Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP009273	468,144	Δ1 bp	coding (91/339 nt)	glnK →	nitrogen assimilation regulatory protein for GlnL, GlnE, and AmtB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	468,144	0	A	.	100.0%	161.4 / NA	36	coding (91/339 nt)	glnK	nitrogen assimilation regulatory protein for GlnL, GlnE, and AmtB
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (21/15);  total (21/15)

CTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAG  >  CP009273/468006‑468286                                                                                                                                           |                                                                                                                                               cttcttCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCCGGGCCTGACCGTC‑CCGAAg                                                                                                                                          <  1:413949/144‑1 (MQ=255)     ttcGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTC‑CCGAAGTGaa                                                                                                                                      <  1:682096/144‑1 (MQ=255)             gCAGAACCATTACCGAATTCTGACCGGAGGGGCTCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTC‑CCGACGGGAAAGGTTTCGGGCGt                                                                                                                         >  2:196908/1‑149 (MQ=255)              cAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGTCTGACCGTC‑CCGAAGTGAAAGGTTTCGGGCGTc                                                                                                                        <  2:475434/149‑1 (MQ=255)              cAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTC‑CCGAAGTGAAAGGTTTCgg                                                                                                                             <  1:73223/144‑1 (MQ=255)                         ccGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTC‑CCGAAGTGAAAGGTTTCGGGCGTCAGAAAg                                                                                                                  >  1:87694/1‑144 (MQ=255)                          cGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTC‑CCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCGTg                                                                                                            >  2:647922/1‑149 (MQ=255)                           gAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAGGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTC‑CCGAAGTGAAAGGTTTCGGGCGTCAGAAAggg                                                                                                                >  1:438868/1‑144 (MQ=255)                           gAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTC‑CCGAAGTGAAAGGTTTCGGGCGtgtgagaggaccagc                                                                                                           >  2:14642/1‑135 (MQ=255)                                cTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTC‑CCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGc                                                                                                           <  1:167328/144‑1 (MQ=255)                                 tGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTC‑CCGAAGTGAAAGGTTTCGGGCGTCGGAAAGGCCATGcc                                                                                                          >  1:88386/1‑144 (MQ=255)                                  gACCGGAGGGGATCTATGAAGCTGTGGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTC‑CCGAAATGACTTGTTTCGGGCGTCAGAAAGGGCATGCCg                                                                                                         <  1:658012/144‑1 (MQ=255)                                   aCCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTC‑CCGCAGTGAAAGGTCTCGGGCGCCAGACAGGGCGTGGCGa                                                                                                        >  1:158358/1‑144 (MQ=255)                                   aCCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTC‑CCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGGGCTGt                                                                                                   >  2:79520/1‑149 (MQ=255)                                     cGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGGAGACGTTCGTGAAGCGTTATCTTCCATAGGTATTCAGGGCCGGACCGTC‑CCCATGTGGAAGGCTTCGGGCGACAGAAAGGGCATGcctggc                                                                                                      >  1:607368/1‑140 (MQ=255)                                     cGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTC‑CCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTAc                                                                                                 >  2:167384/1‑149 (MQ=255)                                            gATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTC‑CCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCg                                                                                               >  1:382896/1‑144 (MQ=255)                                                                gTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTC‑CCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATAAAGCGACAATTTc                                                                      >  2:603922/1‑149 (MQ=255)                                                                 tGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTC‑CCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGGCag                                                                          >  1:351573/1‑143 (MQ=255)                                                                         aaaCCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTC‑CCGAAGTGAAATGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCaaaa                                                             <  2:534356/149‑1 (MQ=255)                                                                         aaaCCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTC‑CCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCaaaa                                                             <  2:214250/149‑1 (MQ=255)                                                                          aaCCATTCAAGCTGGAAGCCGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTC‑CCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGcc                                                                 >  1:483602/1‑144 (MQ=255)                                                                           aCCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTAACCGTC‑CCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAgc                                                           >  2:225731/1‑148 (MQ=255)                                                                                     cTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTC‑CCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGAt                                                 <  2:192017/149‑1 (MQ=255)                                                                                      tGGAAGACGGTCGTGAAGCGTTATTTTCCATTGGTATTCAGGGCCTGACCGTC‑CCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGTCAAAAGTAAAAAt                                                     <  1:468983/144‑1 (MQ=255)                                                                                       ggAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTC‑CCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGAtgt                                               <  2:179488/149‑1 (MQ=255)                                                                                                   tGAAGCGTTACCTTCCATTGGTATTCAGGGCCTGACCGTC‑CCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTCCCGGGGGGCGGAATACAGCGTCAATTTCCTGCCATAAGTAAAAATTGATGTGGCGATTGCtga                                   <  2:484081/149‑1 (MQ=255)                                                                                                           tATCTTCCATTGGTATTCAGGGCCTGACCGTC‑CCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCtgatga                                <  1:555572/144‑1 (MQ=255)                                                                                                               ttCCATTGGTATTCAGGGCCTGACCGTC‑CCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCaa                            >  1:662523/1‑144 (MQ=255)                                                                                                                   aTTGGTATTCAGGGCCTGACCGTC‑CCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCCAAAGTAAAAATTGATGTGGCGATGGCTGATGCCCAACTCGATGaa                   >  2:291932/1‑149 (MQ=255)                                                                                                                   aTTGGTATTCAGGGCCTGACCGTC‑CCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGaa                   >  2:404391/1‑149 (MQ=255)                                                                                                                   aTTGGTATTCAGGGCCTGACCGTC‑CCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATATCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGaa                   <  2:424636/149‑1 (MQ=255)                                                                                                                          ttCAGGGCCTGACCGTC‑CCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACGCGATGCAGt                 >  1:613453/1‑144 (MQ=255)                                                                                                                             aGGGCCTGACCGTC‑CCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATGGCTGATGACCCACTCGAGGAAGTGAACGata         >  2:248935/1‑149 (MQ=255)                                                                                                                                  cTGACCGTC‑CCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGAGCGATATCGTc    >  2:673510/1‑149 (MQ=255)                                                                                                                                    gACCGTC‑CCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAg  <  2:568117/149‑1 (MQ=255)                                                                                                                                           |                                                                                                                                               CTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAG  >  CP009273/468006‑468286

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑