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%	172.2 / NA	44	S253P (TCT→CCT)	rpoD	RNA polymerase, sigma 70 (sigma D) factor
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (19/25);  total (19/25)

CGAAAGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGTCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGTTTGACTA  >  NC_000913/3213756‑3213849                                                |                                               cGAAAGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCt                                              >  1:102728/1‑50 (MQ=255)    aaGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGaa                                           <  1:2253451/50‑1 (MQ=255)    aaGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGaa                                           <  1:1772655/50‑1 (MQ=255)     aGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAg                                          <  1:635710/50‑1 (MQ=255)     aGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAg                                          >  1:1632606/1‑50 (MQ=255)       gTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTa                                        <  1:854092/50‑1 (MQ=255)       gTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTa                                        >  1:1692459/1‑50 (MQ=255)        tCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTAt                                       >  1:1311903/1‑50 (MQ=255)          gCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTAtt                                      >  1:774833/1‑49 (MQ=255)          gCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTAtt                                      >  1:1728859/1‑49 (MQ=255)          gCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTc                                     <  1:2052844/50‑1 (MQ=255)          gCAGTCACGCTACCGCTCAGGAAGAGATACTGAAACTGCCTGAAGTAtt                                      <  1:2093179/49‑1 (MQ=38)           cAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTc                                     >  1:455807/1‑49 (MQ=255)           cAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTc                                     >  1:2512792/1‑49 (MQ=255)              tCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAAc                                 <  1:1645486/50‑1 (MQ=255)                aCGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACa                                <  1:2169234/49‑1 (MQ=255)                 cGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGt                              >  1:2719374/1‑50 (MQ=255)                 cGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGt                              <  1:2451555/50‑1 (MQ=255)                 cGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGt                              <  1:884374/50‑1 (MQ=255)                 cGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGt                              >  1:1975224/1‑50 (MQ=255)                  gCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGtt                             >  1:1905961/1‑50 (MQ=255)                   cTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTc                            <  1:1491328/50‑1 (MQ=255)                   cTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTc                            <  1:852767/50‑1 (MQ=255)                   cTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTc                            <  1:1025895/50‑1 (MQ=255)                    tACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTcc                           >  1:2632205/1‑50 (MQ=255)                      ccGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGc                         <  1:1068947/50‑1 (MQ=255)                        gCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCt                       <  1:743743/50‑1 (MQ=255)                        gCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCt                       <  1:2502031/50‑1 (MQ=255)                          tCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTgg                     >  1:864787/1‑50 (MQ=255)                            aGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTg                   <  1:713426/50‑1 (MQ=255)                             ggAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGc                  >  1:1956001/1‑50 (MQ=255)                               aaGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCg                <  1:2591655/50‑1 (MQ=255)                                 gagaTCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGaa              <  1:967205/50‑1 (MQ=255)                                   gaTCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGc            <  1:222948/50‑1 (MQ=255)                                    aTCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAg             >  1:1491264/1‑48 (MQ=255)                                       cTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGtt        <  1:749048/50‑1 (MQ=255)                                       cTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGtt        <  1:92655/50‑1 (MQ=255)                                       cTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGt         <  1:748115/49‑1 (MQ=255)                                         gAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGttt       >  1:2674186/1‑49 (MQ=255)                                          aaaCTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGTTTGa     >  1:598722/1‑50 (MQ=255)                                           aaCTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGTTTGAc    >  1:2336178/1‑50 (MQ=255)                                            aCTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGTTTGACt   <  1:598511/50‑1 (MQ=255)                                             cTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGTTTGACTa  >  1:688872/1‑50 (MQ=255)                                             cTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGTTTGACTa  <  1:2280064/50‑1 (MQ=255)                                                |                                               CGAAAGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGTCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGTTTGACTA  >  NC_000913/3213756‑3213849

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑