Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_014034	1,608,028	G→T	100%	intergenic (+298/‑49)	RCAP_rcc01484 → / → murD	hypothetical protein/UDP‑N‑acetylmuramoylalanine‑‑D‑glutamate ligase

Read alignment evidence...
	seq id	position		change	freq	score	reads	annotation	genes	product
*	NC_014034	1,608,028	0	G→T	100.0%	240.7	65	intergenic (+298/‑49)	RCAP_rcc01484/murD	hypothetical protein/UDP‑N‑acetylmuramoylalanine‑‑D‑glutamate ligase
Reads supporting (aligned to +/- strand):  new base (17/48):  ref base (0/0):  total (17/48)

GACCGGCGCCTGTCTTCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCCTTGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGGCCGCGCGGCGCGGGCCCAATTCACCCCCGCAGCTTACGG  >  NC_014034/1607928‑1608067                                                                                                     |                                        gcccGCCGCCTGTC.TCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTcc                                       <  1:3387172/99‑1 (MQ=38) gcccGCCGCCTGTC.TCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTcc                                       <  1:2506141/99‑1 (MQ=38) gACCGCCGCCTGTC.TCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGCAAGGGGGGCTGCGCGCCCCCCTCTTGGTcc                                       >  1:7080777/1‑101 (MQ=38) gACCGCCGCCTGTC.TCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTcc                                       >  1:6202014/1‑101 (MQ=38) gACCGCCGCCTGTC.TCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTcc                                       >  1:2612359/1‑101 (MQ=38) gACCGCCGCCTGTC.TCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTcc                                       >  2:5965211/1‑101 (MQ=38)  cccGCCGCCTGTC.TCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCcg                                      <  1:4943096/100‑1 (MQ=38)  cccGCCGCCTGTC.TCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCcg                                      <  2:4030088/100‑1 (MQ=38)  aCCGCCGCCTGTC.TCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCcg                                      <  2:4618502/101‑1 (MQ=38)    cgccgcCTGTC.TCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCcgct                                    <  1:3237997/98‑2 (MQ=38)    cgccgcCTGTC.TCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCcgct                                    <  2:2842064/98‑2 (MQ=38)     gccgcCTGTC.TCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCcgctg                                   <  1:3324079/99‑3 (MQ=38)     gccgcCTGTC.TCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCcgctg                                   <  2:3122759/99‑3 (MQ=38)     gccgcCTGTC.TCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCcgctg                                   <  2:2580720/99‑3 (MQ=38)     cccgcCTGTC.TCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCcgctg                                   <  1:963990/99‑3 (MQ=38)      ccgcCTGTC.TCCGACCTTTTCCCAGCGGATCCTGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCcgctgg                                  <  2:3897858/100‑4 (MQ=38)      ccgcCTGGC.TCCGGCCTTTTACCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCcgttgg                                  <  1:6852234/100‑5 (MQ=37)       cgcCTGTC.TCCGACCTTTTCCCAGCGGATCCGGCGACGGGGTGCGACGCC.TGCGCCGCCGCCCGAAATGGGGGCTTCGCGACCCCCTCTTGGTCcgctggg                                 >  2:1270999/1‑97 (MQ=255)        gcCTGTC.TCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCcgctggcg                                <  2:1289917/101‑6 (MQ=38)        gcCTGTC.TCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCcgctggcg                                >  1:2126229/1‑96 (MQ=38)         ccTGTC.TCCGACCTTTTCCCCGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCcgctgccgc                               <  1:5611919/101‑7 (MQ=38)         ccTGTC.TCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCcgctggcgc                               <  2:6604491/101‑7 (MQ=38)         ccTGTC.TCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCcgctggcgc                               >  1:4221330/1‑95 (MQ=38)         ccTGTC.TCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGCGGGGCTGGGGGGCCCCCTCGTGCTCCgcgcgggc                               >  2:1021488/1‑99 (MQ=255)          cTGTC.TCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCcgctggcggg                              >  1:5835626/1‑94 (MQ=38)          cTGTC.TCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCcgctggcgcg                              >  2:3320279/1‑94 (MQ=38)          cTGTC.TCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCcgctggcgcg                              >  1:1676289/1‑94 (MQ=38)          cTGTC.TCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGGCcgctggcgcg                              >  1:2700449/1‑94 (MQ=38)            tgtctCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCgc.tggcgcgg                            <  1:1914226/97‑1 (MQ=38)            tgtctCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCgc.tggcgcgg                            >  1:1792554/5‑101 (MQ=38)              tctCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCgc.tggcgcggcc                          >  1:3382489/3‑99 (MQ=38)              tctCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCgc.tggcgcggcc                          >  2:389344/3‑99 (MQ=38)               ctCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGCGGCcc                         >  1:4396679/2‑101 (MQ=38)               ctCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGCGGCcc                         <  1:2063782/100‑1 (MQ=38)                tCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGCGGCcca                        <  2:4187750/101‑2 (MQ=38)                tCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGCGGCcca                        <  1:112273/101‑2 (MQ=38)                  cGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAAt                     <  1:3435405/101‑1 (MQ=38)                  cGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAAt                     <  2:4221135/101‑1 (MQ=37)                  cGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAAt                     <  1:1397564/101‑1 (MQ=37)                  cGACCTTTTCCCAGCGGATCCCGCCACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAAt                     <  1:1018659/101‑1 (MQ=37)                    gccTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTc                   <  1:4982609/100‑1 (MQ=37)                    aCCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTc                   <  1:2024743/101‑1 (MQ=37)                    aCCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGAGCGCCCCCCTCTTGGTCCCCTC.GCGCGGCCCCattc                    >  1:6080527/1‑98 (MQ=255)                     ccTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCa                  <  1:2429373/101‑1 (MQ=37)                      cTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCAc                 <  1:7024886/101‑1 (MQ=37)                      cTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCAc                 <  1:2665064/101‑1 (MQ=37)                      cTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCAc                 <  2:6018717/101‑1 (MQ=37)                       ttttCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCAcc                <  1:66641/101‑1 (MQ=37)                       ttttCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCAcc                <  2:3091696/101‑1 (MQ=37)                       ttttCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCAcc                >  2:2462946/1‑101 (MQ=38)                        tttCCCAGCGGATCCCGCGACGGGGTGCGACGTC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCAccc               <  1:5954345/101‑1 (MQ=37)                        tttCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCAccc               <  1:6495165/101‑1 (MQ=38)                         ttCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCAcccc              <  2:4799971/101‑1 (MQ=38)                         ttCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCAcccc              <  2:2004635/101‑1 (MQ=37)                         ttCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCAcccc              <  1:6171719/101‑1 (MQ=37)                          tCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCAccccc             <  2:7051014/101‑1 (MQ=37)                          tCCCAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCAccccc             <  1:3138362/101‑1 (MQ=37)                           cccAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCg            <  1:2674029/101‑1 (MQ=38)                           cccAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCg            >  1:6565181/1‑101 (MQ=38)                            ccAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCGc           <  2:5937329/101‑1 (MQ=38)                             cAGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCGcg          <  1:5662582/101‑2 (MQ=38)                              aGCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCGcgg         >  2:4074717/1‑99 (MQ=37)                               gCGGATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCGcggg        <  2:4286029/101‑4 (MQ=37)                                 ggATCCGGCGGCGGGGTGCGCCGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCGcgggat      <  1:3320096/101‑6 (MQ=25)                                 ggATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCGcgggat      <  1:5294306/101‑6 (MQ=37)                                 ggATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCGcgggat      >  2:2137831/1‑96 (MQ=37)                                 ggATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCGcgggat      >  1:164712/1‑96 (MQ=37)                                  gATCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCGcgggata     >  1:2254267/1‑95 (MQ=37)                                   gtCCCGCCCCGGGGTGCGGCTCC.CGCGTCGCTTCCCGAAAGGCGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCCCCCCCGcgggatat    <  2:3279271/100‑8 (MQ=255)                                   aTCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCGcgggctat    >  2:1135215/1‑94 (MQ=37)                                   aTCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCGcgggatat    <  1:2832441/101‑8 (MQ=37)                                   aTCCCGCGACGGGGTGCGACGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCGcgggatat    <  1:2267924/101‑8 (MQ=37)                                     cccGCGCCGGGGTGCGGCGCC.TGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGTCCGC.TGGCGC.GGCCCAATTCACCCCCGcgggatattt  <  2:2456961/101‑10 (MQ=25)                                                                                                     |                                        GACCGGCGCCTGTCTTCCGACCTTTTCCCAGCGGATCCCGCGACGGGGTGCGACGCCTTGCGGCGCCGCCCGAAAGGGGGGCTGCGCGCCCCCCTCTTGGGCCGCGCGGCGCGGGCCCAATTCACCCCCGCAGCTTACGG  >  NC_014034/1607928‑1608067 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 40 ≤  ATCG