Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP009974	1,920,747	T→C	intergenic (‑376/+179)	RPPX_08560 ← / ← RPPX_08565	16S ribosomal RNA/CoA‑transferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009974	1,920,747	0	T	C	100.0%	14.1 / NA	30	intergenic (‑376/+179)	RPPX_08560/RPPX_08565	16S ribosomal RNA/CoA‑transferase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (12/18);  total (12/18)

CTTGGAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTTGATCGTAGCCCTTACAGC‑‑A‑‑CCTTCCGAATCGTCTAACTCATTGAATCTCAAGGAGTTTGTCGTTCCGTTGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAATTTCA  >  CP009974/1920691‑1920863                                                         |                                                                                                                         cTTGGAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TACCTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCgag                        <  1:2243879/151‑1 (MQ=11)  ttGGAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCgaga                       >  2:4716883/1‑151 (MQ=2)  ttGGAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCgaga                       <  1:3606830/151‑1 (MQ=2)    ggAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGACGTGGGGCGCATTATACGGGGATTCGAGAgg                     >  2:4451016/1‑151 (MQ=2)    ggAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAgg                     <  2:1026015/151‑1 (MQ=2)    ggAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGC‑‑TTTCCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAgg                     <  2:3060508/151‑1 (MQ=2)     gAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTTGAGAggg                    >  1:2175135/1‑151 (MQ=2)     gAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATGATAAGGGGATTGGAGCggg                    >  1:2175116/1‑151 (MQ=2)       aGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCg                  >  1:974192/1‑151 (MQ=2)       aGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTGTCGTTCCGTTGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCg                  <  1:1857849/151‑1 (MQ=11)          gcTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCa               >  2:4412377/1‑151 (MQ=2)          gcTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCa               <  2:1156168/151‑1 (MQ=2)            tGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTCG‑CTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAAc             <  2:923169/151‑1 (MQ=2)             gTCCACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGC‑‑TTTCCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAAcc            <  2:1789953/151‑1 (MQ=2)               cAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCtt          >  1:4597702/1‑151 (MQ=2)               cAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCtt          <  2:1009439/151‑1 (MQ=2)               cAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGC‑‑TTTCCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCtt          >  2:4650512/1‑151 (MQ=2)                aaCCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TATCTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCttt         <  2:3484699/151‑1 (MQ=2)                aaCCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCttt         <  1:714560/151‑1 (MQ=2)                aaCCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCttt         <  1:2547308/151‑1 (MQ=2)                aaCCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCttt         <  2:461927/151‑1 (MQ=11)                aaCCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCttt         <  2:5227266/151‑1 (MQ=2)                  ccATCTTCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTaa       <  1:4357038/151‑1 (MQ=2)                  ccATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTaa       >  1:972799/1‑151 (MQ=2)                     tcatcTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAAttt    <  2:2474804/151‑1 (MQ=2)                     tcatcTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAAttt    >  1:4022223/1‑151 (MQ=2)                     tcatcTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGC‑‑TTTCCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAAttt    <  2:3429108/151‑1 (MQ=2)                      catcTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAATTTc   <  1:415163/151‑1 (MQ=2)                      catcTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAATTTc   >  1:5039975/1‑151 (MQ=2)                       atcTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGCTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATCATAACGCGATTCGCTATGGCGTCAACCTTTAATTTCa  >  2:3751597/1‑151 (MQ=2)                                                         |                                                                                                                         CTTGGAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTTGATCGTAGCCCTTACAGC‑‑A‑‑CCTTCCGAATCGTCTAACTCATTGAATCTCAAGGAGTTTGTCGTTCCGTTGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAATTTCA  >  CP009974/1920691‑1920863

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑