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%	166.8 / NA	46	F563S (TTC→TCC)	rpoD	RNA polymerase, sigma 70 (sigma D) factor
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (18/28);  total (18/28)

CTGGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCGTTCTGAAGTGCTGCG  >  CP009273/3207960‑3208228                                                                                                                                      |                                                                                                                                        cTGGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTa                                                                                                                                    <  1:1108207/139‑1 (MQ=255) cTGGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTa                                                                                                                                    <  1:547893/139‑1 (MQ=255)   gggggATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATc                                                                                                                                  <  1:508815/139‑1 (MQ=255)    ggggATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCg                                                                                                                                 >  1:107376/1‑139 (MQ=255)         tttCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATg                                                                                                                            >  1:2671622/1‑139 (MQ=255)           tCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGat                                                                                                                               >  1:315330/1‑134 (MQ=255)                 aGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCg                                                                                                                     >  1:706075/1‑138 (MQ=255)                     tACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTa                                                                                                                 <  1:4338825/138‑1 (MQ=255)                       ccaccCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTacac                                                                                                              <  1:495711/139‑1 (MQ=255)                           ccTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGAAAAAGTTCTGCGTATGCGTTCCGGTATCGat                                                                                                                               <  1:3755525/118‑1 (MQ=255)                            cTCGAGCTGCCACTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTgg                                                                                                         <  1:2913001/139‑1 (MQ=255)                                   tGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGaagaag                                                                                                   <  1:1221756/138‑1 (MQ=255)                                     ccGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCg                                                                                                                     >  1:1584804/1‑118 (MQ=255)                                       gCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCAGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGt                                                                                              >  1:1202777/1‑139 (MQ=255)                                          cgcttCTGCCACCACCGACAGCCTGCTTGCGGCAACGCACGACGTGCTGGCTGGCCTGCCCGCGCGTGAAGCAAAAGTTCTGCGTCTGCGTTCCCGTCTCGATATGAATACCGACTACCCGATGGAAGAAGTGGGTaaa                                                                                           <  1:4045868/136‑1 (MQ=255)                                              tCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGt                                                                                       <  1:2255255/139‑1 (MQ=255)                                                  cGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCg                                                                                    >  1:4218759/1‑138 (MQ=255)                                                     ccaccGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGt                                                                                >  1:1935553/1‑139 (MQ=255)                                                     ccaccGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGt                                                                                <  1:1459150/139‑1 (MQ=255)                                                       accGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGt                                                                                                  <  1:3530368/119‑1 (MQ=255)                                                                cggcgtgcgGCAACGCACGACGGGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTGCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAAc                                                                     <  1:3833893/137‑1 (MQ=255)                                                                cTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGa                                                                       <  1:2049022/137‑1 (MQ=255)                                                                cTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGa                                                                       <  1:3078823/137‑1 (MQ=255)                                                                cTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGa                                                                       <  1:3519512/137‑1 (MQ=255)                                                                 tgcgtgcgGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAg                                                                                        >  1:1359179/1‑119 (MQ=255)                                                                   cgtgcgGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTa                                                                                                                                    >  1:3637537/1‑73 (MQ=255)                                                                   cgtgcgGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGGATCGATATGAACCCCGACTACCCGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACgaa                                                                  >  1:2967613/1‑137 (MQ=255)                                                                          cAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATc                                                                                                                                  <  1:1422504/68‑1 (MQ=255)                                                                             cGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGAt                                                        <  1:447117/139‑1 (MQ=255)                                                                              gCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATc                                                                                                                                  <  1:1113354/64‑1 (MQ=255)                                                                                    cgTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGGATGCGTTCCGGTATCGATATGAaca                                                                                                                        >  1:3593564/1‑68 (MQ=255)                                                                                     gTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGGATCGATATGAACACCGACTACACGCTGGAAGAAGTTGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATcgaagcga                                                <  1:795486/139‑1 (MQ=255)                                                                                      tGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATcgaagcgaa                                               >  1:437693/1‑139 (MQ=255)                                                                                        ctggctggCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAaca                                                                                                                        >  1:3285017/1‑64 (MQ=255)                                                                                               gcCTGACCGCGCGTGAAGCAAAAGTTCTGCGGATGCGTTCCGGTCTCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTga                                       >  1:3352033/1‑137 (MQ=255)                                                                                                       gcgcgTGAAGCAAAAGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGc                              <  1:506579/139‑1 (MQ=255)                                                                                                       gagcgTGAAGCAAAAGTTCTGCTGATGCGTTCCGGTATCGATATGAACCCCGACTCCACGCTGGAAGAAGTGGGTAAACAGTTCGACTTTACCCGCCAACGTATCCCTCAGATCGAAGCGAAGGCGCTGCGCAAACTGc                              <  1:3571894/137‑1 (MQ=255)                                                                                                                  aaaaGTTCTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAg                    <  1:2878350/138‑1 (MQ=255)                                                                                                                         cTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCGTTCTg            <  1:499023/139‑1 (MQ=255)                                                                                                                         cTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCGTTCTg            <  1:2838640/139‑1 (MQ=255)                                                                                                                         cTGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCGTTCTg            >  1:851623/1‑139 (MQ=255)                                                                                                                          tGCGTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCGTTCTGa           >  1:1759606/1‑139 (MQ=255)                                                                                                                             gTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGCCGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCGTTCTGAAg         <  1:3023702/138‑1 (MQ=255)                                                                                                                             gTATGCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCGTTCTGAAg         <  1:706525/138‑1 (MQ=255)                                                                                                                                 gCGTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCGTTCTGAAGtgct     >  1:1033489/1‑138 (MQ=255)                                                                                                                                   gTTCCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCGTTCTGAAGTGCTGCg  <  1:1180532/139‑1 (MQ=255)                                                                                                                                      |                                                                                                                                        CTGGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCGTTCTGAAGTGCTGCG  >  CP009273/3207960‑3208228

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑