Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP009273	2,860,429	Δ1 bp	coding (482/993 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
*	CP009273	2,860,427	0	T	.	100.0%	183.3 / NA	41	coding (484/993 nt)	rpoS	RNA polymerase, sigma S (sigma 38) factor
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (28/13);  total (28/13)

AACTGGCTTATCCAGTTGCTCTGCGATCTCTTCCGCACTTGGTTCATGGTCCAGCTTATGGGACAACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGGTTTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAA  >  CP009273/2860293‑2860555                                                                                                                                       |                                                                                                                                 aaCTGGCTTATCCAGTTGCTCTGCGATCTCTTCCGCACTTGGTTCATGGTCCAGCTTATGGGACAACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATGGGCAAACGAATGATACGGG‑GTGGTGCATAATCGc                                                                                                                   >  2:70503/1‑149 (MQ=255) aaCTGGCTTATCCAGTTGCTCTGCGATCTCTTCCGCACTTGGTTCATGGTCCAGCTTATGGGACAACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATCGTACGGG‑TTGGTTCATAATCGc                                                                                                                   >  2:114970/1‑149 (MQ=255) aaCTGGCTTATCCAGTTGCTCTGCGATCTCTTCCGCACTTGGTTCATGGTCCAGCTTATGGGACAACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGc                                                                                                                   >  2:137170/1‑149 (MQ=255)      gCTTATCCAGTTGCTGTGCGATCGCTTCCGCACTTGGTTAATGGTCCAGCTTATGGGACAACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCCGCAAACGAATAGTCCGCG‑TTGGTTCATAATCgt                                                                                                                   >  1:81229/1‑143 (MQ=255)         tATCCCGTTGCTCTGCGATCTCTTCCGCACTTGGTTCATGGTCCAGCGTATGGGACAACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCg                                                                                                                <  1:371044/144‑1 (MQ=255)              aGTTGCTCTGCGATCTCTTCCGCACTTGGTTCATGGTCCAGCTTATGGGACAACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTCCGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGtt                                                                                                      >  2:193492/1‑148 (MQ=255)                  gCTCTGCGATCTTTTCCGCACTTGGTTCATGGTCCAGCTTATGGGACAACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGc                                                                                                  <  2:24729/149‑1 (MQ=255)                      tGCGATCTCTTCCGCACTTGGTTCATGGTCCAGCTTATGGGACAACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTAATAATCGCCCGTTCAATCGTCTGGCGAAt                                                                                              >  2:303606/1‑149 (MQ=255)                         gATCTCTTCCGCACGTGGTTCATGGTCCAGCTTATGGGACAACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGa                                                                                                >  1:391194/1‑144 (MQ=255)                             tctTCCGCACTTGGTTCATGGTCCAGCTTATGGGACAACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAg                                                                                       >  2:681543/1‑149 (MQ=255)                                tCCGCACTTGGTTCATGGTCCAGCTTATGGGACAACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCACCCGTTCAATCGTCTGGCGAATCCACCAGGtt                                                                                    >  2:377231/1‑149 (MQ=255)                                                 gTCCAGCTTATGGGACAACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTgag                                                                        <  1:104709/144‑1 (MQ=255)                                                    cAGCTTATGGGACAACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGaa                                                                >  2:600963/1‑149 (MQ=255)                                                         tATGGGACAACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCCGGTTGCGTATGTTGGGAAGCGGaa                                                                >  1:441496/1‑144 (MQ=255)                                                                 aaCTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGtt                                                        >  1:206586/1‑144 (MQ=255)                                                                 aaCTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCggg                                                   >  2:74110/1‑149 (MQ=255)                                                                  tcTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTc                                                       <  1:555614/143‑1 (MQ=255)                                                                   cTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTc                                                 <  2:572688/149‑1 (MQ=255)                                                                    tCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAAGGAATAGTACGGG‑TTGGTTTATAATCGCCCGTTCAATCGTCTGGCCGATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGGTCCg                                                     >  1:441940/1‑144 (MQ=255)                                                                    tCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCCGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGGCa                                                >  2:613575/1‑149 (MQ=255)                                                                      aCGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAGACCACGTTCAGGGTCaaa                                              >  2:336283/1‑149 (MQ=255)                                                                      aCGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCaaa                                              >  2:117348/1‑149 (MQ=255)                                                                        gTGCGGTTGGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTc                                                 <  1:207411/144‑1 (MQ=255)                                                                           cGGTTCGCAGGTACACGTTCAGCTCCCTCACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTtct                                         <  2:622703/149‑1 (MQ=255)                                                                              ttCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCCCGTTCCGGGTCAACCtt                                           >  1:299164/1‑144 (MQ=255)                                                                              ttCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACtt                                           <  1:338186/144‑1 (MQ=255)                                                                                cGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTtct                                         >  1:176326/1‑144 (MQ=255)                                                                                     gTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACcgcgcg                               <  2:558275/149‑1 (MQ=255)                                                                                     gTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACcgcgcg                               <  2:487020/149‑1 (MQ=255)                                                                                           gTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCGAACTTCTCTACCGCGCgg                              >  1:189191/1‑144 (MQ=255)                                                                                                          gATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTg               >  1:591119/1‑144 (MQ=255)                                                                                                          gATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCctc          <  2:193575/149‑1 (MQ=255)                                                                                                          gATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCAACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGcccac          >  2:250898/1‑147 (MQ=255)                                                                                                             gtgAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGcac            >  1:235771/1‑142 (MQ=255)                                                                                                                 aTCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGACGCGGAAACCACGTTCCGGGTCAAACTTCTCGACCGCGCGGATCAGCCCCAGGTTGCCctcct        >  1:280214/1‑142 (MQ=255)                                                                                                                  tctgCAAACGAATAGTACGGG‑TTGGTTCATACTCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTc       <  1:32254/141‑1 (MQ=255)                                                                                                                   cGGCAAACGAATAGGACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCg      <  1:66978/144‑1 (MQ=255)                                                                                                                     gCAAACGAATAGTACGGG‑TTGGTTCATAATGGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTACGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGAGCCGCCCCAGGGTCCCCTCTTCGAt    >  1:537024/1‑144 (MQ=255)                                                                                                                     gCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGAt    >  1:606706/1‑144 (MQ=255)                                                                                                                     gCAAACGAATAGTACGGG‑TTGGTGCATAATAGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACGACGTTCCGGGTCGAACTTCTCTACCGCGCGGATCAGCCCCCGGTTGCCCTCTTCGAt    >  1:463631/1‑144 (MQ=255)                                                                                                                       aaaCGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAAGCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGGAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGCTGCCCCCTTCGATaa  >  1:8600/1‑144 (MQ=255)                                                                                                                                       |                                                                                                                                 AACTGGCTTATCCAGTTGCTCTGCGATCTCTTCCGCACTTGGTTCATGGTCCAGCTTATGGGACAACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGGTTTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAA  >  CP009273/2860293‑2860555

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑