Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,867,455	G→A	Q33* (CAG→TAG)	rpoS ←	RNA polymerase sigma factor RpoS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,867,455	0	G	A	100.0%	60.0 / NA	25	Q33* (CAG→TAG)	rpoS	RNA polymerase sigma factor RpoS
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (12/13);  total (12/13)

AGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTGTTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGT  >  NC_000913/2867211‑2867700                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                                      aGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTctac                                                                                                                                                                                                                                                 <  1:137425/251‑1 (MQ=255)                                                    ctctCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAAcc                                                                                                                                                                                                                           >  2:269115/1‑222 (MQ=255)                                                    ctctCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAAcc                                                                                                                                                                                                                           <  1:269115/222‑1 (MQ=255)                                                     tctcGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCt                                                                                                                                                                                             >  1:66421/1‑251 (MQ=255)                                                        cGATCATACTGCGGCGAGAGGCGACAGCTCCACGCAGTGCGCGACTCGCAAAATAAACTTTTTCTTCGGCCGTTAACAGTGGTGAATCACCAATCTCACCAGGGTAAAGCTGAGTCGCGTCCATCACACGCTTTGTGGCTCTCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACGCCGTTCTCATCAAATTCCGCTTCTTCa                                                                                                                                                                                          <  2:197316/251‑1 (MQ=255)                                                            catcCGGCGGCGAGAGGCGACATCTCGACGCAGTTCGCGACGCGCAAAATGAACTTCTTCTTCGGCCGTTAACAGTGGAGAATACCCAATCTCACCACGGTAGAGCTGAGTCGCGTCCAACACACGCTGTGTAGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTACGGCCTTTTCGTCCAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCAttt                                                                                                                                                                                       >  2:208839/1‑250 (MQ=255)                                                             atcCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGATTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGTGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCACAACTCCGTTCTCATCAAATTCCGCATCTTCATTTaa                                                                                                                                                                                     <  2:7841/251‑1 (MQ=255)                                                                   cggcgAGAGACGACATCCCCACGCAGTGCGCGCCGAGCAAAATAACCTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCACACAAAGGTAAAGCTGAGTCGCGTCCAAAACACGCTGTGTGGCTCCCTGCGATAACAGATCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTAATAAGGCCTTTTCGTCACAACACTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATg                                                                                                                                                                               >  2:177740/1‑251 (MQ=255)                                                                                          cAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTc                                                                                                                                                         >  2:291458/1‑250 (MQ=255)                                                                                          cAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCa                                                                                                                                                        <  1:289777/251‑1 (MQ=255)                                                                                                        cAAAATAAACGTCGTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATGCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTa                                                                                                                                          <  2:92603/251‑1 (MQ=255)                                                                                                              aaaCTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAAGCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCATCTTATTCTGACTCATAAGGTGGCTCCTACCCGTg                                                                                                                                    <  1:117508/251‑1 (MQ=255)                                                                                                                        ttcGGCCGTTAACAGGGGTGAAGAACCCATCTCACCAAGGTAAAGCTGAGGCGAGCACAACACACGCTGTGTGGCTCCCTGCGATAACAGTGCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTAGTCTACTAAGTCCTTTTCGTCAAAAACCTCAACTCCGTGCTCATCAAATTCCGCATGTTCATTTAAATCATGTACTTGCATCTTATTCTGACTCATATGGGTGCTCCTACCCTGGATCCCTTGa                                                                                                                           <  2:128513/250‑1 (MQ=255)                                                                                                                         tcGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGa                                                                                                                           <  1:291458/249‑1 (MQ=255)                                                                                                                         tcGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACg                                                                                                                         >  1:140251/1‑251 (MQ=255)                                                                                                                                        ggtgAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTTCTAAGGCCTAGTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTTCTTCTGTTCATTTAAATCATGCACTTTCAGCGTCTGCTGACGCATAAGGGGGCTCCTTCCCGTGATCCCTTGACGGAACATTCAAGCaaa                                                                                                          <  1:208839/251‑1 (MQ=255)                                                                                                                                          tgAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTACTACCCGTGATCCCTTGACGGAACATTCAAGCaaa                                                                                                          >  1:161601/1‑249 (MQ=255)                                                                                                                                             aTAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCt                                                                                                     >  1:76943/1‑251 (MQ=255)                                                                                                                                               aaCCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTACGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCAGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAACGCCTgg                                                                                                   >  2:29001/1‑251 (MQ=255)                                                                                                                                                                              gTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACg                                                                    >  2:50349/1‑251 (MQ=255)                                                                                                                                                                                              gtgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAAt                                                                        <  1:82695/231‑1 (MQ=255)                                                                                                                                                                                              gtgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAAt                                                                        >  2:82695/1‑231 (MQ=255)                                                                                                                                                                                                                                   cGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTg               >  2:262179/1‑251 (MQ=255)                                                                                                                                                                                                                                             gggTTCCTATTCTACTAAGGCCTGTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACACATAAGGTGGCGCCTGCCCGTGATCCCTTGACGGAACATTCAATCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGCTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTcc     <  2:161601/251‑1 (MQ=255)                                                                                                                                                                                                                                                 tCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACGCCGTTCTCATCAAATGCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGGTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGt  <  2:124215/250‑1 (MQ=255)                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                                      AGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTGTTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCGGT  >  NC_000913/2867211‑2867700

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑