Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,213,531	T→G	I162S (ATC→AGC)	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	3,213,531	0	T	G	100.0%	123.1 / NA	33	I162S (ATC→AGC)	rpoD	RNA polymerase, sigma 70 (sigma D) factor
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (17/16);  total (17/16)

GACTGACCCGGTACGCATGTACATGCGTGAAATGGGCACCGTTGAACTGTTGACCCGCGAAGGCGAAATTGACATCGCTAAGCGTATTGAAGACGGGATCAACCAGGTTCAATGCTCCGTTGCTGAATATCCGGAAGCGATCACCTATCTGCTGGAACAGTACGATCGTGTTGAAGCAGAAGAAGCGCGTCTGTCCGATCTGATCACCGGCTTTGTTGACCCGAACGCAGAAGAAGATCTGGCACCTACCGCCACTCACGTCGGTTCTGAGCTTTCCCAGGAAGATCTGGACGATGACGAAGATGAAGACGAAGAAGATGGCGATGACGACAGCGCCGATGATGACAACAGCATCGACCCGGAACTGGCTCGCGAAAAATTTGCGGAACTACGCGCTCAGTACGTTGTAACGCGTGACACCATCAAAG  >  NC_000913/3213328‑3213755                                                                                                                                                                                                            |                                                                                                                                                                                                                                 gACTGACCCGGTACGCATGTACATGCGTGAAATGGGCACCGTTGAACTGTTGACCCGCGAAGGCGAAATTGACATCGCTAAGCGTATTGAAGACGGGATCAACCAGGTTCAATGCTCCGTTGCTGAATATCCGGAAGCGATCACCTATCTGCTGGAACAGTACGATCGTGTTGAAGCAGAAGAAGCGCGTCTGTCCGATCTGAGCACCgg                                                                                                                                                                                                                            <  2:321452/210‑1 (MQ=255)                 aTGTACATGCGTGAAATGGGCACCGTTGAACTGTTGACCCGCGAAGGCGAAATTGACATCGCTAAGCGTATTGAAGACGGGATCAACCAGGTTCAATGCTCCGTTGCTGAATATCCGGAAGCGATCACCTATCTGCTGGAACAGTACGATCGTGTTGAAGCAGAAGAAGCGCGTCTGTCCGATCTGAGCACCGGCTTTGTTGACCCGAACGCAGAAGAAGATCTGGCACCTACCGCCACt                                                                                                                                                                              <  1:27072/240‑1 (MQ=255)                       aTGCGTGAAATGGGCACCGTTGAACTGTTGACCCGCGAAGGCGAAATTGACATCGCTAAGCGTATTGAAGACGGGATCAACCAGGTTCAATGCTCCGTTGCTGAATATCCGGAAGCGATCACCTATCTGCTGGAACAGTACGATCGTGTTGAAGCAGAAGAAGCGCGTCTGTCCGATCTGAGCACCGGCTTTGTTGACCCGAACGCAGAAGAAGATCTGGCACCTACCGCCACTCACGt                                                                                                                                                                         <  2:322948/239‑1 (MQ=255)                                        cGTTGAACTGTTGACCCGCGAAGGCGAAATTGACATCGCTAAGCGTATTGAAGACGGGATCAACCAGGTTCAATGCTCCGTTGCTGAATATCCGGAAGCGATCACCTATCTGCTGGAACAGTACGATCGTGTTGAAGCAGAAGAAGCGCGTCTGTCCGATCTGAGCACCGGCTTTGTTGACCCGAACGCAGAAGAAGATCTGGCACCTACCGCCACTCACGTCGGTTCTGAGCTTTccc                                                                                                                                                        >  1:335934/1‑239 (MQ=255)                                                  ttGACCCGCGAAGGCGAAATTGACATCGCTAAGCGTATTGAAGACGGGATCAACCAGGTTCAATGCTCCGTTGCTGAATATCCGGAAGCGATCACCTATCTGCTGGAACAGTACGATCGTGTTGAAGCAGAAGAAGCGCGTCTGTCCGATCTGAGCACCGGCTTTGTTGACCCGAACGCAGAAGAAGATCTGGCACCTACCGCCACTCACGTCGGTTCTGAGCTTTCCCAGGAAGATCTg                                                                                                                                             >  1:300525/1‑240 (MQ=255)                                                            aaGGCGAAATTGACATCGCTAAGCGTATTGAAGACGGGATCAACCAGGTTCAATGCTCCGTTGCTGAATATCCGGAAGCGATCACCTATCTGCTGGAACAGTACGATCGTGTTGAAGCAGAAGAAGCGCGTCTGTCCGATCTGAGCACCGGCTTTGTTGACCCGAACGCAGAAGAAGATCTGGCACCTACCGCCACTCACGTCGGTTCTGAGCTTTCCCAGGAAGATCTGGACGATGACg                                                                                                                                   >  1:51118/1‑240 (MQ=255)                                                                cGAAATTGACATCGCTAAGCGTATTGAAGACGGGATCAACCAGGTTCAATGCTCCGTTGCTGAATATCCGGAAGCGATCACCTATCTGCTGGAACAGTACGATCGTGTTGAAGCAGAAGAAGCGCGTCTGTCCGATCTGAGCACCGGCTTTGTTGACCCGAACg                                                                                                                                                                                                           <  1:135249/164‑1 (MQ=255)                                                                cGAAATTGACATCGCTAAGCGTATTGAAGACGGGATCAACCAGGTTCAATGCTCCGTTGCTGAATATCCGGAAGCGATCACCTATCTGCTGGAACAGTACGATCGTGTTGAAGCAGAAGAAGCGCGTCTGTCCGATCTGAGCACCGGCTTTGTTGACCCGAACGCAGAAGAAGATCTGGCACCTACCg                                                                                                                                                                                   <  1:223203/188‑1 (MQ=255)                                                                  aaaTTGACATCGCTAAGCGTATTGAAGACGGGATCAACCAGGTTCAATGCTCCGTTGCTGAATATCCGGAAGCGATCACCTATCTGCTGGAACAGTACGATCGTGTTGAAGCAGAAGAAGCGCGTCTGTCCGATCTGAGCACCGGCTTTGTTGACCCGAACGCAGAAGAAGATCTGGCACCTACCGCCACTCACGTCGGTTCTGAGCTTTCCCAGGAAGATCTGGACGATGACGAAGAt                                                                                                                              <  1:321953/239‑1 (MQ=255)                                                                              cTAAGCGTATTGAAGACGGGATCAACCAGGTTCAATGCTCCGTTGCTGAATATCCGGAAGCGATCACCTATCTGCTGGAACAGTACGATCGTGTTGAAGCAGAAGAAGCGCGTCTGTCCGATCTGAGCACCGGCTTTGTTGACCCGAACGCAGAAGAAGATCTg                                                                                                                                                                                             <  2:85435/164‑1 (MQ=255)                                                                                    gTATTGAAGACGGGATCAACCAGGTTCAATGCTCCGTTGCTGAATATCCGGAAGCGATCACCTATCTGCTGGAACAGTACGATCGTGTTGAAGCAGAAGAAGCGCGTCTGTCCGATCTGAGCACCGGCTTTGTTGACCCGAACGCAGAAGAAGATCTGGCACCTACCGCCACTCACGTCGGTTCTGAGCTTTCCCAGGAAGATCTGGACGATGACGAAGATGAAGACGAAGAAGATGGc                                                                                                            <  1:134173/239‑1 (MQ=255)                                                                                                    cAACCAGGTTCAATGCTCCGTTGCTGAATATCCGGAAGCGATCACCTATCTGCTGGAACAGTACGATCGTGTTGAAGCAGAAGAAGCGCGTCTGTCCGATCTGAGCACCGGCTTTGTTGACCCGAACGCAGAAGAAGATCTGGCACCTACCGCCACTCACGTCGGTTCTGAGCTTTCCCAGGAAGATCTGGACGATGACGAAGATGAAGACGAAGAAGATGGCGATGACGACAGCGCCg                                                                                            <  1:60617/239‑1 (MQ=255)                                                                                                     aaCCAGGTTCAATGCTCCGTTGCTGAATATCCGGAAGCGATCACCTATCTGCTGGAACAGTACGATCGTGTTGAAGCAGAAGAAGCGCGTCTGTCCGATCTGAGCACCGGCTTTGTTGACCCGAACGCAGAAGAAGATCTGGCACCTACCGCCACTCACGTCGGTTCTGAGCTTTCCCAGGAAGATCTGGACGATGACGAAGATGAAGACGAAGAAGATGGCGATGACGACAGCGCCgat                                                                                          <  1:261756/240‑1 (MQ=255)                                                                                                               aaTGCTCCGTTGCTGAATATCCGGAAGCGATCACCTATCTGCTGGAACAGTACGATCGTGTTGAAGCAGAAGAAGCGCGTCTGTCCGATCTGAGCACCGGCTTTGTTGACCCGAACGCAGAAGAAGATCTGGCACCTACCGCCACTCACGTCGGTTCTGAGCTTTCCCAGGAAGATCTGGACGATGACGAAGATGAAGACGAAGAAGATGGCGATGACGACAGCGCCGATGATGacaac                                                                                 >  1:140733/1‑239 (MQ=255)                                                                                                                                       aaGCGATCACCTATCTGCTGGAACAGTACGATCGTGTTGAAGCAGAAGAAGCGCGTCTGTCCGATCTGAGCACCGGCTTTGTTGACCCGAACGCAGAAGAAGATCTGGCACCTACCGCCACTCACGTCGGTTCTGAGCTTTCCCAGGAAGATCTGGACGATGACGAAGATGAAGACGAAGAAGATg                                                                                                              <  2:176213/186‑1 (MQ=255)                                                                                                                                        aGCGATCACCTATCTGCTGGAACAGTACGATCGTGTTGAAGCAGAAGAAGCGCGTCTGTCCGATCTGAGCACCGGCTTTGTTGACCCGAACGCAGAAGAAGATCTGGCACCTACCGCCACTCACGTCGGTTCTGAGCTTTCCCAGGAAGATCTGGACGATGACGAAGATGAAGACGAAGAAGATGGCGATGACGACa                                                                                                  >  2:253868/1‑197 (MQ=255)                                                                                                                                        aGCGATCACCTATCTGCTGGAACAGTACGATCGTGTTGAAGCAGAAGAAGCGCGTCTGTCCGATCTGAGCACCGGCTTTGTTGACCCGAACGCAGAAGAAGATCTGGCACCTACCGCCACTCACGTCGGTTCTGAGCTTTCCCAGGAAGATCTGGACGATGACGAAGATGAAGACGAAGAAGATGGCGATGACGACAGCGCCgatgat                                                                                       <  2:139696/208‑1 (MQ=255)                                                                                                                                                        ctgGAACAGTACGATCGTGTTGAAGCAGAAGAAGCGCGTCTGTCCGATCTGAGCACCGGCTTTGTTGACACGAACGCAGAAGAAGATCTGGCACCTACCGCCACTCACGTCGGTTCTGAGCTTTCCCAGGAAGATCTGGACGATGACGAAGATGAAGACGAAGAAGATGGCGATGACGACAGCGCCGATGATGACAACAGCATc                                                                           >  2:178183/1‑204 (MQ=255)                                                                                                                                                           gAACAGTACGATCGTGTTGAAGCAGAAGAAGCGCGTCTGTCTGATCTGAGCACCGGCTTTGTTGACCCGAACGCAGAAGAAGATCTGGCACCTACCGCCACTCACGTCGGTTCTGAGCTTTCCCAGGAAGATCTGGACGATGACGAAGATGAAGACGAAGAAGATGGCGATGACGACAGCGCCGATGATGACAACAGCATCGACCCGGAACTGGCTCGCGAAAAATTTGCGGAACTAcg                                     >  1:89714/1‑239 (MQ=255)                                                                                                                                                           gAACAGTACGATCGTGTTGAAGCAGAAGAAGCGCGTCTGTCCGATCTGAGCACCGGCTTTGTTGACCCGAACGCAGAAGAAGATCTGGCACCTACCGCCACTCACGTCGGTTCTGAGCTTTCCCAGGAAGATCTGGACGATGACGAAGATGAAGACGAAGAAGATGGCGATGACGACAGCGCCGATGATGACAACAGCATCGACCCGGAACTGGCTCGCGAAAAATTTGCGGAACTAcg                                     >  2:185484/1‑239 (MQ=255)                                                                                                                                                              cAGTACGATCGTGTTGAAGCAGAAGAAGCGCGTCTGTCCGATCTGAGCACCGGCTTTGTTGACCCGAACGCAGAAGAAGATCTGGCACCTACCGCCACTCACGTCGGTTCTGAGCTTTCCCAGGAAGATCTGGACGATGACGAAGATGAAGACGAAGAAGATGGCGATGACGACAGCGCCGATGATGACAACAGCATCGACCCGGAACTGGCTCGCGAAAAATTTGCGGAACTACgcgc                                  <  2:51117/239‑1 (MQ=255)                                                                                                                                                                gTACGATCGTGTTGAAGCAGAAGAAGCGCGTCTGTCCGATCTGAGCACCGGCTTTGTTGACCCGAACGCAGAAGAAGATCTGGCACCTACCGCCACTCACGTCGGTTCTGAGCTTTCCCAGGAAGATCTGGACGATGACGAAGATGAAGACGAAGAAGATGGCGATGACGACAGCGCCGATGATGACAACAGCATCGACCCGGAACTGGCTCGCGAAAAATTTGCGGAACTACGCGCTCa                               <  2:335923/240‑1 (MQ=255)                                                                                                                                                                 tACGATCGTGTTGAAGCAGAAGAAGCGCGTCTGTCCGATCTGAGCACCGGCTTTGTTGACCCGAACGCAGAAGAAGATCTGGCACCTACCGCCACTCACGTCGGTTCTGAGCTTTCCCAGGAAGATCTGGACGATGACGAAGATGAAGACGAAGAAGATGGCGATGACGACAGCGCCGATGATGACAACAGCATCGACCCGGAACTGGCTCGCGAAAAATTTGCGGAACTACGCGCTc                                >  2:254050/1‑238 (MQ=255)                                                                                                                                                                  aCGATCGTGTTGAAGCAGAAGAAGCGCGTCTGTCCGATCTGAGCACCGGCTTTGTTGACCCGAACGCAGAAGAAGATCTGGCACCTACCGCCACTCACGTCGGTTCTGAGCTTTCCCAGGAAGATCTGGACGATGACGAAGATGAAGACGAAGAAGATGGCGATGACGACAGCGCCGATGATGACAACAGCATCGACCCGGAACTGGCTCGCGAAAAATTTGCGGAACTACGCGCCCAg                              >  1:223313/1‑239 (MQ=255)                                                                                                                                                                    gATCGTGTTGAAGCAGAAGAAGCGCGTCTGTCCGATCTGAGCACCGGCTTTGTTGACCCGAACGCAGAAGAAGATCTGGCACCTACCGCCACTCACGTCGGTTCTGAGCTTTCCCAGGAAGATCTGGACGATGACGAAGATGAAGACGAAGAAGATGGCGATGACGACAGCGCCGATGATGACAACAGCATCGACCCGGAACTGGCTCGCGAAAAATTTGCGGAACTACGCGCTCAGTa                            <  2:316394/239‑1 (MQ=255)                                                                                                                                                                         tgtTGAAGCAGAAGAAGCGCGTCTGTCCGATCTGAGCACCGGCTTTGTTGACCCGAACGCAGAAGAAGATCTGGCACCTACCGCCACTCACGTCGGTTCTGAGCTTTCCCAGGAAGATCTGGACGATGACGAAGATGAAGACGAAGAAGATGGCGATGACGACAGCGCCGATGATGACAACAGCATCGACCCGGAACTGGCTCGCGAAAAATTTGCGGAACTACGCGCTCAGTACGTTGt                      >  1:328678/1‑240 (MQ=255)                                                                                                                                                                           ttGAAGCAGAAGAAGCGCGTCTGTCCGATCTGAGCACCGGCTTTGTTGACCCGAACGCAGAAGAAGATCTGGCACCTACCGCCACTCACGTCGGTTCTGAGCTTTCCCAGGAAGATCTGGACGATGACGAAGATGAAGACGAAGAAGATGGCGATGACGACAGCGCCGATGATGACAACAGCATCGACCCGGAACTGGCTCGCGAAAAATTTGCGGAACTACGCGCTCAGTACGTTGTaa                    >  2:117273/1‑240 (MQ=255)                                                                                                                                                                           ttGAAGCAGAAGAAGCGCGTCTGTCCGATCTGAGCACCGGCTTTGTTGACCCGAACGCAGAAGAAGATCTGGCACCTACCGCCACTCACGTCGGTTCTGAGCTTTCCCAGGAAGATCTGGACGATGACGAAGATGAAGACGAAGAAGATGGCGATGACGACAGCGCCGATGATGACAACAGCATCGACCCGGAACTGGCTCGCGAAAAATTTGCGGAACTACGCGCTCAGTACGTTGTaa                    >  1:66147/1‑240 (MQ=255)                                                                                                                                                                                gCAGAAGAAGCGCGTCTGTCCGATCTGAGCACCGGCTTTGTTGACCCGAACGCAGAAGAAGATCTGGCACCTACCGCCACTCACGTCGGTTCTGAGCTTTCCCAGGAAGATCTGGACGATGACGAAGATGAAGACGAAGAAGATGGCGATGACGACAGCGCCGATGATGACAACAGCATCGACCCGGAACTGGCTCGCGAAAAATTTGCGGAACTACGCGCTCAGTACGTTGTAAcgcg                >  1:351675/1‑239 (MQ=255)                                                                                                                                                                                            cgTCTGTCCGATCTGAGCACCGGCTTTGTTGACCCGAACGCAGAAGAAGATCTGGCACCTACCGCCACTCACGTCGGTTCTGAGCTTTCCCAGGAAGATCTGGACGATGACGAAGATGAAGACGAAGAAGATGGCGATGACGACAGCGCCGATGATGACAACAGCATCGACCCGGAACTGGCTCGCGAAAAATTTGCGGAACTACGCGCTCAGTACGTTGTAACGCGTGACACCATCaaa   >  1:142791/1‑240 (MQ=255)                                                                                                                                                                                              tCTGTCCGATCTGAGCACCGGCTTTGTTGACCCGAACGCAGAAGAAGATCTGGCACCTACCGCCACTCACGTCGGTTCTGAGCTTTCCCAGGAAGATCTGGACGATGACGAAGATGAAGACGAAGAAGATGGCGATGACGACAGCGCCGATGATGACAACAGCATCGACCCGGAACTGGCTCGCGAAAAATTTGCGGAACTACGCGCTCAGTACGTTGTAACGCGTGACACCa        >  2:102614/1‑233 (MQ=255)                                                                                                                                                                                              tCTGTCCGATCTGAGCACCGGCTTTGTTGACCCGAACGCAGAAGAAGATCTGGCACCTACCGCCACTCACGTCGGTTCTGAGCTTTCCCAGGAAGATCTGGACGATGACGAAGATGAAGACGAAGAAGATGGCGATGACGACAGCGCCGATGATGACAACAGCATCGACCCGGAACTGGCTCGCGAAAAATTTGCGGAACTACGCGCTCAGTACGTTGTAACGCGTGACACCATCAAAg  >  2:8906/1‑239 (MQ=255)                                                                                                                                                                                                  tCCGATCTGAGCACCGGCTTTGTTGACCCGAACGCAGAAGAAGATCTGGCACCTACCGCCACTCACGt                                                                                                                                                                         <  2:185488/68‑1 (MQ=255)                                                                                                                                                                                                            |                                                                                                                                                                                                                                 GACTGACCCGGTACGCATGTACATGCGTGAAATGGGCACCGTTGAACTGTTGACCCGCGAAGGCGAAATTGACATCGCTAAGCGTATTGAAGACGGGATCAACCAGGTTCAATGCTCCGTTGCTGAATATCCGGAAGCGATCACCTATCTGCTGGAACAGTACGATCGTGTTGAAGCAGAAGAAGCGCGTCTGTCCGATCTGATCACCGGCTTTGTTGACCCGAACGCAGAAGAAGATCTGGCACCTACCGCCACTCACGTCGGTTCTGAGCTTTCCCAGGAAGATCTGGACGATGACGAAGATGAAGACGAAGAAGATGGCGATGACGACAGCGCCGATGATGACAACAGCATCGACCCGGAACTGGCTCGCGAAAAATTTGCGGAACTACGCGCTCAGTACGTTGTAACGCGTGACACCATCAAAG  >  NC_000913/3213328‑3213755

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑