Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,430,200:1	+T	13.8%	coding (375/1164 nt)	PP_3045 →	ATP‑dependent protease ClpP

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,430,200	1	.	T	13.8%	90.2 / 11.5	29	coding (375/1164 nt)	PP_3045	ATP‑dependent protease ClpP
Reads supporting (aligned to +/- strand):  ref base . (14/11);  new base T (2/2);  total (16/13)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.05e-01

TTCAACACAAACGGAGGTGACCTGTTCGAGGGGCTTGCCATCCACAACGCGCTGAGCCGCTTGGGTGAACGTTGCACCGGCCGAGTCGATGCCTTGGCCGCAAGTGCAGGCAGCGTGGCAGTCTGCGGCGCTCACCGTGTGGTCATGGCA‑TCGAATGCCATGCTGATGATCCATAACCCTTACACCTGGGTTGGCGGTGATGCCGAGGACCTTCGTCGGGTGGCGGACGTGCTTGATCAGGCCTTCGAGGCAATGATCGCAGCCTATAAGGCCAAGGCTCCGAACATCG  >  NC_002947/3430051‑3430339                                                                                                                                                       |                                                                                                                                            ttCAACACAAACGGAGGTGACCTGTTCGAGGGGCTTGCCATCCACAACGCGCTGAGCCGCTTGGGTGAACGTTGCACCGGCCGAGTCGATGCCTTGGCCGCAAGTGCAGGCAGCGTGGCAGTCTGCGGCGCTCACCGTGTGGTCATGGCa                                                                                                                                              >  2:225805/1‑150 (MQ=255)       acaAACGGAGGTGACCTGTTCGAGGGGCTTGCCATCCACAACGCGCTGAGCCGCTTGGGTGAACGTTGCACCGGCCGAGTCGATGCCTTGGCCGCAAGTGCAGGCAGCGTGGCAGTCTGCGGCGCTCACCGTGTGGTCATGGCA‑TCGAAt                                                                                                                                       >  1:181908/1‑150 (MQ=255)         aaaCGGAGGTGACCTGTTCGAGGGGCTTGCCATCCACAACGCGCTGAGCCGCTTGGGTGAACGTTGTAAGCGCCGAGTCGATGCCTTGGCCGCAAGTGCAGGCAGCGTGGCAGTCTGCGGCGCTCACCGTGTGGTCATGGCA‑TCGAATGc                                                                                                                                     <  1:470967/150‑1 (MQ=255)            cGGAGGTGACCTGTTCGAGGGGCTTGCCATCCACAACGCGCTGAGCCGCTTGGGTGAACGTTGCACCGGCCGAGTCGATGCCTTGGCCGCAAGTGCAAGCAGCGTGGCAGTCTGCGGCGCTCACCGTGTGGTCATGGCA‑TCGAATGCCAt                                                                                                                                  <  1:44487/150‑1 (MQ=255)              gAGGTGACCTGTTCGAGGGGCTTGCCATCCACAACGCGCTGAGCCGCTTGGGTGAACGTTGCACCGGCCGAGTCGATGCCTTGGCCGCAAGTGCAGGCAGCGTGGCAGTCTGCGGCGCTCACCGTGTGGTCATGGCATTCG‑ATGCCATga                                                                                                                                <  1:225805/150‑2 (MQ=255)                      cTGTTCGAGGGGCTTGCTTTCCACAACGCGCGGAGCCGCTTGGGTGAACGTTGCCCCGGCCGAGTCGATGCCTTGGCCGCAAGTGCAGGCAGCGTGGGAGTCTGCGGCGCTTACCGTGTGGTCATGGCA‑TCGACTGCTATGCtcatggcc                                                                                                                        <  2:152782/150‑4 (MQ=255)                      cTGTTCGAGGGGCTTGCCATCCACAACGCGCTGAGCCGCTTGGGTGAACGTTGCACCGGCCGAGTCGATGCCTTGGCCGCAAGTGCAGGCAGCGTGGCAGTCTGCGGCGCTCACCGTGTGGTCATGGCA‑TCGAATGCCATGCTGTTGATc                                                                                                                        >  2:350637/1‑150 (MQ=255)                            gAGGGGCTTGCCATCCACAACGCGCTGAGCCGCTTGGGTGAACGTTGCACCGGCCGAGTCGATGCCTTGGCCGCAAGTGCAGGCAGCGTGGCAGTCTGCGGCGCTCACCGTGTGGTCATGGCA‑TCGAATGCCATGCtga                                                                                                                             >  1:245582/1‑139 (MQ=255)                            gAGGGGCTTGCCATCCACAACGCGCTGAGCCGCTTGGGTGAACGTTGCACCGGCCGAGTCGATGCCTTGGCCGCAAGTGCAGGCAGCGTGGCAGTCTGCGGCGCTCACCGTGTGGTCATGGCA‑TCGAATGCCATGCtga                                                                                                                             <  2:245582/139‑1 (MQ=255)                                   ttGCCATCCACAACGCGCTGAGCCGCTTGGGTGAACGTTGCACCGGCCGAGTCGATGCCTTGGCCGCAAGTGCAGGCAGCGTGGCAGTCTGCGGCGCTCACCGTGTGGTCATGGCA‑TCGAATGCCATGCTGATGATCCATAACCCTTaca                                                                                                           >  2:127162/1‑150 (MQ=255)                                                   gcTGAGCCGCTTGGGTGAACGTTGCACCGGCCGAGTCGATGCCTTGGCCGCAAGTGCAGGCAGCGTGGCAGTCTGCGGCGCTCACCGTGTGGTCATGGCA‑TCGAATGCCATGCTGATGATCCATAACCCTTACACCTGGGTTGGCGGTGa                                                                                           <  1:44373/150‑1 (MQ=255)                                                           gCTGGGGTGAACGTTGCACCGGCCGAGTCGATGCCTTGGCCGCAAGTGCAGGCAGCGTGGCAGTCTGCGGCGCTCACCGGGTGGTCATGGCA‑TCGAATGCCAGGCTGATGATCCATAACCCTTACACCTGGGTTCGCGGTGATGCCGAgg                                                                                   >  2:535192/1‑150 (MQ=255)                                                              tGGGTGAACGTTGCACCGGCCGAGTCGATGCCTTGGCCGCAAGTGCAGGCAGCGTGGCAGTCTGCGGCGCTCACCGTGTGGTCATGGCA‑TCGAATGCCATGCTGATGATCCATAACCCTTACACCTGGGTTGGCGGTGATGCCGAGGAcc                                                                                <  1:127162/150‑1 (MQ=255)                                                                 gTGAACGTTGCACCGGCCGAGTCGATGCCTTGGCCGCAAGTGCAGGCAGCGTGGCAGTCTGCGGCGCTCACCGTGTGGTCATGGCA‑TCGAATGCCATGCTGATGATCCATAACCCTTACACCTGGGTTGGCGGCGATGCCGAGGACCTtc                                                                             >  2:61254/1‑150 (MQ=255)                                                                                gCCGAGTCGATGCCTTGGCCGCAAGTGCAGGCAGCGTGGCAGTCTGCGGCGCTCACCGTGTGGTCATGGCA‑TCGAATGCCATGCTGATGATCCATAACCCTTACACCTGGGTTGGCGGTGATGCCGAGGACCTTCGTCGGGTGGCGGACg                                                              >  2:565225/1‑150 (MQ=255)                                                                                          tGCCTTGGCCGCAAGTGCAGGCAGCGTGGCAGTCTGCGGCGCTCACCGTGTGGTCATGGCATTCG‑ATGCCATgac                                                                                                                               >  1:543809/1‑73 (MQ=38)                                                                                          tGCCTTGGCCGCAAGTGCAGGCAGCGTGGCAGTCTGCGGCGCTCACCGTGTGGTCATGGCATTCG‑ATGCCATgac                                                                                                                               <  2:543809/75‑3 (MQ=38)                                                                                          tGCCTTGGCCGCAAGTGCAGGCAGCGTGGCAGTCTGCGGCGCTCACCGTGTGGTCATGGCA‑TCGAATGCCATGCTCATGCTCCATAACCCTTGCACCGGGGTTGGCGGTGATGCCGAGGACCTTCGTCGGGTGGCGGACGTGCTTGATCa                                                    <  1:230282/150‑1 (MQ=255)                                                                                             cTTGGCCGCAAGTGCAGGCAGCGTGGCAGTCTGCGGCGCTCACCGTGTGGTCATGGCA‑TCGAATGCCATGCTGATGATCCATAACCCTTACACCTGGGTTGGCGGTGATGCCGAGGACCTTCGTCGGGTGGCGGACGTGCTTGATCAGGc                                                 >  2:318200/1‑150 (MQ=255)                                                                                                ggCCGCAAGTGCAGGCAGCGTGGCAGTCTGCGGCGCTCACCGTGTGGTCATGGCA‑TCGAATGCCATGCTGATGATCCCTAACCCTTACACCTGGGTTGGCGGTTATGCGGAGGTTCTTCGTCGGGTGGCGGACGTGCTTGATCAGGCCtt                                              <  1:565225/150‑1 (MQ=255)                                                                                                   cGCAAGTGCAGGCAGCGTGGCAGTCTGCGGCGCTCACCGTGTGGTCATGGCA‑TCGAATGCCATGCTGATGATCCATAACCCTTACACCTGGGGTGGCGGTGATGCCGAGGCCCTTCGTCGGGTGGCGGACGTGCTTGATCAGGCCTTCGa                                           >  1:397612/1‑150 (MQ=255)                                                                                                                  cGTGGCAGTCTGCGGCGCTCACCGTGTGGTCATGGCA‑TCGAATGCCATGCTGATGATCCATAACCCTTACACCTGGGTTGGCGGCGATGCCGAGGACCTTCGTCGGGTGGCGGACGTGCTTGATCAGGCCTTCGAGGCAATGATCGCAGc                            <  1:61254/150‑1 (MQ=255)                                                                                                                          tCTGCGGCGCTCACCGTGTGGTCATGGCA‑TCGAAGGCGATGCTGATGATCCATAACGCTTACACCTGGGTTGCGTGTGATGCCGGGGACCTTCGTCGGGTGGCGGACGTGCTTGATCAGGCCTTCGAGGCAATGATCGCAGCCTATAAgg                    >  2:21232/1‑150 (MQ=255)                                                                                                                              cggcgCTCACCGTGTGGTCATGGCA‑TCGAATGCCATGCTGATGATCCATAACCCTTACACCTGGGTTGGCGGTGATGCCGAGGACCTTCGTCGGGTGGCGGACGTGCTTGATCAGGCCTTCGAGGCAATGATCGCAGCCTATAAGGCCaa                <  2:225199/150‑1 (MQ=255)                                                                                                                              cggcgCTCACCGTGTGGTCATGGCA‑TCGAATGCCATGCTGATGATCCATAACCCTTACACCTGGGTTGGCGGTGATGCCGAGGACCTTCGTCGGGTGGCGGACGTGCTTGATCAGGCCTTCGAGGCAATGATCGCAGCCTATAAGGCCaa                >  1:225199/1‑150 (MQ=255)                                                                                                                                    tCACCGTGTGGTCATGGCA‑TCGAATGCCATGCTGATGATCCATAACCCTTACACCTGGGTTGGCGGTGATGCCGAGGACCTTCGTCGGGTGGCGGACGTGCTTGATCAGGCCTTCGAGGCAATGATCGCAGCCTATAAGGCCAAGGCTcc          >  2:268571/1‑150 (MQ=255)                                                                                                                                          tgtgGTCATGGCA‑TCGAATGCCATGCTGATGATCCATAACCCTTACACCTGGGTTGGCGGTGATGCCGAGGACCTTCGTCGGGTGGCGGACGTGCTTGATCAGGCCTTCGAGGCAATGATCGCAGCCTATAAGGCCAAGGCTCCGAACAt    >  1:197738/1‑150 (MQ=255)                                                                                                                                            tcagcATGGCATTCG‑ATGCCATGCTGATGATCCATAACCCTTACACCTGGGTTGGCGGTGATGCCGAGGACCTTCGTCGGGTGGCGGACGTGCTTGATCAGGCCTTCGAGGCAATGATCGCAGCCTATAAGGCCAAGGCTCCGAACATCg  >  1:400106/5‑150 (MQ=255)                                                                                                                                                     cA‑TCGAATGCCATGCTGATGATCCATAACCCTTACACCTGGGTTGGCGGTGATGCCGAGGACCTTCGTCGGGTGGCGGACGTGCTTGATCAgg                                                  <  1:495132/93‑1 (MQ=255)                                                                                                                                                     cA‑TCGAATGCCATGCTGATGATCCATAACCCTTACACCTGGGTTGGCGGTGATGCCGAGGACCTTCGTCGGGTGGCGGACGTGCTTGATCAgg                                                  >  2:495132/1‑93 (MQ=255)                                                                                                                                                       |                                                                                                                                            TTCAACACAAACGGAGGTGACCTGTTCGAGGGGCTTGCCATCCACAACGCGCTGAGCCGCTTGGGTGAACGTTGCACCGGCCGAGTCGATGCCTTGGCCGCAAGTGCAGGCAGCGTGGCAGTCTGCGGCGCTCACCGTGTGGTCATGGCA‑TCGAATGCCATGCTGATGATCCATAACCCTTACACCTGGGTTGGCGGTGATGCCGAGGACCTTCGTCGGGTGGCGGACGTGCTTGATCAGGCCTTCGAGGCAATGATCGCAGCCTATAAGGCCAAGGCTCCGAACATCG  >  NC_002947/3430051‑3430339

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑