Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,898,828	(T)5→4	coding (130/1878 nt)	bglF ←	PTS beta‑glucoside transporter subunit IIABC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,898,824	0	T	.	100.0%	182.5 / NA	44	coding (134/1878 nt)	bglF	PTS beta‑glucoside transporter subunit IIABC
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (29/15);  total (29/15)

TAACCGCCAGGAAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTCTTTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATGTT  >  NZ_CP009273/3898735‑3898909                                                                                          |                                                                                      tagccGCCAGGAAGACATCGGCCCCATGGTTACCTATGACCACCTGAAACTGGCCCCCGCTTTCCACCACCATAATAATACCGGGGGTCt                                                                                       <  2:620958/87‑1 (MQ=255) tAACCGCCAGGAAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTCt                                                                                       <  1:333024/90‑1 (MQ=255)   aCCGCCAGGAAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTCttt                                                                                     <  2:129718/90‑1 (MQ=255)    ccGCCAGGAAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTCtttt                                                                                    <  2:70134/90‑1 (MQ=255)         aGGAAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTa                                                                              >  2:436119/1‑90 (MQ=255)         aGGAAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTa                                                                              <  1:724735/90‑1 (MQ=255)                 aTCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCCCCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCt                                                                      <  2:200369/90‑1 (MQ=255)                        acaTGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCgctt                                                               >  2:473339/1‑90 (MQ=255)                                 ccTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCAt                                                      <  1:758369/90‑1 (MQ=255)                                   tATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATcc                                                    >  2:234825/1‑90 (MQ=255)                                           ccTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCtttaattt                                            >  2:465619/1‑90 (MQ=255)                                           ccTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCtttaattt                                            >  1:612412/1‑90 (MQ=255)                                           ccTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGGC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCtttaattt                                            >  1:613073/1‑90 (MQ=255)                                                    ggCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTaa                                   >  1:138557/1‑90 (MQ=255)                                                    ggCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTaa                                   >  2:813357/1‑90 (MQ=255)                                                    ggCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTaa                                   >  2:335301/1‑90 (MQ=255)                                                     gCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAAt                                  >  1:579428/1‑90 (MQ=255)                                                     gCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAAt                                  >  1:510052/1‑90 (MQ=255)                                                          cGCTTTCCGCCACCATAATAATACCGGGGGTC‑TTTTCAGTGCCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGt                             <  2:816473/90‑1 (MQ=255)                                                          cGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGt                             <  1:234825/90‑1 (MQ=255)                                                                ccaccaccaTAATAATACCGGGGGTC‑TTTTCAGTA‑CTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCaa                      <  1:625746/90‑1 (MQ=255)                                                                      ccaTAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGt                             >  2:449238/1‑78 (MQ=255)                                                                      ccaTAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGt                             <  1:449238/78‑1 (MQ=255)                                                                        ataataataCCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCa               >  1:8041/1‑90 (MQ=255)                                                                         taataataCCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAg              <  1:120693/90‑1 (MQ=255)                                                                         taataataCCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAg              <  2:510052/90‑1 (MQ=255)                                                                               taCCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTcac        <  1:248399/90‑1 (MQ=255)                                                                                aCCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCtttaattt                                            <  2:461852/53‑1 (MQ=255)                                                                                aCCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCtttaattt                                            >  1:461852/1‑53 (MQ=255)                                                                                aCCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTcaca       >  1:814742/1‑90 (MQ=255)                                                                                aCCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTcaca       >  2:387475/1‑90 (MQ=255)                                                                                aCCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTcaca       <  2:129020/90‑1 (MQ=255)                                                                                aCCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTcaca       >  2:222813/1‑90 (MQ=255)                                                                                aCCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTc          >  2:302766/1‑87 (MQ=255)                                                                                aCCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTc          <  1:302766/87‑1 (MQ=255)                                                                                aCCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATACATCAGACTcaca       >  2:709857/1‑90 (MQ=255)                                                                                  cGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCaa                      <  2:98767/73‑1 (MQ=255)                                                                                  cGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCaa                      >  1:98767/1‑73 (MQ=255)                                                                                   gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATc                <  1:307795/78‑1 (MQ=255)                                                                                   gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATc                >  2:307795/1‑78 (MQ=255)                                                                                   gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATg    >  2:281448/1‑90 (MQ=255)                                                                                   gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATg    >  2:486531/1‑90 (MQ=255)                                                                                   gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATg    >  2:713700/1‑90 (MQ=255)                                                                                   gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATg    >  1:903712/1‑90 (MQ=255)                                                                                   gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATg    >  2:856882/1‑90 (MQ=255)                                                                                   gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATg    >  2:339273/1‑90 (MQ=255)                                                                                     gggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATGtt  >  2:534101/1‑90 (MQ=255)                                                                                     gggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATGtt  >  2:830231/1‑90 (MQ=255)                                                                                          |                                                                                      TAACCGCCAGGAAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTCTTTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATGTT  >  NZ_CP009273/3898735‑3898909

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑