Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,064,422	C→G	8.4%	T83R (ACG→AGG)	PP_2676 →	substrate‑binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,064,422	0	C	G	8.4%	166.5 / 3.8	57	T83R (ACG→AGG)	PP_2676	substrate‑binding protein
Reads supporting (aligned to +/- strand):  ref base C (20/30);  new base G (3/2);  total (24/33)
Fisher's exact test for biased strand distribution p-value = 6.39e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCAGGCGCAGGTGCGCAACTATGACGCGATCATCGCTGCCGGCGAGCTCAAGGTGGCGGTGTACAAGGATTTCGCCCCCTACAGTTTTCAGGACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTGCGCGACTACATCTGGCGTGGCAGCCCGCTGCGTCATCAGCAATTGGCCGACCTGATGATGCGGGTGCCTTA  >  NC_002947/3064279‑3064557                                                                                                                                                 |                                                                                                                                         ccAGGCGCAGGTGCGCAACTATGACGCGATCATCGCTGCCGGCGAGCTCAAGGTGGCGGTGTACAAGGATTTCGCCCCCTACAGTTTTCAGGACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCtt                                                                                                                                    <  1:10470/150‑1 (MQ=255)     gcgcAGGTGCGCAACTATGACGCGATCATCGCTGCCGGCGAGCTCAAGGTGGCGGTGTACAAGGATTTCGCCCCCTACAGTTTTCAGGACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTgggg                                                                                                                                <  2:1325069/150‑1 (MQ=255)     gcgcAGGTGCGCAACTATGACGCGATCATCGCTGCCGGCGAGCTCAAGGTGGCGGTGTACAAGGATTTCGCCCCCTACAGTTTTCAGGACCAC‑GGCCAGCCGCGTGGTGTCGAGGTGGAGCTGGCGCAGGCCCTGGCTACGGCCTTgggg                                                                                                                                >  1:105420/1‑150 (MQ=255)            tGCGCAACTATGACGCGATCATCGCTGCCGGCGAGCTCAAGGTGGCGGTGTACAAGGATTTCGCCCCCTACAGTTTTCAGGACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑cc                                                                                                                        >  2:1027798/1‑150 (MQ=255)            tGCGCAACTATGACGCGATCATCGCTGCCGGCGAGCTCAAGGTGGCGGTGTACAAGGATTTCGCCCCCTACAGTTTTCAGGACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑cc                                                                                                                        >  2:1028032/1‑150 (MQ=255)                 aaCTATGACGCGATCATCGCTGCCGGCGAGCTCAAGGTGGCGGTGTACAAGGATTTCGCCCCCTACAGTTTTCAGGACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCaa                                                                                                                   <  1:704388/150‑1 (MQ=255)                         cgcgATCATCGCTGCCGGCGAGCTCAAGGTGGCGGTGTACAAGGATTTCGCCCCCTACAGTTTTCAGGACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTg                                                                                                           >  1:511406/1‑150 (MQ=255)                              tcatcGCTACCGGCGAGCTCACGGTGGCGGTGTGCCAGGAGTACGCCCCCTACAGTTTTCAGGACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGgcgc                                                                                                      <  2:1084987/150‑1 (MQ=255)                                 tcGCTGCGGGCGAGCTCAAGGTGGCGGTGTACAAGGATTTCGCCCCCTACAGTTTTCAGGACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCAc                                                                                                   <  2:204227/150‑1 (MQ=255)                                      gCCGGCGAGCTCAAGTGGGCGGTGTACAAGGATTTCGCCCCCTACAGTTTTCAGGACAACAAGCCA‑CTCCGTGGGGTAGCTGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGga                                                                                              <  1:811353/150‑1 (MQ=255)                                          gCGAGCTCAAGGTGGCGGTGTACAAGGATTTCGCCCCCTACAGTTTTCAGGACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGaaa                                                                                          >  1:627886/1‑150 (MQ=255)                                           cGAGCTCAAGGTGGTGGTGTACAAGGATTTCGCCCCCTACAGTTTTCAGGACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGaaaa                                                                                         <  2:1420699/150‑1 (MQ=255)                                                  aaGGTGGCGGTGTACAAGGATTTCGCCCCCTACAGTTTTCAGGACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTcgac                                                                                  >  1:1117767/1‑150 (MQ=255)                                                              tACAAGGATTTCGCCCCCTACAGTTTTCAGGACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTgcgc                                                                      >  1:936940/1‑150 (MQ=255)                                                                cAAGGATTTCGCCCCCTACAGTTTTCAGGACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGCCGCTGACCTGcgcgg                                                                    >  1:1091667/1‑149 (MQ=255)                                                                 aaGGATTTCGCCCCCTACAGTTTTCAGGACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCTACGGCCTTGGGGGTACG‑CCTGCAACAGATCTGGGCGCCAGCCGGAGAAAAGCTCGACGATGACCTGCGCGAc                                                                   >  1:454772/1‑150 (MQ=255)                                                                 aaGGATTTCGCCCCCTACAGTTTTCAGGACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTGCGCGAc                                                                   >  1:795689/1‑150 (MQ=255)                                                                 aaGGATTTCGCCCCCTACAGTTTTCAGGACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTGCGCGAc                                                                   >  2:954232/1‑150 (MQ=255)                                                                 aaGGATTTCGCCCCCTACAGTTTTCAGGACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTGCGCGAc                                                                   <  1:547154/150‑1 (MQ=255)                                                                      tttCGCCCCCTACAGTTTTCAGGACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTGCGCGACTACAt                                                              <  2:1091667/150‑1 (MQ=255)                                                                         cGCCCCCTACAGGTTTCAGGACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTGCGCGACTACATCTg                                                           <  2:128266/150‑1 (MQ=255)                                                                           cccccTACAGTTTTCAGGACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTGCGCGACTACATCTGGc                                                         <  2:511406/150‑1 (MQ=255)                                                                           cccccTACAGTTTTCAGGACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTGCGCGACTACATCTGGc                                                         <  2:1022894/150‑1 (MQ=255)                                                                             cccTACAGTTTTCAGGACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTGCGCGACTACATCTGGCGt                                                       >  1:1007511/1‑150 (MQ=255)                                                                              ccTACAGTTTTCAGGACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATg                                                                              >  1:563672/1‑126 (MQ=255)                                                                              ccTACAGTTTTCAGGACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATg                                                                              <  2:563672/126‑1 (MQ=255)                                                                              ccTACAGTTTTCAGGACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTGCGCGACTACATCTGGCGTg                                                      <  2:627886/150‑1 (MQ=255)                                                                               cTACAGTTTTCAGGACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTGCGCGACTACATCTGGCGTgg                                                     <  2:936940/150‑1 (MQ=255)                                                                                     ttttCAGGACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTgcgc                                                                      <  2:1408497/127‑1 (MQ=255)                                                                                     ttttCAGGACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTgcgc                                                                      >  1:1408497/1‑127 (MQ=255)                                                                                           ggACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTggg                                                                                                                                 <  1:578070/63‑1 (MQ=255)                                                                                           ggACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTggg                                                                                                                                 >  2:578070/1‑63 (MQ=255)                                                                                            gACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTGCGCGACTACATCTGGCGTGGCAGCCCGCTGCGt                                        >  1:38756/1‑150 (MQ=255)                                                                                               cAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTATG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTGCGCGACTACATCTGGCGTGGCAGCCCGCTGCGtcat                                     <  2:777791/150‑1 (MQ=255)                                                                                               cAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTGCGCGACTACATCTGGCGTTGCAGCCCGCTGCGtcat                                     <  2:164928/150‑1 (MQ=255)                                                                                               cAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTGCGCGACTACATCTGGCGTGGCAGCCCGCTGCGtcat                                     <  1:954232/150‑1 (MQ=255)                                                                                                      cAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCAAGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTGCGCGACTACATCTGGCGTGGCAGCCCGCTGCGTCATCAGCaa                               >  1:442996/1‑150 (MQ=255)                                                                                                       aGCCGCGTGGTGTAGACGTGGCGCTGGCGCTCGGCCCGGCCAGGGCATTGGGAGTACC‑CCCGCAACTGACCGGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTGCGCGACTACATCTGGCGTGGCAGCCCGCTGCGTCATCAGCAAt                              <  2:1007511/150‑1 (MQ=255)                                                                                                        gCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTGCGCGACTACATCTGGCGTGGCAGCCCGCTGCGTCATCAGCAAtt                             <  2:1345939/150‑1 (MQ=255)                                                                                                              tggtgTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGATC‑TAGGCATAGGTGCTGCAACTGATCTGGGCGCCACCCTGAGAAAAGCTCGACGATGACCTGCGCGACTACATCTGGCGTGGCAGCCCGCTGCGTCATCAGCAATTGGCCGa                       <  1:1028032/150‑1 (MQ=255)                                                                                                              tggtgTCGATGTGGAGCTGGCGCAGGCCCTCGCCCACGCCTTTCAGGCACG‑CCTGCAAGTGATCTGGGCGCCAGCCAGAGAAAAGCTCGACGATGACCTGCGCGACTACATCTGGCGTGGCAGCCCGCTGCGTCATCAGCAATTGGCCGa                       <  1:1027798/150‑1 (MQ=255)                                                                                                                gtgtCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTGCGCGACTACATCTGGc                                                         <  2:182406/114‑1 (MQ=255)                                                                                                                gtgtCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTGCGCGACTACATCTGGc                                                         >  1:182406/1‑114 (MQ=255)                                                                                                                 tgtCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTGCGCGACTACATCTGGCGTGGCAGCCCGCTGCGTCATCAGCAATTGGCCGACCt                    <  2:490225/150‑1 (MQ=255)                                                                                                                     gATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTGCGCGACTACATCTGGCGTGGCAGCCCGCTGCGTCATCAGCAATTGGCCGACCtgatg                <  2:795689/150‑1 (MQ=255)                                                                                                                     gATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCACGACGATGACCTGCGCGACTACATCTGGCGTGGCAGCCCGCTGCGTCATCAGCAATTGGCCGACCtgatg                >  1:366778/1‑150 (MQ=255)                                                                                                                        gtgGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑cc                                                                                                                        >  1:1185752/1‑43 (MQ=255)                                                                                                                        gtgGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑cc                                                                                                                        <  2:1185752/43‑1 (MQ=255)                                                                                                                           gAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTGCGCGACTACATCTGGCGTGGCAGCCCGCTGCGTCATCAGCAATTGGCCGACCTGATGATGCgg          <  2:1326255/150‑1 (MQ=255)                                                                                                                           gAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTGCGCGACTACATCTGGCGTGGCAGCCCGCTGCGTCATCAGCAATTGGCCGACCTGATGATGCgg          <  2:1101844/150‑1 (MQ=255)                                                                                                                                ccccaaGGCCGTGGCCAGGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTGCGCGACTACATCTGGCGTGGCAGCCCGCTGCGTCATCAGCAATTGGCCGACCTGATGATGCGGGTGcc     >  2:91031/6‑150 (MQ=255)                                                                                                                                 cccaaGGCCGTGGCCAGGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTGCGCGACTACATCTGGCGt                                                       <  2:243219/95‑1 (MQ=255)                                                                                                                                 cccaaGGCCGTGGCCAGGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTGCGCGACTACATCTGGCGt                                                       >  1:243219/5‑99 (MQ=255)                                                                                                                                  ccaaGGCCGTGGCCAGGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTGCGCGCCTACCTCTGGCGTGGCAGCCCGCTGCGGCCTCAGCACTTGGCCGACCGGATGATGCGGGTGCCtt   >  2:400287/4‑150 (MQ=255)                                                                                                                                   gcAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTGCGCGACTACATCTGGCGTGGCAGCCCGCTGCGTCATCAGCAATTGGCCGACCTGATGATGCGGGTGCCTTa  <  2:1117767/150‑1 (MQ=255)                                                                                                                                               cACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTcgac                                                                                  <  1:36381/58‑1 (MQ=255)                                                                                                                                               cACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTcgac                                                                                  >  2:36381/1‑58 (MQ=255)                                                                                                                                                 |                                                                                                                                         CCAGGCGCAGGTGCGCAACTATGACGCGATCATCGCTGCCGGCGAGCTCAAGGTGGCGGTGTACAAGGATTTCGCCCCCTACAGTTTTCAGGACCAC‑GGCCAGCCGCGTGGTGTCGATGTGGAGCTGGCGCAGGCCCTGGCCACGGCCTTGGGGGTACG‑CCTGCAACTGATCTGGGCGCCACCCGGAGAAAAGCTCGACGATGACCTGCGCGACTACATCTGGCGTGGCAGCCCGCTGCGTCATCAGCAATTGGCCGACCTGATGATGCGGGTGCCTTA  >  NC_002947/3064279‑3064557

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: ‑