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%	125.0 / NA	30	coding (134/1878 nt)	bglF	PTS beta‑glucoside transporter subunit IIABC
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (19/11);  total (19/11)

TAACCGCCAGGAAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTCTTTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATG  >  NZ_CP009273/3898735‑3898907                                                                                          |                                                                                    tAACCGCCAGGAAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTCt                                                                                     >  2:369473/1‑90 (MQ=255)       ccAGGAAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTCttttcag                                                                               >  1:108496/1‑87 (MQ=255)            aaGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACct                                                                         <  2:529179/90‑1 (MQ=255)                 aTCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCt                                                                    >  2:302262/1‑90 (MQ=255)                         caTGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCgcttt                                                            >  2:262020/1‑90 (MQ=255)                               tACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTc                                                      <  2:430912/90‑1 (MQ=255)                                   tATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATcc                                                  >  1:120530/1‑90 (MQ=255)                                          accTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCtttaatt                                           >  1:388269/1‑90 (MQ=255)                                           ccTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCtttaattt                                          >  2:74228/1‑90 (MQ=255)                                           ccTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCtttaattt                                          >  1:79377/1‑90 (MQ=255)                                                    ggCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTaa                                 >  2:395978/1‑90 (MQ=255)                                                    ggCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTaa                                 >  2:220042/1‑90 (MQ=255)                                                                ccaccaccaTAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCa                     <  2:120530/90‑1 (MQ=255)                                                                 caccaccaTAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCaa                    <  1:74228/90‑1 (MQ=255)                                                                     accaTAATAATACCGGGGGTC‑TTTTCAGTACGTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCa                >  2:446385/1‑90 (MQ=255)                                                                      ccaTAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCAt               >  2:188586/1‑90 (MQ=255)                                                                      ccaTAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCAt               >  1:364357/1‑90 (MQ=255)                                                                       caTAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATc              <  1:512950/90‑1 (MQ=255)                                                                       caTAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATc              <  2:446215/90‑1 (MQ=255)                                                                        ataataataCCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCa             >  2:231222/1‑90 (MQ=255)                                                                        ataataataCCGGGGGGC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACATAATCGCGTTGCGCAATGCATCa             >  1:339368/1‑90 (MQ=255)                                                                         taataataCCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAg            <  1:468898/90‑1 (MQ=255)                                                                             aataCCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTc        <  1:231222/90‑1 (MQ=255)                                                                             aataCCGGGGGTC‑‑TTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTca       <  2:441446/90‑1 (MQ=255)                                                                                aCCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTcaca     >  2:217886/1‑90 (MQ=255)                                                                                aCCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTcaca     >  1:349/1‑90 (MQ=255)                                                                                 ccGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACaa    <  2:79377/90‑1 (MQ=255)                                                                                   gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATc              >  2:315133/1‑78 (MQ=255)                                                                                   gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATc              <  1:315133/78‑1 (MQ=255)                                                                                   gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATg  >  1:360679/1‑90 (MQ=255)                                                                                   gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCCTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATg  >  1:414586/1‑90 (MQ=255)                                                                                   gggggTC‑TTTACAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATg  >  1:121495/1‑90 (MQ=255)                                                                                          |                                                                                    TAACCGCCAGGAAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTCTTTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATG  >  NZ_CP009273/3898735‑3898907

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑