Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	3,856,021	T→G	24.8%	pseudogene (943/1617 nt)	glvC ←	pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	3,856,021	0	T	G	24.8%	48.7 / 8.8	44	pseudogene (943/1617 nt)	glvC	pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component
Reads supporting (aligned to +/- strand):  ref base T (11/21);  new base G (8/3);  total (20/24)
Fisher's exact test for biased strand distribution p-value = 3.83e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.96e-01

CCCATGTTGCCCACCACACCAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGTAATTCCCACCAGCATGGC‑GGTTAA‑GGTT‑GCGGG‑AA‑TCA‑GC‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGC  >  CP009273/3855876‑3856166                                                                                                                                                    |                                                                                                                                                        cccATGTTGCCCACCACACCAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGTAATTCCCACCAGCATGGC‑GGTTAA‑GGTT‑GCg                                                                                                                                                    <  1:352204/150‑1 (MQ=255)             accacaccaAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGTAATTCCCACCAGCATGGC‑GGGTAA‑AGGT‑GCGGG‑GA‑TTA‑GC‑AAg                                                                                                                                    >  2:658297/1‑150 (MQ=255)              ccacaccaAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGTAATTCCCACCAGCATGGC‑GGTTTA‑AGGT‑GCGGG‑GA‑TCA‑GC‑aaac                                                                                                                                   >  1:722029/1‑148 (MQ=255)                       agagATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGTAATTCCCACCAGCATGGC‑GTTTAA‑GGTT‑GCGGG‑AA‑TCA‑GC‑AAGCCCGCCA‑Ctt                                                                                                                         <  2:711417/150‑1 (MQ=255)                        gagaTACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGTAATTCCCACCAGCATGGCGGGTTAA‑GG‑T‑GCGGG‑GA‑TCA‑GCAAAGCCCCCCC‑Ctt                                                                                                                         >  2:162893/1‑150 (MQ=255)                              cATTACGGCCGACATTGAGGCCGCCAGCACGGCGTGTCCCGAAAACAGCAACGGTGAAAGGAACAGGAAGGAAATTCCCAGCGGTTCGGAAATTCCCACCAGCAGGGG‑GGTTAA‑GGTT‑GCGGA‑AA‑TCA‑GC‑AAGCCCGCCA‑CTTTTACCCg                                                                                                                  <  1:962026/150‑1 (MQ=255)                                        gACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGTAATTCCCACCAGCATGGC‑GGTTTA‑GGGT‑GCGGG‑GA‑TCA‑GC‑AAGCCCGCCC‑CTTTTTCCCGAtttttccgg                                                                                                        >  2:841387/1‑145 (MQ=255)                                            tggAGGCCCCCAGCGCGGCGTCTCCCGCAAACAGCACCGGAAAAATGAGGGGGAGTGTAAATCCCGGGGTTTCGGTAATCCCCCCCAGCATGG‑‑GGTTAG‑GGTT‑GGGGGAAA‑CCA‑CC‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCgg                                                                                                    <  2:811861/148‑1 (MQ=255)                                              gAGCCCGCCAGCCCGGGGTGTCCCGCAAACGACAACGTTGAAAAGACGAGGAAGGTAATTCCCAGGGTTTCGATAATCCCCCCCAGCGTGGC‑‑GTTAA‑GGGT‑GGGGG‑AACCCA‑AC‑AACCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCa                                                                                                  <  2:738736/150‑1 (MQ=255)                                                    gccAGCACGGCGTGTACCGAAAACAGCAAGGGTAAAATAAACAGGAAGGTAAATCCCAGCGGTTCGGTATTCCCCCCCAGCATGGC‑GGTTAG‑GGTT‑GCGGA‑AA‑CCA‑GC‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAg                                                                                            <  1:162893/150‑1 (MQ=255)                                                      cAGCACGGCGTGTCCCGAAAACAGCAAGGATGAAATGAACAGGAAGGTAAATTCCAGCGTTTCGGAAATCCCCACCAGCAGGGC‑GTTTAG‑GGTT‑GGGGA‑AA‑TCA‑GC‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTa                                                                                          <  1:658297/150‑1 (MQ=255)                                                            gggggggaCCGAAAACAGCACGGGTGAAATCCCCATGAGGGTAAATTCCCGCGTTTCGTTAATTCCCCCCAGCATGGC‑GTTTAA‑GGGG‑GGGGG‑AA‑TAA‑GC‑AAGCCCGCCA‑CGGGTACCCGATTTTCCGGTGCGGCAGTGAAGTACATCGc                                                                                    <  1:208885/143‑1 (MQ=255)                                                                    ccGCAAACAGAAAGGGTAAAAGAAACAGGAAGGTAAATCCCAGCGGTTCGGTAATCCCCACCAGCAGGGC‑GGTTAG‑GGTG‑GGGGG‑AA‑TCA‑GC‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACATCGCTAAAGaa                                                                             <  1:469081/149‑1 (MQ=255)                                                                    ccGCAAACAACAAGGGTAAAATGAACGGGAAGATAAATTCCGGGGGTTCGGTAATCCCCCCCAGCAGGGC‑GGTAAG‑GGTT‑GCGGC‑AA‑TCA‑GC‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACATCGCTAAAGaaa                                                                            <  1:871773/150‑1 (MQ=255)                                                                     cGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGTAATTCCCACCAGCATGGC‑GGTTAA‑AGTT‑GCGGG‑AA‑TCA‑GC‑AAACCCGCCA‑CCTTTAACCGATTTTTCGGTGCGGCAGGGAAGGACATCGCTTaaaaaa                                                                            >  2:548865/1‑149 (MQ=255)                                                                      gaaaaCAGAAAGGGTAAAATGAACAGGAAGGTAAATCCCGGCGGTTGGTTAATCCCCCCCAGCA‑GGG‑TGTTAA‑GGGT‑GGGGGAAA‑TCA‑GC‑AACCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACATCGCTAAAGAAATg                                                                          <  2:514181/148‑1 (MQ=255)                                                                         aaCAGCAACGGTAAAATAAACAGGAAGGTAAATCCCAGCGGTTGGGTAATCCCCACCAGCATGGG‑GGTTAA‑GGTG‑GGGGG‑AA‑TCA‑GC‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACATCGCTAAAGAAATGccc                                                                       <  1:148295/150‑1 (MQ=255)                                                                               acgggTAAAATGAACAGGAAGGTAAATTCCGGCGGTTCGGTAATCCCCCCCAGCAGGGC‑GTTTAA‑GGTT‑GCGGA‑AA‑TCA‑GC‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACATCGCTAAAGAAATGCCCACGGCa                                                                 <  2:510282/147‑1 (MQ=255)                                                                                  ggTAAAATGAACAGGAAGGTAAATCCCAGGGGTTCGGTAATCCCCCCCAGCAGGGC‑GGTTAA‑GGTT‑GCGGG‑AA‑TCA‑GC‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACATCGCTAAAGAAATGCCCACGGCACCa                                                              <  1:841387/150‑1 (MQ=255)                                                                                      aaaTGAACAGGAAGGTAAATTCCAGCGGTTCGGTAATTCCCACCAGCATGGC‑GGTTAA‑GGTT‑GCGGG‑AA‑TCA‑GC‑AAGCCCGCCC‑CTTTTACCCCATTTTCCGGTGCGGCAGTGAAGTACATCGGTAAAGAAAATCCCACGGCAccc                                                              >  1:612258/1‑145 (MQ=255)                                                                                       aaTGAACAGGAAGGTAAATTCCAGCGGTTCGGTAATTCCCACCAGCATGGC‑GGTTAA‑GGGT‑TCGGG‑AA‑TCA‑GC‑AAGCCCGCCC‑CTTTTTCCCCATTTTTCGGGGGGGGAGTGAAGGACATCCCTAAAGAAATGCCCACGGCACCAAAGAt                                                         >  2:948556/1‑150 (MQ=255)                                                                                       aaTAAACAGGAAGGTAAATCCCGGCGTTTCGTTAATCCCCCCCAGCGTGGC‑GGTTAA‑GGTT‑GCGGA‑AA‑CCA‑GC‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACATCGCTAAAGAAATGCCCACGGCACCAAAGAt                                                         <  2:517310/150‑1 (MQ=255)                                                                                        aTGAACAGGAAGGTAAATTCCAGCGGTTCGGTAATTCCCACCAGCATGGC‑GGTTAA‑GGGT‑GCGGG‑AA‑TCA‑GC‑AAGCCCGCCACCTTTTACCC‑ATTTTCCGGTGCGGCAGTGAAGCACATCGCTAAAGAAATGCCCACGGCACCAAAAAtt                                                        >  1:728014/1‑150 (MQ=255)                                                                                             cAGGAAGGTAAATTCCAGCGGTTCGGTAATTCCCACCAGCATGGC‑GGTTAAGGGTT‑TCGGG‑AA‑‑CA‑GC‑AAGGCCCCCC‑CTTTTACCCCATTTTTCGGGGCGGCCGTGAAGAACATCGCCAAAAAAAAACCCACGGCTCCCAACAttttttt                                                   >  2:398309/1‑148 (MQ=255)                                                                                                   gatAAATTCCAGCGGTTCGGTATTCCCCACCAGCAGGGC‑GTTAAG‑GGTG‑GCGGG‑AA‑TCA‑GC‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTAcc                                             <  1:80703/148‑1 (MQ=255)                                                                                                    gTAAATTCCAGCGGTTCGGTAATTCCCACCAGCATGGC‑GGTTAA‑GGTT‑GCGGG‑AA‑TCA‑GC‑AAACCCGCCA‑CTTTTACCCGATTTTTCGGTGCGGCAGTGAAGTACATCGCTAAAGAAAAGCCCACGGCACCAAAGATTTTTTAGTTACCg                                            >  1:458131/1‑150 (MQ=255)                                                                                                        aTTCCAGCGGTTCGGTAATTCCCACCAGCATGGC‑GGTTAA‑GGGT‑GCGGG‑GA‑TCA‑GC‑AAACCCGCCA‑CTTTTTCCCGATTTTTCGGGGCGGCAGTGAAGTACATCGCCAAAGAAATGCCCACGGCACCAAAGATTTTTTAGTTACCggg                                          >  1:793977/1‑146 (MQ=255)                                                                                                           ccggCGGTGCGTTAATCCCCACCAGCGGGGC‑GGTAAG‑GGTT‑GCGGA‑AA‑TCA‑GA‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAgg                                      <  2:422138/146‑1 (MQ=255)                                                                                                             aGCGGTTCGGTAATTCCCACCAGCATGGC‑GGTTTA‑GGTT‑TCGGG‑GA‑ACA‑GC‑AAGACCGCCC‑CTTTTACCCGAATTTTCGGCGCGGCAGGGAAGAACATAGCCTAAGAAATGCCCACGGCACCAAAAATTTTTTAGTTACCGTGCAGGGc                                    >  1:23964/1‑149 (MQ=255)                                                                                                               cGGTTCGGTAATTCCCACCAGCATGGC‑GGTTAA‑GGTT‑GCGGG‑AA‑TCA‑GC‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGGACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCaa                                  >  1:639445/1‑149 (MQ=255)                                                                                                                    cGGTAATCCCCCCCAGCGTGGC‑GGTTAA‑GGTG‑GGGGA‑AA‑TCA‑GC‑AACCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCAAAACCg                             <  2:557436/149‑1 (MQ=255)                                                                                                                     ggTAATTCCCACCAGCATGGC‑GGTTAA‑GGTT‑GCGGG‑GA‑TCA‑GC‑AAGCCCCCCA‑CCTTTTCCCGATTTTCCGGTGCGGCAGTGAAGAACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCAAAACCGcc                           >  1:646064/1‑150 (MQ=255)                                                                                                                     ggTAATTCCCACCAGCATGGC‑GGTTAA‑GGGT‑GCGGG‑GA‑TCA‑GC‑AAGCCCGCCC‑CTTTTTCCCGATTTTTCGGGGCGGCAGTGAAGGACATCGCTAAAGAAAAGCCCACGGCCCCCAAGATTTTTTAGTTAACGTGCCGGGCAAAAACGcc                           >  1:916264/1‑150 (MQ=255)                                                                                                                        aaTTCCCACCAGCATGGC‑GGTTAA‑CGGT‑GGGGG‑GA‑TCACGA‑AACCCCGCAA‑C‑TTTAACCGAATTTCCCGTGCGGCAGAGAAGTACATCGCTCAAGAAATGACCAATGCACCCAAGATATTTGAGTGTCCGTTCAAGGGAAAAACggcgta                        >  1:635860/1‑145 (MQ=255)                                                                                                                          ttCCCACCAGCATGGC‑GGTTAA‑AGTT‑GCGGG‑AA‑TTA‑GC‑AAGCCCGCCA‑CTTTTACCCGATTTTTCCGTGCGGCTGCGGAGAACAATGCTCAAGAAAATACCACTGCCCCCAAAATTTTTTTGTTTCCCGGCAAGGCTAAAACGcccttcg                      >  2:399338/1‑145 (MQ=255)                                                                                                                            cccACCAGCAGGGG‑GGTAAA‑GGTG‑GCGGA‑AA‑TAA‑GC‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCAAAACCGCCTTCCgg                     <  2:821516/149‑1 (MQ=255)                                                                                                                              caccaGCATGGC‑GGTTAA‑GGTT‑GCGGG‑GA‑TCA‑GC‑AAGCCCCCCA‑CCTTTACCCGGCTTTCCGGGGCGGGAGGGGAGGACCTCGCTCAAAAAAATCCCACCGCACCAAAGATTTTTTAGTTACCGGGCAGGGGAAAAACGCCTTCCGGGa                   >  2:402980/1‑149 (MQ=255)                                                                                                                                  aGCATGGC‑GGTTAA‑GGTG‑GGGGG‑AA‑TCA‑GC‑ACGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCAAAACCGCCTTCCGGGaacaac              <  2:630384/150‑1 (MQ=255)                                                                                                                                         ggggTTAG‑GGTG‑GGGGA‑AA‑CCA‑AA‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCAAAACCGCCTTCCGGGAACAACGATTTc        <  2:975099/148‑1 (MQ=255)                                                                                                                                             ttAG‑GGTG‑GCGGG‑AA‑CCA‑AC‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCAAAACCGCCTTCCGGGAACAACGATTTCAGCg    <  2:130477/150‑1 (MQ=255)                                                                                                                                             ttAA‑GGTT‑GCGGG‑AA‑TCA‑GC‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCAAAACCGCCTTCCGGGAACAACGATTTCAGCg    >  1:909811/1‑150 (MQ=255)                                                                                                                                             ttAA‑GGTT‑GCGGG‑AA‑TCA‑GC‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCAAAACCGCCTTCCGGGAACAACGATTTCAGCg    >  1:45238/1‑150 (MQ=255)                                                                                                                                              tAA‑GGTTGGGGGG‑AA‑CCA‑GC‑AGGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCAAAACCGCCTTCCGGGAACAACGATTTCAGCg    <  2:646064/150‑1 (MQ=255)                                                                                                                                               aa‑GGTG‑GGGGA‑AA‑TCA‑AC‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGc  <  2:977004/150‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                        CCCATGTTGCCCACCACACCAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGTAATTCCCACCAGCATGGC‑GGTTAA‑GGTT‑GCGGG‑AA‑TCA‑GC‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGC  >  CP009273/3855876‑3856166

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑