Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,213,803	T→C	S253P (TCT→CCT)	rpoD →	RNA polymerase, sigma 70 (sigma D) factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,213,803	0	T	C	100.0%	335.8 / NA	81	S253P (TCT→CCT)	rpoD	RNA polymerase, sigma 70 (sigma D) factor
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (35/46);  total (35/46)

CGAAAGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGTCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGTTTGAC  >  NC_000913/3213756‑3213847                                                |                                             cGAAAGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCt                                            <  1:1960112/50‑1 (MQ=255)  gAAAGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCt                                            >  1:4653494/1‑49 (MQ=255)  gAAAGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCt                                            >  1:3799796/1‑49 (MQ=255)  gAAAGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCt                                            >  1:5032403/1‑49 (MQ=255)  gAAAGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCt                                            >  1:2149349/1‑49 (MQ=255)  gAAAGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTg                                           <  1:615430/50‑1 (MQ=255)   aaaGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGa                                          <  1:2905234/50‑1 (MQ=255)   aaaGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGa                                          <  1:4598926/50‑1 (MQ=255)   aaaGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGa                                          <  1:483741/50‑1 (MQ=255)    aaGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGaa                                         <  1:3952524/50‑1 (MQ=255)    aaGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGaa                                         <  1:4750253/50‑1 (MQ=255)      ggTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGt                                       <  1:5307621/50‑1 (MQ=255)       gTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTa                                      <  1:720358/50‑1 (MQ=255)        tCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTAt                                     <  1:2558460/50‑1 (MQ=255)        tCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTAt                                     >  1:756835/1‑50 (MQ=255)         cGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTAtt                                    >  1:3447569/1‑50 (MQ=255)          gCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTAtt                                    <  1:4297012/49‑1 (MQ=255)          gCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTAtt                                    >  1:4245694/1‑49 (MQ=255)          gCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTc                                   <  1:5832470/50‑1 (MQ=255)          gCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCATGAAGTAtt                                    <  1:4595521/49‑1 (MQ=39)           cAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCa                                  <  1:5496662/50‑1 (MQ=255)           cAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCa                                  <  1:3609984/50‑1 (MQ=255)            aGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCaa                                 <  1:1560124/50‑1 (MQ=255)            aGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCa                                  >  1:5894945/1‑49 (MQ=255)             gTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCaaa                                <  1:4611052/50‑1 (MQ=255)             gTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCaaa                                <  1:5531126/50‑1 (MQ=255)             gTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCaaa                                >  1:267678/1‑50 (MQ=255)              tCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCaaa                                >  1:3301094/1‑49 (MQ=255)              tCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAAc                               <  1:1066612/50‑1 (MQ=255)                aCGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAg                             >  1:5307085/1‑50 (MQ=255)                  gCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGtt                           >  1:1226454/1‑50 (MQ=255)                  gCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGtt                           >  1:2182252/1‑50 (MQ=255)                  gCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGtt                           <  1:3593697/50‑1 (MQ=255)                   cTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTc                          <  1:5046861/50‑1 (MQ=255)                    tACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTcc                         >  1:893917/1‑50 (MQ=255)                    tACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTcc                         >  1:1978751/1‑50 (MQ=255)                    tACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTcc                         >  1:2767836/1‑50 (MQ=255)                     aCCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCg                        >  1:4360214/1‑50 (MQ=255)                      ccGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTcc                         <  1:3777022/48‑1 (MQ=255)                      ccGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTcc                         <  1:4023408/48‑1 (MQ=255)                      ccGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCg                        <  1:4759436/49‑1 (MQ=255)                      ccGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGc                       >  1:3577022/1‑50 (MQ=255)                        gCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCt                     <  1:2878856/50‑1 (MQ=255)                        gCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCt                     <  1:283237/50‑1 (MQ=255)                        gCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCt                     <  1:2714662/50‑1 (MQ=255)                        gCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCt                     <  1:1615992/50‑1 (MQ=255)                         cTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTg                    <  1:925483/50‑1 (MQ=255)                         cTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTg                    <  1:3066852/50‑1 (MQ=255)                           cAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGt                  >  1:804304/1‑50 (MQ=255)                            aGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTgg                   <  1:3370266/48‑1 (MQ=255)                            aGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGt                  <  1:1631588/49‑1 (MQ=255)                            aGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTg                 >  1:2982208/1‑50 (MQ=255)                             ggAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGc                <  1:1222713/50‑1 (MQ=255)                             ggAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGc                <  1:3559972/50‑1 (MQ=255)                              gAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGcc               <  1:747554/50‑1 (MQ=255)                              gAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGcc               <  1:5031262/50‑1 (MQ=255)                              gAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGcc               >  1:2514069/1‑50 (MQ=255)                               aaGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGcc               >  1:1876220/1‑49 (MQ=255)                               aaGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGcc               >  1:1503004/1‑49 (MQ=255)                               aaGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGcc               >  1:5621126/1‑49 (MQ=255)                                   gaTCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAg           >  1:2836087/1‑49 (MQ=255)                                   gaTCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGc          <  1:4938335/50‑1 (MQ=255)                                    aTCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAg           >  1:5063991/1‑48 (MQ=255)                                    aTCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCa         <  1:1778434/50‑1 (MQ=255)                                    aTCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCa         <  1:4979157/50‑1 (MQ=255)                                    aTCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCa         <  1:5321543/50‑1 (MQ=255)                                     tCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAg        >  1:1887501/1‑50 (MQ=255)                                     tCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAg        >  1:3155098/1‑50 (MQ=255)                                      ccTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGt       >  1:17584/1‑50 (MQ=255)                                      ccTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGt       >  1:986674/1‑50 (MQ=255)                                       cTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGtt      <  1:5351855/50‑1 (MQ=255)                                       cTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGtt      <  1:4411632/50‑1 (MQ=255)                                        tGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGttt     >  1:3720819/1‑50 (MQ=255)                                         gAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGttt     >  1:1588071/1‑49 (MQ=255)                                          aaaCTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGttt     <  1:5175242/48‑1 (MQ=255)                                          aaaCTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGttt     <  1:1858466/48‑1 (MQ=255)                                          aaaCTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGTTTg    <  1:5457091/49‑1 (MQ=255)                                          aaaCTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGTTTGa   >  1:4600377/1‑50 (MQ=255)                                          aaaCTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGTTTGa   >  1:4581144/1‑50 (MQ=255)                                           aaCTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGTTTGAc  >  1:3314651/1‑50 (MQ=255)                                           aaCTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGTTTGAc  <  1:1236145/50‑1 (MQ=255)                                                |                                             CGAAAGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGTCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGTTTGAC  >  NC_000913/3213756‑3213847

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑