Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP009273	3,208,093	T→C	F563S (TTC→TCC)	rpoD →	RNA polymerase, sigma 70 (sigma D) factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	3,208,093	0	T	C	100.0%	196.8 / NA	59	F563S (TTC→TCC)	rpoD	RNA polymerase, sigma 70 (sigma D) factor
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (20/39);  total (20/39)

TGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGC  >  CP009273/3208028‑3208157                                                                  |                                                                 tgcgGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCg                                                                >  1:1470249/1‑68 (MQ=255)  gcgGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCgg                                                               <  1:1580501/68‑1 (MQ=255)   cgGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGt                                                              <  1:1207063/68‑1 (MQ=255)   cgGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGt                                                              <  1:1780101/68‑1 (MQ=255)     gCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTAt                                                            >  1:4145616/1‑68 (MQ=255)     gCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTAt                                                            >  1:3221768/1‑68 (MQ=255)     gCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTAt                                                            <  1:6118733/68‑1 (MQ=255)        aCGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGa                                                         <  1:4550444/68‑1 (MQ=255)        aCGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGa                                                         <  1:1328325/68‑1 (MQ=255)        aCGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGa                                                         <  1:413400/68‑1 (MQ=255)        aCGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGa                                                         <  1:1834459/68‑1 (MQ=255)          gCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGata                                                       >  1:5830341/1‑68 (MQ=255)          gCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGata                                                       <  1:359120/68‑1 (MQ=255)            acgacgTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATg                                                     >  1:4509713/1‑68 (MQ=255)             cgacgTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGa                                                    <  1:1807350/68‑1 (MQ=255)              gacgTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGaa                                                   <  1:3668544/68‑1 (MQ=255)               acgTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAac                                                  <  1:2869692/68‑1 (MQ=255)                cgTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAacc                                                 >  1:2286153/1‑67 (MQ=255)                  tGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACAcc                                               <  1:1378533/68‑1 (MQ=255)                   gctggctgGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACAGCg                                              <  1:2446151/68‑1 (MQ=255)                   gctggctgGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCg                                              <  1:3490825/68‑1 (MQ=255)                   gctggctgGCCTGACCGCGCGTGAAGCAAAAGGTCTGCGTATGCGTTCCGGTATCGATATGAACACCg                                              <  1:1482981/68‑1 (MQ=255)                    ctggctggCCTGACCGCGCGTGAAGCTAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGa                                             >  1:211143/1‑68 (MQ=255)                    ctggctggCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGa                                             <  1:5898781/68‑1 (MQ=255)                     tggcttgcCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGAc                                            <  1:6039161/68‑1 (MQ=255)                      ggctggcCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACt                                           <  1:4133927/68‑1 (MQ=255)                        ctggcCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTac                                         >  1:1377908/1‑68 (MQ=255)                           gcCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACg                                      >  1:82524/1‑68 (MQ=255)                           gcCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACg                                      <  1:2603234/68‑1 (MQ=255)                           gcCTGACCGCGCGTGAAGCAAAAGTGCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACg                                      <  1:5281829/68‑1 (MQ=255)                             cTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCt                                    <  1:3562083/68‑1 (MQ=255)                              tGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCta                                   <  1:324539/68‑2 (MQ=255)                              tGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTg                                   <  1:2853064/68‑1 (MQ=255)                              tGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTg                                   <  1:172273/68‑1 (MQ=255)                               gACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACCCGCTgg                                  >  1:1256499/1‑68 (MQ=255)                                aCCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGga                                 >  1:5456663/1‑68 (MQ=255)                                aCCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGga                                 <  1:4190373/68‑1 (MQ=255)                                 ccGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGgaa                                >  1:1613385/1‑68 (MQ=255)                                      cgTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACA‑CGACTACACGCTGGAAGAAGTg                          >  1:4951517/1‑68 (MQ=255)                                       gTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTg                          <  1:2787092/68‑1 (MQ=255)                                       gTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTg                          <  1:820174/68‑1 (MQ=255)                                       gTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTg                          <  1:881922/68‑1 (MQ=255)                                       gTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTg                          <  1:2838936/68‑1 (MQ=255)                                       gTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTg                          <  1:3153428/68‑1 (MQ=255)                                       gTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTg                          <  1:3829130/68‑1 (MQ=255)                                        tGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTgg                         <  1:4268439/68‑1 (MQ=255)                                        tGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTgg                         <  1:120340/68‑1 (MQ=255)                                         gAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTggg                        <  1:4497878/68‑1 (MQ=255)                                                aaGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAg                 <  1:204924/68‑1 (MQ=255)                                                 aGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGt                <  1:531602/68‑1 (MQ=255)                                                 aGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGt                <  1:1265089/68‑1 (MQ=255)                                                   ttCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTc              >  1:4872459/1‑68 (MQ=255)                                                     cTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGa            <  1:2115320/68‑1 (MQ=255)                                                       gCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACg          >  1:5369960/1‑68 (MQ=255)                                                            tGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTAcc     >  1:5562944/1‑68 (MQ=255)                                                            tGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTAcc     >  1:4091095/1‑68 (MQ=255)                                                              cGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAACCAGTTCGACGTTACCcg   >  1:5310426/1‑68 (MQ=255)                                                              cGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCcg   >  1:4051522/1‑68 (MQ=255)                                                              cGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGT‑GGTAAACACTTACACGTTTCCcgc  >  1:2718559/1‑68 (MQ=255)                                                                  |                                                                 TGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGC  >  CP009273/3208028‑3208157

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑