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%	259.6 / NA	59	coding (134/1878 nt)	bglF	PTS beta‑glucoside transporter subunit IIABC
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (40/19);  total (40/19)

TAACCGCCAGGAAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTCTTTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATGTT  >  NZ_CP009273/3898735‑3898909                                                                                          |                                                                                      tAACCGCCAGGAAGACATCGGCCACATGGTTACCTATGACCACCTGAAGCTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTCt                                                                                       <  2:372706/90‑1 (MQ=255)   aCCGCCAGGAAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTCttt                                                                                     <  2:1111444/90‑1 (MQ=255)       ccAGGAAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTCttttcag                                                                                 >  2:749869/1‑87 (MQ=255)         aGGAAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTa                                                                              >  1:11907/1‑90 (MQ=255)         aGGAAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTa                                                                              >  2:390961/1‑90 (MQ=255)                cATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGc                                                                       >  2:1079927/1‑90 (MQ=255)                  tCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCtt                                                                     >  1:1063367/1‑90 (MQ=255)                   cGGCCACATGGTTACCTATGACCTCCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTg                                                                    <  1:478125/90‑1 (MQ=255)                        acaTGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCgctt                                                               >  2:733466/1‑90 (MQ=255)                        acaTGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCgctt                                                               >  2:1177602/1‑90 (MQ=255)                        acaTGGTTACCTATGACCACCTGAAACTGGCCACCGCATTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCgctt                                                               >  1:825745/1‑90 (MQ=255)                               tACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTc                                                        <  2:665922/90‑1 (MQ=255)                                   tATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATcc                                                    >  2:266821/1‑90 (MQ=255)                                     tGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACTTCTGCTTGCGCTTTGCTTTCATCCtt                                                  >  1:953866/1‑90 (MQ=255)                                       accaccTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACct                                                                           <  2:722855/63‑1 (MQ=255)                                       accaccTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACct                                                                           >  1:722855/1‑63 (MQ=255)                                       accaccTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCttta                                                <  2:264580/90‑1 (MQ=255)                                         caccTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCtttaat                                              >  2:1094114/1‑90 (MQ=255)                                          accTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCtttaatt                                             >  2:914489/1‑90 (MQ=255)                                          accTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCtttaatt                                             >  2:103383/1‑90 (MQ=255)                                           ccTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCtttaattt                                            >  1:290476/1‑90 (MQ=255)                                           ccTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCtttaattt                                            >  1:811858/1‑90 (MQ=255)                                                aaCTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAAc                                       <  1:414171/90‑1 (MQ=255)                                                    ggCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTaa                                   >  1:719180/1‑90 (MQ=255)                                                    ggCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTaa                                   >  2:494486/1‑90 (MQ=255)                                                     gCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAAt                                  <  2:795673/90‑1 (MQ=255)                                                     gCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAAt                                  >  2:739367/1‑90 (MQ=255)                                                               tCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTgcgc                        <  1:739367/90‑1 (MQ=255)                                                                 caccaccaTAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCaa                      <  2:910910/90‑1 (MQ=255)                                                                 caccaccaTAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCaa                      <  1:390961/90‑1 (MQ=255)                                                                   ccaccaTAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATg                    >  2:353521/1‑90 (MQ=255)                                                                    caccaTAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGc                   >  2:326067/1‑90 (MQ=255)                                                                       caTAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATc                <  2:524652/90‑1 (MQ=255)                                                                       caTAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATc                <  2:1180784/90‑1 (MQ=255)                                                                         taataataCCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAg              <  1:304206/90‑1 (MQ=255)                                                                            taataCCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGGCt           <  2:825745/90‑1 (MQ=255)                                                                              ataCCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTca         <  1:458619/90‑1 (MQ=255)                                                                               taCCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTcac        >  1:556862/1‑90 (MQ=255)                                                                                aCCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTcaca       >  1:1116633/1‑90 (MQ=255)                                                                                aCCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTcaca       >  2:362861/1‑90 (MQ=255)                                                                                aCCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTcaca       >  1:76050/1‑90 (MQ=255)                                                                                aCCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTcaca       <  1:770647/90‑1 (MQ=255)                                                                                aCCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTcaca       >  2:674095/1‑90 (MQ=255)                                                                                aCCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTcaca       >  1:638512/1‑90 (MQ=255)                                                                                 ccGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACaa      <  2:607998/90‑1 (MQ=255)                                                                                   gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTgcgc                        <  1:371998/70‑1 (MQ=255)                                                                                   gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTgcgc                        >  2:371998/1‑70 (MQ=255)                                                                                   gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCaa                      >  2:143170/1‑72 (MQ=255)                                                                                   gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCaa                      <  1:143170/72‑1 (MQ=255)                                                                                   gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATg    >  1:1215613/1‑90 (MQ=255)                                                                                   gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATg    >  1:70477/1‑90 (MQ=255)                                                                                   gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATg    >  1:244704/1‑90 (MQ=255)                                                                                   gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATg    >  2:280639/1‑90 (MQ=255)                                                                                   gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATg    >  1:1004231/1‑90 (MQ=255)                                                                                   gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATg    >  2:1034044/1‑90 (MQ=255)                                                                                   gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATg    >  1:999703/1‑90 (MQ=255)                                                                                   gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATg    >  1:505660/1‑90 (MQ=255)                                                                                   gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTAAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATg    >  2:33387/1‑90 (MQ=255)                                                                                     gggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAg              >  2:407047/1‑78 (MQ=255)                                                                                     gggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAg              <  1:407047/78‑1 (MQ=255)                                                                                     gggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATGtt  >  2:287704/1‑90 (MQ=255)                                                                                     gggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATGtt  >  2:75799/1‑90 (MQ=255)                                                                                          |                                                                                      TAACCGCCAGGAAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTCTTTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATGTT  >  NZ_CP009273/3898735‑3898909

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑