Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,349,419	G→A	9.7%	G576D (GGT→GAT)	PP_2944 →	sensor histidine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,349,419	0	G	A	9.7%	111.3 / 3.5	41	G576D (GGT→GAT)	PP_2944	sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base G (21/16);  new base A (2/2);  total (23/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.54e-01

CTGGAAATGAGCGTGCTGGACGAGGGCGAAGGCATTGCCCCTGAAAACCTGCAGAAGATCTTTGCCCATGGCTTCACCACGCGCAAGGACGGGCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTACCCTGAG‑GATCCCGCTGATCGCGGTGACGGAGCCTGCATGAGTGACATGATCAATCGCCGGATCCTGCTGATCGATGACATGCCGACTATCCACGAGGA  >  NC_002947/3349277‑3349565                                                                                                                                               |                                                                                                                                                    cTGGAAATGAGCGTGCTGGACGAGGGCGAAGGCATTGCCCCTGAAAACCTGCAGAAGATCTTTGCCCATGGCTTCACCACGCGCAAGGACGGGCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCt                                                                                                                                               <  6:139265/149‑1 (MQ=255)   ggAAATGAGCGTGCTGGACGAGGGCGAAGGCATTGCCCCTGAAAACCTGCAGAAGATCTTTGCCCATGGCTTCACCACGCGCAAGGACGGGCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGa                                                                                                                                             >  1:4487/1‑149 (MQ=255)    gAAATGAGCGTGCTGGACGAGGGCGAAGGCATTGCCCCTGAAAACCTGCAGAAGATCTTTGCCCATGGCTTCACCACGCGCAAGGACGGGCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGa                                                                                                                                             <  1:292300/148‑1 (MQ=255)    gAAATGAGCGTGCTGGACGAGGGCGAAGGCATTGCCCCTGAAAACCTGCAGAAGATCTTTGCCCATGGCTTCACCACGCGCAAGGACGGGCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGAc                                                                                                                                            >  5:181684/1‑149 (MQ=255)        tGAGCGTGCTGGACGAGGGCGAAGGCATTGCCCCTGAAAACCTGCAGAAGATCTTTGCCCATGGCTTCACCACGCGCAAGGACGGGCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGATCACCTGACCGca                                                                                                                                        >  3:267898/1‑149 (MQ=255)        tGAGCGTGCTGGACGAGGGCGAAGGCATTGCCCCTGAAAACCTGCAGAAGATCTTTGCCCATGGCTTCACCACGCGCAAGGACGGGCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGATCACCTGACCGca                                                                                                                                        >  3:263542/1‑149 (MQ=255)               gCTGGACGAGGGCGAAGGCATTGCCCCTGAAAACCTGCAGAAGATCTTTGCCCATGGCTTCACCACGCGCAAGGACGGGCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGACCGCACACAGc                                                                                                                                  >  2:203142/1‑148 (MQ=255)                 tGGACGAGGGCGAAGGCATTGCCCCTGAAAACCTGCAGAAGATCTTTGCCCATGGCTTCACCACGCGCAAGGACGGGCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGACCGCACACAGCGAc                                                                                                                               >  2:197555/1‑149 (MQ=255)                                       cccTGAAAACCTGCAGAAGATCTTTGCCCATGGCTTCACCACGCGCAAGGACGGGCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGAcc                                                                                                                                           <  1:202985/115‑1 (MQ=255)                                       cccTGAAAACCTGCAGAAGATCTTTGCCCATGGCTTCACCACGCGCAAGGACGGGCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGAcc                                                                                                                                           >  2:202985/1‑115 (MQ=255)                                            aaaaCCTGCAGAAGATCTTTGCCCATGGCTTCACCACGCGCAAGGACGGGCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTAc                                                                                                     <  6:181684/148‑1 (MQ=255)                                            aaaaCCTGCAGAAGATCTTTGCCCATGGCTTCACCACGCGCAAGGACGGGCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGAGCTGTCTTTAcc                                                                                                    >  1:176550/1‑149 (MQ=255)                                                 cTGCAGAAGATCTTTGCCCATGGCTTCACCACGCGCAAGGACGGGCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTACCCTGAg                                                                                               <  1:203142/149‑1 (MQ=255)                                                  tGCAGAAGATCTTTGCCCATGGCTTCACCACGCGCAAGGACGGGCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTACCCTGAg                                                                                               >  2:236106/1‑148 (MQ=255)                                                    cAGAAGATCTTTGCCCATGGCTTCACTACGCGCAAGGACGGGCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTACCCTGAG‑GAt                                                                                           >  1:170105/1‑149 (MQ=255)                                                    cAGAAGATCTTTGCCCATGGCTTCACCACGCGCAAGGACGGGCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTACCCTGAg                                                                                               <  1:236106/146‑1 (MQ=255)                                                                  ccATGGCTTCACCACGCGCAAGGACGGGCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTACCCTGAG‑GATCCCGCTGATCGCgg                                                                             >  3:242845/1‑149 (MQ=255)                                                                    aTGGCTTCACCACGCGCAAGGACGGGCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTACCCTGAG‑GATCCCGCTGATCGCGGt                                                                            >  1:305472/1‑148 (MQ=255)                                                                    aTGGCTTCACCACGCGCAAGGACGGGCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTACCCTGAG‑GATCCCGCTGATCGCGGt                                                                            >  3:79987/1‑148 (MQ=255)                                                                       gCTTCACCACGCGCAAGGACGGGCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTACCCTGAG‑GATCCCGCTGATCGCGGTGAc                                                                         <  2:305472/148‑1 (MQ=255)                                                                       gCTTCACCACGCGCAAGGACGGGCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGACCGCACACAGCGACGGCCCTGGCGTGGGTGCTGTCTTTACCCTGAG‑GATCCCGCTGATCGCGGTGACg                                                                        <  2:4487/149‑1 (MQ=255)                                                                         ttCACCACGCGCAAGGACGGGCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTACCCTGAG‑GATCCCGCTGATCGCGGTGACg                                                                        >  5:305002/1‑147 (MQ=255)                                                                             ccacGCGCAAGGACGGGCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTACCCTGAG‑GATCCCGCTGATCGCGGTGACGGAGCCt                                                                  >  5:105051/1‑149 (MQ=255)                                                                              cacGCGCAAGGACGGGCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTACCCTGAG‑GATCCCGCTGATCGCGGTGACGGAGCCTg                                                                 >  3:27104/1‑149 (MQ=255)                                                                                  cgcAAGGACGGGCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTACCCTGAGAGATCCCGCTGATCGCGGTGACGGAGCCTGCAt                                                              <  1:197555/149‑1 (MQ=255)                                                                                   gcAAGGACGGGCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTACCCTGAG‑GATCCCGCTGATCGCGGTGACGGAGCCTGCAt                                                              >  1:279129/1‑147 (MQ=255)                                                                                     aaGGACGGGCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTACCCTGAG‑GATCCCGCTGATCGCGGTGACGGAGCCTGCATGAGt                                                          <  4:27104/149‑1 (MQ=255)                                                                                     aaGGACGGGCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTACCCTGAG‑GATCCCGCTGATCGCGGTGACGGAGCCTGCATGAGt                                                          <  6:105051/149‑1 (MQ=255)                                                                                     aaGGACGGGCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTACCCTGAG‑GATCCCGCTGATCGCGGTGACGGAGCCTGCATGAGt                                                          <  2:177330/149‑1 (MQ=255)                                                                                     aaGGACGGGCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTACCCTGAG‑GATCCCGCTGATCGCGGTGACGGAGCATGCATGAGt                                                          >  6:308741/1‑149 (MQ=255)                                                                                             gCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTACCCTGAG‑GATCCCGCTGATCGCGGTGACGGAGCCTGCATGAGTGACATGAt                                                  <  4:242845/149‑1 (MQ=255)                                                                                                        gCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTACCCTGAG‑GATCCCGCTGATCGCGGTGACGGAGCCTGCATGAGTGACATGATCAATCGCCGGa                                       >  8:257075/1‑149 (MQ=255)                                                                                                             cacaGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTACCCTGAG‑GATCCCGCTGATCGCGGTGACGGAGCCTGCATGAGTGACATGATCAATc                                             <  7:44441/138‑1 (MQ=255)                                                                                                             cacaGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTACCCTGAG‑GATCCCGCTGATCGCGGTGACGGAGCCTGCATGAGTGACATGATCAATc                                             >  8:44441/1‑138 (MQ=255)                                                                                                                        ccTGGCCGCCATCGAGATGAATGGTCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTACCCTGAG‑GATCCCGCTGATCGCGGTGACGGAGCCTGCATGa                                                            >  7:4943/1‑112 (MQ=255)                                                                                                                         cTGGCCGCCATCGAGATGAATGGTCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTACCCTGAG‑GATCCCGCTGATCGCGGTGACGGAGCCTGCATGAGTGACATGATCAATCGCCGGATCCTGCTGATCGATGAc                      <  1:209397/149‑1 (MQ=255)                                                                                                                               gccATCGAGATGAATGGTCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTACCCTGAG‑GATCCCGCTGATCGCGGTGACGGAGCCTGCATGAGTGACATGATCAATCGCCGGATCCTGCTGATCGATGACATGcc                 >  6:187127/1‑148 (MQ=255)                                                                                                                                      agaTGAATGATCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTACCCTGAG‑GATCCCGCTGATCGCGGTGACGGAGCCTGCATGAGTGACATGATCAATCGCCGGATCCTGCTGATCGATGACATGCCGACTATcc         <  4:263542/149‑1 (MQ=255)                                                                                                                                      agaTGAATGAGCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTACCCTGAG‑GATCCCGCTGATCGCGGTGACGGAGCCTGCATGAGTGACATGATCAATCGCCGGATCCTGCTGATCGATGACATGCCGACTATcc         <  4:267898/149‑1 (MQ=255)                                                                                                                                           aaTGGTCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTACCCTGAG‑GATCCCGCTGATCGCGGTGACGGAGCCTGCATGAGTGACATGATCAATCGCCGGATCCTGCTGATCGATGACATGCCGACTATCCACGa     <  4:79987/148‑1 (MQ=255)                                                                                                                                             tGGTCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTACCCTGAG‑GATCCCGCTGATCGCGGTGACGGAGCCTGCATGAGTGACATGATCAATCGCCGGATCCTGCTGATCGATGACATGCCGACTATCCACGAGGa  >  3:178546/1‑149 (MQ=255)                                                                                                                                              ggTCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTACCCTGAG‑GATCCCGCTGATCGCGGTGACGGAGCCTGCATGAGTGACATGa                                                   >  7:66096/1‑99 (MQ=255)                                                                                                                                              ggTCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTACCCTGAG‑GATCCCGCTGATCGCGGTGACGGAGCCTGCATGAGTGACATGa                                                   <  8:66096/99‑1 (MQ=255)                                                                                                                                               |                                                                                                                                                    CTGGAAATGAGCGTGCTGGACGAGGGCGAAGGCATTGCCCCTGAAAACCTGCAGAAGATCTTTGCCCATGGCTTCACCACGCGCAAGGACGGGCATGGCTTCGGCTTGCACAGTTGCGCCCTGGCCGCCATCGAGATGAATGGTCACCTGACCGCACACAGCGACGGCCCTGGCTTGGGTGCTGTCTTTACCCTGAG‑GATCCCGCTGATCGCGGTGACGGAGCCTGCATGAGTGACATGATCAATCGCCGGATCCTGCTGATCGATGACATGCCGACTATCCACGAGGA  >  NC_002947/3349277‑3349565

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑