Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	3,207,739	A→C	100%	D445A (GAT→GCT)	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	3,207,739	0	A	C	100.0%	112.3 / NA	32	D445A (GAT→GCT)	rpoD	RNA polymerase, sigma 70 (sigma D) factor
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (17/15);  total (17/15)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CGAAAGCCCGCCGTGCGAAGAAAGAGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTATGCTGATGCCGGAAGACAAGATCCGCAAAGTGCTGAAGATCGCCAAAGAGCCAATCTCCATGGAAACGCCGATCGGTGATGATGAAGATTCGCATCTGGGGGATTTCATCGAGGAT‑ACCACCCTCGAGCTGCCGCTGGATT  >  CP009273/3207514‑3208005                                                                                                                                                                                                                                  |                                                                                                                                                                                                                                                                            cGAAAGCCCGCCGTGCGAAGAAAGAGATGGTTGAAGCGAACTTACGTATGGTTATTTCTATCGCTAAGAAATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATcaac                                                                                                                                                                                                                            <  1:246374/275‑1 (MQ=255)                                   aGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAgg                                                                                                                                                                                                                                                                        >  1:77262/1‑197 (MQ=255)                                       aaCTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGgcgcg                                                                                                                                                                                                                                                                    <  2:77262/197‑1 (MQ=255)                                                   gTTATTTCTATCGCTAAGAAATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGgcgcg                                                                                                                                                                                                                                                                    >  2:141752/1‑185 (MQ=255)                                                       tttCTATCGCTAAGAAATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCACGCAcc                                                                                                                                                                                                                                                                <  1:141753/185‑1 (MQ=255)                                                                               aCCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGgcgc                                                                                                                                                                                                                                                                     >  2:108207/1‑156 (MQ=255)                                                                                   tGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCAc                                                                                                                                                                                                                                                                 <  1:108207/156‑1 (MQ=255)                                                                                                                                                       aaTACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGgcgc                                                                                                                                                                                                                                                                     >  2:173694/1‑84 (MQ=255)                                                                                                                                                           ccgccgTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCAc                                                                                                                                                                                                                                                                 <  1:173696/84‑1 (MQ=255)                                                                                                                                                                          gTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGt                                                                                                                                                                                                                                                  >  2:81371/1‑84 (MQ=255)                                                                                                                                                                             ctcCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAgg                                                                                                                                                                                                                                                                        >  1:170077/1‑59 (MQ=255)                                                                                                                                                                              tcCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCat                                                                                                                                                                                                                                              <  1:81371/84‑1 (MQ=255)                                                                                                                                                                              tcCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCACGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTATGCTGATGCCGGAAGACAAGATCCGCAAAGTGCTGAAGATCGCCAAAGAGCCCATCTCCATGGAAACGCCGACCGGTGATGATGAAGATTCGCATCt                                               >  1:40532/1‑275 (MQ=255)                                                                                                                                                                                 aCCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGgcgcg                                                                                                                                                                                                                                                                    <  2:170076/59‑1 (MQ=255)                                                                                                                                                                                     aCGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGa                                                                                                                                                     >  2:229677/1‑166 (MQ=255)                                                                                                                                                                                        cAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCa                                                                                                                                                                                                     >  1:184718/1‑115 (MQ=255)                                                                                                                                                                                         aaCCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGt                                                                                                                                                 <  1:229680/166‑1 (MQ=255)                                                                                                                                                                                            cTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGAtg                                                                                                                                                                                                 <  2:184715/115‑1 (MQ=255)                                                                                                                                                                                             tggtggATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGt                                                                                                                                                                                                                                                  >  1:28608/1‑65 (MQ=255)                                                                                                                                                                                                tggATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGgcgcg                                                                                                                                                                                                                                                                    >  2:413388/1‑44 (MQ=255)                                                                                                                                                                                                 ggATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCat                                                                                                                                                                                                                                              <  2:28608/65‑1 (MQ=255)                                                                                                                                                                                                    tCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCAcc                                                                                                                                                                                                                                                                <  1:413397/44‑1 (MQ=255)                                                                                                                                                                                                     ccGTCAGGCGATCACCCGCTCTATCGCGGCTCAGgcgc                                                                                                                                                                                                                                                                     >  2:47110/1‑38 (MQ=255)                                                                                                                                                                                                        tCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAAc                                                                                                                                                            >  1:88952/1‑140 (MQ=255)                                                                                                                                                                                                         cAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCAc                                                                                                                                                                                                                                                                 <  1:47110/38‑1 (MQ=255)                                                                                                                                                                                                         cAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCCCa                                                                                                                                                                                                                     >  1:216994/1‑82 (MQ=255)                                                                                                                                                                                                            gCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGc                                                                                                                                                        <  2:88952/140‑1 (MQ=255)                                                                                                                                                                                                             cGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCg                                                                                                                                                                                                                 <  2:216991/82‑1 (MQ=255)                                                                                                                                                                                                                          tATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCg                                                                                                                                                                                                                 >  1:257083/1‑69 (MQ=255)                                                                                                                                                                                                                          tATCGCGGCCCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACCAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGCCGCCGGAAGAACTGGCTGAACGTATGCTGATGCCGGAAGACAAGAGTCGCAAAGTGCTGAAGATGGCGAAAGAACCAATCTCAATGGAAACGCCGAACGGAGATGAAGAAGATTTGAATCAGGGGGATGTCATGGGGGATAACCACGC‑CGNNCTGGCACTGGAtn  >  2:375912/1‑274 (MQ=255)                                                                                                                                                                                                                             cgcgGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTg                                                                                                                                                                                                                                       >  1:404932/1‑44 (MQ=255)                                                                                                                                                                                                                              gcgGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTAtt                                                                                                                                                                                                             <  2:257079/69‑1 (MQ=255)                                                                                                                                                                                                                                  |                                                                                                                                                                                                                                                                            CGAAAGCCCGCCGTGCGAAGAAAGAGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTATGCTGATGCCGGAAGACAAGATCCGCAAAGTGCTGAAGATCGCCAAAGAGCCAATCTCCATGGAAACGCCGATCGGTGATGATGAAGATTCGCATCTGGGGGATTTCATCGAGGAT‑ACCACCCTCGAGCTGCCGCTGGATT  >  CP009273/3207514‑3208005

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑