Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	REL606	3,145,995	C→T	I44I (ATC→ATT)	rpoD →	RNA polymerase sigma factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	REL606	3,145,995	0	C	T	100.0%	147.4 / NA	38	I44I (ATC→ATT)	rpoD	RNA polymerase sigma factor
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (19/19);  total (19/19)

CTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGATGC  >  REL606/3145923‑3146062                                                                         |                                                                    cTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCCGATCAGATCGAAGACattatc                                                                  >  2:172618/1‑76 (MQ=255)   aTCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATTATCCa                                                                >  2:269258/1‑76 (MQ=255)   aTCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATTATCCa                                                                <  2:286796/76‑1 (MQ=255)    tCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATTATCCaa                                                               <  2:566090/76‑1 (MQ=255)      tGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATTATCCAAAt                                                             >  2:444849/1‑76 (MQ=255)       gACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATTATCCAAATg                                                            >  1:474490/1‑76 (MQ=255)         ccTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATTATCCAAATGAt                                                          <  1:503542/76‑1 (MQ=255)                 gAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATTATCCAAATGATCAACGACa                                                  >  2:131118/1‑76 (MQ=255)                  aGGTCAATGTCCATCTGCCGGAANATATCNTCGATGCAGATCAGNTCAAAGACATTATCCACATGATCAACGACAt                                                 >  2:144582/1‑76 (MQ=255)                   ggTCAATGACCATCTGCCGGAAGATATCGTGGATTCAGATCAGATCGAAGACATTATCCAAATGATCAATGACATg                                                >  1:1065321/1‑76 (MQ=255)                      cAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATTATCCAAATGATCAACGACATGGGc                                             >  2:95714/1‑76 (MQ=255)                      cAATGACCAACTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATTATCCAAATGATCAACCACATGGGc                                             <  1:38088/76‑1 (MQ=255)                         tGACCATCTGCCGGAAGATATCGTCGATTCAGNTCAGATCGAAGACATTATCCAAATGATCAACGACATGGGNAtc                                          >  2:1093410/1‑75 (MQ=255)                          gACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATTATCCAAATGATCAACGACATGGGCATTc                                         <  1:650264/76‑1 (MQ=255)                           gccATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATTATCCAAATGATCAACGACATGGGCAttaa                                        <  2:15931/75‑3 (MQ=255)                           aCCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATTATCCAAATGATCAACGACATGGGCATTCa                                        <  2:182958/76‑1 (MQ=255)                                   ccGGAAGATATCGTCGATTCAGATCAGATCGAANACATTATCCAAATGATCAACGANATGGGCATACNGGTGATgg                                >  2:972464/1‑76 (MQ=255)                                    cGGAAGATATCGTCGATTCAGATCAGATCTAAGACATTATCCAAATGATCAACGACATGGGCATTCAGGTGATGga                               <  2:545407/76‑1 (MQ=255)                                      gAAGATATCGTCGACTCAGATCAGGTCGCAGNCATTATCCTAATGANCAACGNCATGGGCATTCAGGTGATGgaag                             <  2:148502/76‑1 (MQ=255)                                       aaGATATCGTCGATTCAGATCAGATCGAAGACATTATCCAAATGATCAACGACATGGGCATTCAGGTGATGgaaga                            >  2:681602/1‑76 (MQ=255)                                          atatCGTCGATTCAGATCAGATCGAAGACATTATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGc                         <  1:592261/76‑1 (MQ=255)                                             tcgtcgATTCAGATCAGATCGAAGACATTATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCAcc                      >  1:855390/1‑76 (MQ=255)                                             tcgtcgATTCAGATCAGATCGAAGACATTATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCAcc                      >  2:638001/1‑76 (MQ=255)                                                tcgATTCAGATCAGATCGAAGACATTATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGa                   >  1:694184/1‑76 (MQ=255)                                                 cgATTCAGATCAGATCGAAGACATTATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGAt                  <  2:872911/76‑1 (MQ=255)                                                  gATTCAGATCAGATCGAAGACATTATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCggcgt                 >  2:803477/1‑73 (MQ=255)                                                  gATTCAGATCAGATCGAAGACATTATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCggcgt                 >  2:803471/1‑73 (MQ=255)                                                    ttCAGATCAGATCGAAGACATTATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGcc               >  2:578225/1‑76 (MQ=255)                                                     tcagatcagaTCGAAGACATTATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCg              >  1:196100/1‑76 (MQ=255)                                                        gatcagatcGAAGACATTATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCgatg           >  2:136053/1‑76 (MQ=255)                                                        gatcagatcGAAGACATTATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCgatg           <  2:900397/76‑1 (MQ=255)                                                        gatcagatcGAAGACATTATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCgatg           <  1:360491/76‑1 (MQ=255)                                                        gatcagatcGAAGACATTATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATCCCgatg           <  1:68047/76‑1 (MQ=255)                                                           cagatcGAAGACATTATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATc        >  1:848336/1‑76 (MQ=255)                                                            agatcGAAGACATTATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCt       <  1:165701/76‑1 (MQ=255)                                                             gatcGAAGACATTATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTg      <  2:626298/76‑1 (MQ=255)                                                             gatcGAAGACATTATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTg      <  2:922843/76‑1 (MQ=255)                                                               tcGAAGACATTATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGAt    <  2:294290/76‑1 (MQ=255)                                                                 gAAGACATTATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGATgc  <  2:462104/76‑1 (MQ=255)                                                                         |                                                                    CTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGATGC  >  REL606/3145923‑3146062

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑