Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_pgi	2,867,401	Δ1 bp	coding (151/993 nt)	rpoS ←	RNA polymerase, sigma S (sigma 38) factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_pgi	2,867,401	0	T	.	100.0%	91.3 / NA	20	coding (151/993 nt)	rpoS	RNA polymerase, sigma S (sigma 38) factor
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (11/9);  total (11/9)

TCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTGTTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCAT  >  NC_000913_3_pae_pgi/2867263‑2867526                                                                                                                                           |                                                                                                                              tctcGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTG‑GGCTCCCTGCGa                                                                                                                   <  1:14716/150‑1 (MQ=255)  ctcGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTG‑GGCTCCCTGCGAt                                                                                                                  >  2:10991/1‑150 (MQ=255)          tcCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTCACAGTGGTGAATAACCAATCTCTCCAAGGTAAATTTTAGTCGCGTCCAACACACGCTGTG‑GGCTCCCTGCGATAACAGTTc                                                                                                          >  3:36122/1‑150 (MQ=255)                                         tGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTG‑GGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTcc                                                                           >  2:154270/1‑150 (MQ=255)                                           cgcgACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTG‑GGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTg                                                                         <  1:14312/150‑1 (MQ=255)                                           cgcgACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTG‑GGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTg                                                                         <  2:163813/150‑1 (MQ=255)                                             cgACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATATCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTG‑GGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTGtt                                                                       >  4:48864/1‑150 (MQ=255)                                              gACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTG‑GGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTGTTc                                                                      >  1:173887/1‑150 (MQ=255)                                              gACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTG‑GGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTGTTc                                                                      >  2:164711/1‑150 (MQ=255)                                                cgcgCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTG‑GGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTGTTcta                                                                    >  3:32239/1‑150 (MQ=255)                                                                 ttcttcGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTG‑GGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTGTTCTACTAAGGCCTTTTCGTCa                                                   >  1:46247/1‑150 (MQ=255)                                                                     tcGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTG‑GGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTGTTCTACTAAGGCCTTTTCGTCaaaaa                                               <  1:10991/150‑1 (MQ=255)                                                                                cAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTG‑GGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTGTTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCg                                    <  1:121136/150‑1 (MQ=255)                                                                                       gAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTG‑GGCTCCCTGCGATAACAGt                                                                                                            <  4:31358/71‑1 (MQ=255)                                                                                       gAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTG‑GGCTCCCTGCGATAACAGt                                                                                                            >  3:31358/1‑71 (MQ=255)                                                                                       gAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTG‑GGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTGTTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtcat                             <  4:36122/150‑1 (MQ=255)                                                                                       gAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTG‑GGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTGTTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtcat                             >  2:113567/1‑150 (MQ=255)                                                                                                                  tGAGTCGCGTCCAACACACGCTGTG‑GGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTGTTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCAt  <  1:164711/150‑1 (MQ=255)                                                                                                                                   acGCTGTG‑GGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTGCTGTTCTACTAAGGCCTTTTCGt                                                     >  1:113711/1‑82 (MQ=255)                                                                                                                                   acGCTGTG‑GGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTGTTCTACTAAGGCCTTTTCGt                                                     <  2:113711/82‑1 (MQ=255)                                                                                                                                           |                                                                                                                              TCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTGTTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCAT  >  NC_000913_3_pae_pgi/2867263‑2867526

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑