                                                                                            cgcgCCAGCCGGAAATTTTATTGACTCACCCGTTGCCGGAAAGTCGTCTGGCAGATGCCCGCAACCGTGCTAATCAGATGCGCCCGATGGTGGTGCAGTCGTCGGAAGATTTCTATCTGGCGAAAGCGCGCACACTgggg  <  2:443681/140‑1 (MQ=255)                                                                                                                            cgcgCCAGCCGGAAATTTTATTGACTCACCCGTTGCCGGAAAGTCGTCTGGCAGATGCCCGCAACCGTGCTAATCAGATGCGCCCGATGGTGGTGCAGTCGTCGGAAGATTTCTATCTGGCGAAAGCGCGCACACTgggg  >  1:588008/1‑140 (MQ=255)                                                                                                                                  |                                                                                                                                      TCACCCAGCAAAATGAACAGGAAGCGGACCGCATTGGTATTCAGGTGCTGCAACGCTCGGGATTCGATCCGCAGGCGATGCCAACCTTCCTCGAAAAATTACTCGATCAGGCGCGTTACTCCTCGCGCCCGCCGGAAATTTTATTGACTCACCCGTTGCCGGAAAGTCGTCTGGCAGATGCCCGCAACCGTGCTAATCAGATGCGCCCGATGGTGGTGCAGTCGTCGGAAGATTTCTATCTGGCGAAAGCGCGCACACTGGGG  >  NC_000913/2616680‑2616942

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑