Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,385,277	T→A	8.4%	intergenic (+22/‑41)	lldP → / → lldD	L‑lactate permease/L‑lactate dehydrogenase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,385,277	0	T	A	8.4%	162.7 / 5.9	58	intergenic (+22/‑41)	lldP/lldD	L‑lactate permease/L‑lactate dehydrogenase
Reads supporting (aligned to +/- strand):  ref base T (26/27);  new base A (2/3);  total (28/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-01

GTCGGCAAGGAATCCGACCTGTTCCGCTTCACCGTCAAGCACAGCCTGTTCTTCGCCACCATCGTCGGCCTGATCACCCTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGCCTCTACCGACTATCGCGCCGCGGCCCAACGCAAGCTGCCCCCCTTCCTGTTCCACTACGCTGACGGCGGCGCCTACGCCGAGCACACCCTGCGC  >  NC_002947/5385133‑5385425                                                                                                                                                  |                                                                                                                                                     gTCGGCAAGGAATCCGACCTGTTCCGCTTCACCGTCAAGCACAGCCTGTTCTTCGCCACCATCGTCGGCCTGATCACCCTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCTGGCGC‑CGTcgcgc                                                                                                                                                 <  1:1257499/150‑1 (MQ=255)    ggCAAGGAATCCGACCTGTTCCGCTTCACCGTCAAGCACAGCCTGTTCTTCGCCACCATCGTCGGCCTGATCACCCTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGGCGGGGGC‑CTTCGCGCGcc                                                                                                                                              >  2:277956/1‑150 (MQ=255)       aaGGAATCCGACCTGTTCCGCTTCACCGTCAAGCACAGCCTGTTCTTCGCCACCATCGTCGGCCTGATCACCCTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCgg                                                                                                                                           >  1:334985/1‑150 (MQ=255)       aaGGAATCCGACCTGTTCCGCTTCACCGTCAAGCACAGCCTGTTCTTCGCCACCATCGTCGGCCTGATCACCCTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCgg                                                                                                                                           >  2:580604/1‑150 (MQ=255)          gAATCCGACCTGTTCCGCTTCACCGTCAAGCACAGCCTGTTCTTCGCCACCATCGTCGGCCTGATCACCCTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCAc                                                                                                                                        >  1:430723/1‑150 (MQ=255)            aTCCGACCTGTTCCGCTTCACCGTCAAGCACAGTCTGTTCTTCGCCACCATCGTCGGCCTGATCACCCTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGCGCGACG‑GCGCCCGGcccct                                                                                                                                      <  2:342683/150‑5 (MQ=255)                 aCCTGTTCCGCTTCACCGTCAAGCACAGCCTGTTCTTCGCCACCATCGTCGGCCTGATCACCCTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCcaca                                                                                                                                 <  2:1027029/150‑1 (MQ=255)                     gTTCCGCTTCACCGTCAAGCACAGCCTGTTCTTCGCCACCATCGTCGGCCTGATCACCCTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGCGCGACG‑GCGCCCGGcccctttc                                                                                                                                   >  2:1272037/1‑137 (MQ=255)                     gTTCCGCTTCACCGTCAAGCACAGCCTGTTCTTCGCCACCATCGTCGGCCTGATCACCCTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGCGCGACG‑GCGCCCGGcccctttc                                                                                                                                   <  1:1272037/144‑8 (MQ=255)                     gTTCCGCTTCACCGTCAAGCACAGCCTGTTCTTCGCCACCATCGTCGGCCTGATCACCCTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCa                                                                                                                             >  2:858483/1‑150 (MQ=255)                            ttCACCGTCAAGCACAGCCTGTTCTTCGCCACCATCGTCGGCCTGATCACCCTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGc                                                                                                                      <  1:226243/150‑1 (MQ=255)                              cACCGTCAAGCACAGCCTGTTCTTCGCCACCATCGTCGGCCTGATCACCCTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCga                                                                                                                    <  2:253066/150‑1 (MQ=255)                                  gTCAAGCACAGCCTGTTCTTCGCCACCATCGTCGGCCTGATCACCCTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAAt                                                                                                                >  2:770182/1‑150 (MQ=255)                                       gCACAGCCTGTTCTTCGCCACCATCGTCGGCCTGATCACCCTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGCGCGACG‑GCGCCCGGc                                                                                                                                          <  1:17653/119‑1 (MQ=255)                                       gCACAGCCTGTTCTTCGCCACCATCGTCGGCCTGATCACCCTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGCGCGACG‑GCGCCCGGc                                                                                                                                          >  2:17653/1‑119 (MQ=255)                                            gCCTGTTCTTCGCCACCATCGTCGGCCTGATCACCCTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGC‑ACGCTGCGAGAATCCATGATCAtt                                                                                                     <  2:665218/150‑1 (MQ=255)                                             ccTGTTCTTCGCCACCATCGTCGGCCTGATCACCCTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCAtt                                                                                                     >  1:775231/1‑150 (MQ=255)                                             ccTGTTCTTCGCCACCATCGTCGGCCTGATCACCCTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCAtt                                                                                                     >  2:420742/1‑150 (MQ=255)                                                  tcttgGCCACCATCGTCGGCCTGATCACCCTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGc                                                                                                <  1:218285/150‑1 (MQ=255)                                                  tcttcGCCACCATCGTCGGCCTGATCACCCTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGc                                                                                                <  1:330911/150‑1 (MQ=255)                                                  tcttcGCCACCATCGTCGGCCTGATCACCCTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGc                                                                                                <  1:556729/150‑1 (MQ=255)                                                        ccaccaTCGTCGGCCTGATCACCCTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGCCTCTAc                                                                                          >  1:1050467/1‑150 (MQ=255)                                                         caccaTCGTCGGCCTGATCACCCTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGCCTCTAcc                                                                                         >  2:345975/1‑150 (MQ=255)                                                         caccaTCGTCGGCCTGATCACCCTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGCCTCTAcc                                                                                         <  2:1050467/150‑1 (MQ=255)                                                            caTCGTCGGCCTGATCACCCTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATTGATGATCATTTCTGCCTCTACCGAc                                                                                      <  1:495107/150‑1 (MQ=255)                                                                    gCCTGATCACCCTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGCCTCTACCGACTATCgcgc                                                                              >  1:468575/1‑150 (MQ=255)                                                                          tCACCCTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGCCTCTACCGACTATCGCGCCGCGGc                                                                        <  2:1064107/150‑1 (MQ=255)                                                                              ccTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTcc                                                                                                                                     <  1:134630/85‑1 (MQ=255)                                                                              ccTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTcc                                                                                                                                     >  2:134630/1‑85 (MQ=255)                                                                               cTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGCCTCTACCGACTATCGCGCCGCGGCCCAAc                                                                   <  2:430723/150‑1 (MQ=255)                                                                               cTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGCCTCTACCGACTATCGCGCCGCGGCCCAAc                                                                   <  1:420742/150‑1 (MQ=255)                                                                                   tCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGCCTCTACCGACTATCGCGCCGCGGCCCAACGCaa                                                               <  1:1088303/150‑1 (MQ=255)                                                                                   tCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCAAGATCATTTCTGCCTCTACCGACTATCGCGCCGCGGCCCAACGCaa                                                               >  1:771945/1‑150 (MQ=255)                                                                                      aGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGCCTCTACCGACTATCGCGCCGCGGCCCAACGCAAg                                                              <  2:385575/148‑1 (MQ=255)                                                                                      aGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGCCTCTACCGACTATCGCGCCGCGGCCCAACGCAAg                                                              >  1:385575/1‑148 (MQ=255)                                                                                        gCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGCCTCTACCGACTATCGCGCCGCGGCCCAACGCAAGCTGc                                                          >  1:971608/1‑150 (MQ=255)                                                                                          ttACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGCCTCTACCGACTATCGCGCCGCGGCCCAACGCAAGCTGccc                                                        <  2:558827/150‑1 (MQ=255)                                                                                          ttACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGCCTCTACCGACTATCGCGCCGCGGCCCAACGCAAGCTGccc                                                        <  2:334985/150‑1 (MQ=255)                                                                                                    aCCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCGCTCCCACAAGCAACGCTGCGAGAATCCa                                                                                                             <  2:405344/87‑1 (MQ=255)                                                                                                    aCCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCa                                                                                                             >  1:405344/1‑87 (MQ=255)                                                                                                      cGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGCCTCTACCGACTATCGCGCCGCGGCCCAACGCAAGCTGCCCCCCTTCCTGTTc                                            >  1:966421/1‑150 (MQ=255)                                                                                                        gCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGAGCGGCTTGCTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGCCTCTACCGACTATCGCGCCGCGGCCCAACGCAAGCTGCCCCCCTTCCTGTTCCa                                          <  1:719840/150‑1 (MQ=255)                                                                                                         cATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGCCTCTACCGACTATCgcgc                                                                              <  2:154537/113‑1 (MQ=255)                                                                                                         cATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGCCTCTACCGACTATCgcgc                                                                              >  1:154537/1‑113 (MQ=255)                                                                                                          aTGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGCCTCTACCGACTATCGCGCCGCGGCCCAACGCAAGCTGCCCCCCTTCCTGTTCCACt                                        >  2:628791/1‑150 (MQ=255)                                                                                                            gCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGCCTCTACCGACTATCGCGCCGCGGCCCAACGCAAGCTGCCCCCCTTCCTGTTCCACTAc                                      <  1:628791/150‑1 (MQ=255)                                                                                                              tGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGAGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGCCTCTACCGACTATCGCGCCGCGGCCCAACGCAAGCTGCCCCCCTTCCTGTTCCACTACGc                                    >  1:1222585/1‑150 (MQ=255)                                                                                                                 ttCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGCCTCTACCGACTATCGCGCCGCGGCCCAACGCAAGCTGCCCCCTTTCCTGTTCCACTACGCTGa                                 >  2:1144435/1‑150 (MQ=255)                                                                                                                         tAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCTGCACTCCCACAAACACCACTGCGAGAATCCATGATCATTTCTGCCTCTACCGACTATCGCGCCGCGGCCCAACGCAAGCTGCCCCCCTTCCTGTTCCACTACGCTGACGgcggcg                         >  1:157732/1‑150 (MQ=255)                                                                                                                           aaGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGCCTCTACCGACTATCGCGCCGCGGCCCAACGCAAGCTGCCCCCCTTcc                                                 <  1:1001685/124‑1 (MQ=255)                                                                                                                           aaGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGCCTCTACCGACTATCGCGCCGCGGCCCAACGCAAGCTGCCCCCCTTcc                                                 >  2:1001685/1‑124 (MQ=255)                                                                                                                             gTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGCCTCTACCGACTATCGCGCCGCGGCCCAACGCAAGCTGCCCCCCTTCCTGTTCCACTACGCTGACGGCGGCGCCTa                     <  1:345975/150‑1 (MQ=255)                                                                                                                                   ggggCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGCCTCTACCGACTATCGCGCCGCGGCCCAACGCAAGCTGCCCCCCTTCCTGTTCCACTACGCTGACGGCGGCGCCTACGCCGa               <  2:775231/150‑1 (MQ=255)                                                                                                                                    gggCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGCCTCTACCGACTATCGCGCCGCGGCCCAACGCAAGCTGCCCCCCTTCCTGTTCCACTACGCTGACGGCGGCGCCTACGCCGAg              >  1:184412/1‑150 (MQ=255)                                                                                                                                      gCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGCCTCTACCGa                                                                                       >  2:561224/1‑75 (MQ=255)                                                                                                                                      gCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGCCTCTACCGa                                                                                       <  1:561224/75‑1 (MQ=255)                                                                                                                                         gggCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGCCTCTACCGACTATCGCGCCGCGGCCCAACGCAAGCTGCCCCCCTTCCTGTTCCACTACGCTGACGGCGGCGCCTACGCCGAGCacac         <  1:770182/150‑1 (MQ=255)                                                                                                                                                 gTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGCCTCTACCGACTATCGCGCCGCGGCCCAACGCAAGCTGCCCCCCTTCCTGTTCCACTACGCTGACGGCGGCGCCTACGCCGAGCACACCCTgcgc  >  2:127565/1‑150 (MQ=255)                                                                                                                                                  |                                                                                                                                                     GTCGGCAAGGAATCCGACCTGTTCCGCTTCACCGTCAAGCACAGCCTGTTCTTCGCCACCATCGTCGGCCTGATCACCCTGGTCCAGGCTTACTGGCTGACCGGCATGCTGGTTCATCACTAAAGTGAAAGGGGCCGGGCGC‑CGTCGCGCGCCCGGCACTCCCACAAGCAACGCTGCGAGAATCCATGATCATTTCTGCCTCTACCGACTATCGCGCCGCGGCCCAACGCAAGCTGCCCCCCTTCCTGTTCCACTACGCTGACGGCGGCGCCTACGCCGAGCACACCCTGCGC  >  NC_002947/5385133‑5385425

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑