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%	136.2 / NA	41	F563S (TTC→TCC)	rpoD	RNA polymerase, sigma 70 (sigma D) factor
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (12/29);  total (12/29)

CGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCG  >  CP009273/3208030‑3208156                                                                |                                                                cgGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGt                                                             <  1:3967438/68‑1 (MQ=255) cgGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGt                                                             <  1:2059468/68‑1 (MQ=255)   gCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTAt                                                           >  1:4018832/1‑68 (MQ=255)   gCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTAt                                                           <  1:663405/68‑1 (MQ=255)      aCGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAATAGTTCTGCGTATGCGTTCCGGTATCGa                                                        <  1:159443/68‑1 (MQ=255)      aCGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGa                                                        <  1:2283958/68‑1 (MQ=255)        gCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGata                                                      <  1:2279051/68‑1 (MQ=255)        gCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGata                                                      <  1:5398762/68‑1 (MQ=255)        gCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGata                                                      <  1:9414/68‑1 (MQ=255)          acgacgTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATg                                                    <  1:766761/68‑1 (MQ=255)             acgTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAac                                                 >  1:5309662/1‑68 (MQ=255)              cgTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAaca                                                >  1:5427708/1‑68 (MQ=255)                tGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACAcc                                              >  1:2224295/1‑68 (MQ=255)                 gctggctgGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCg                                             <  1:3564305/68‑1 (MQ=255)                  ctggctggCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGa                                            <  1:28637/68‑1 (MQ=255)                    ggctggcCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACt                                          >  1:4806753/1‑68 (MQ=255)                     gctggcCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGCCTa                                         >  1:33907/1‑68 (MQ=255)                        ggcCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTacac                                      <  1:2399880/68‑1 (MQ=255)                         gcCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACg                                     <  1:5321623/68‑1 (MQ=255)                         gcCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACg                                     <  1:1470678/68‑1 (MQ=255)                         gcCTGACAGCGCGGGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACg                                     <  1:4867084/68‑1 (MQ=255)                           cTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCt                                   >  1:4638573/1‑68 (MQ=255)                            tGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTg                                  <  1:4745942/68‑1 (MQ=255)                             gACCGCGCGTGAAGCATAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTgg                                 <  1:4778090/68‑1 (MQ=255)                             gACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTgg                                 <  1:19665/68‑1 (MQ=255)                             gACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTgg                                 <  1:3969362/68‑1 (MQ=255)                             gACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTgg                                 <  1:4310707/68‑1 (MQ=255)                                  cgcgTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGgaagaa                            <  1:4579981/68‑1 (MQ=255)                                     gTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTg                         <  1:3712855/68‑1 (MQ=255)                                     gTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGAAATGAACACCGACTACACGCTGGAAGAAGTg                         <  1:3480017/68‑1 (MQ=255)                                     gTGAAGCAAAAGTTCTGCGTATGCGGTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTg                         <  1:136237/68‑1 (MQ=255)                                              aaGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAg                <  1:3008168/68‑1 (MQ=255)                                               aGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGATGAAGTGGGTAAACAGt               >  1:2156391/1‑68 (MQ=255)                                               aGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGt               <  1:1990752/68‑1 (MQ=255)                                                 ttCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTc             >  1:231875/1‑68 (MQ=255)                                                   cTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGa           <  1:4118679/68‑1 (MQ=255)                                                   cTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACACTTCGa           <  1:3981333/68‑1 (MQ=255)                                                         aTGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTAc     <  1:917497/68‑1 (MQ=255)                                                            cGTTCCGGTATCGATATGAACACTGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCcg  >  1:2028284/1‑68 (MQ=255)                                                            cGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCcg  >  1:3894569/1‑68 (MQ=255)                                                            cGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCcg  >  1:1929199/1‑68 (MQ=255)                                                                |                                                                CGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCG  >  CP009273/3208030‑3208156

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑