Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,311,742	G→A	8.3%	intergenic (‑210/+68)	PP_1144 ← / ← rapA	membrane protein/RNA polymerase‑associated protein RapA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,311,742	0	G	A	8.3%	125.9 / 2.5	48	intergenic (‑210/+68)	PP_1144/rapA	membrane protein/RNA polymerase‑associated protein RapA
Reads supporting (aligned to +/- strand):  ref base G (17/27);  new base A (2/2);  total (19/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.37e-02

GCAGTATAGGAAGGAGTACTTAAGCCTTCCTGACTAATGGCACAATGATTTCTACGATTTGGTTATAACTCCAATCGCAGTGAGGAAT‑AAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCATTGCCAGGCCATCT  >  NC_002947/1311595‑1311879                                                                                                                                                     |                                                                                                                                           gCAGTATAGGAAGGAGTACTTAAGCCTTCCTGACTAATGGCACAATGATTTCTACGATTTGGTTATAACTCCAATCGCAGTGAGGAAT‑TAATTTGGGGCCCTAATGCCTTCCTTTGGGAGCGGGCGAGACAGCGAAGCATACACTGCgg                                                                                                                                           >  7:99536/1‑149 (MQ=255) gCAGTATAGGAAGGAGTACTTAAGCCTTCCTGACTAATGGCACAATGATTTCTACGATTTGGTTAAAACTCCAATCGCAGTGAGGAAT‑AAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCgg                                                                                                                                           <  2:295784/149‑1 (MQ=255) gCAGTATAGGAAGGAGTACTTAAGACTTCCTGTCTAATGGCTGTATGATTTATACGATTTTGTTATAACTCCAATCGCAGTGTGGAAT‑AAATTTGGGGCCCTTATGCCTTCCTGTGTGTGCGGGCGAGCCCGCGAAGGATCCACTGCgg                                                                                                                                           <  8:10494/149‑1 (MQ=255)  cAGTATAGGAAGGAGTACTTAAGCCTTCCTGACTAATGGCACAATGATTTCTACGATTTGGTTATAACTCCAATCGCAGTGAGGAATAAAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCgg                                                                                                                                           <  1:249053/149‑1 (MQ=255)      ataGGAAGGAGTACTTAAGCCTTCCTGACTAATGGCACAATGATTTCTACGATTTGGTTATAACTCCAATCGCAGTGAGGAAT‑AAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGa                                                                                                                                       <  6:207674/148‑1 (MQ=255)       taGGAAGGAGTACTTAAGCCTTCCTGACTAATGGCACAATGATTTCTACGATTTGGTTATAACTCCAATCGCAGTGAGGAAT‑AAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGAt                                                                                                                                      <  2:97359/148‑1 (MQ=255)           aaggaGTACTTAAGCCTTCCTGACTAATGGCACAATGATTTCTACGATTTGGTTATAACTCCAATCGCAGTGAGGAAT‑AAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACCGCAGTGGATGcttc                                                                                                                                 <  2:83700/149‑4 (MQ=255)             ggaGTACTTAAGCCTTCCTGACTAATGGCACAATGATTTCTACGATTTGGTTATAACTCCAATCGCAGTGAGGAAT‑AAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCg                                                                                                                               <  8:268545/149‑1 (MQ=255)               aGTACTTAAGCCTTCCTGACTAATGGCACAATGATTTCTACGATTTGGTTATAACTCCAATCGCAGTGAGGAAT‑AAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGc                                                                                                                             >  6:61937/1‑149 (MQ=255)                    ttAAGCCTTCCTGACTAATGGCACAATGATTTCTACGATTTGGTTATAACTCCAATCGCAGTGAGGAAT‑AAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGGGGATGCCACCGGCTTTGc                                                                                                                        >  6:881/1‑149 (MQ=255)                      aaGCCTTCCTGACTAATGGCACAATGATTTCTACGATTTGGTTATAACTCCAATCGCAGTGAGGAAT‑AAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGGACCATCCAAAGCGGGGGCTGCCACCCGCGTTGCCg                                                                                                                      >  2:178650/1‑149 (MQ=255)                          cTTCCTGACTAATGGCACAATGATTTCTACGATTTGGTTATAACTCCAATCGCAGTGAGGAAT‑AAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCg                                                                                                                      <  6:20931/145‑1 (MQ=255)                          cTTCCTGACTAATGGCACAATGATTTCTACGATTTGGTTATAACTCCAATCGCAGTGAGGAAT‑AAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCg                                                                                                                      >  5:20931/1‑145 (MQ=255)                               tGACTAATGGCACAATGATTTCTACGATTTGGTTATAACTCCAATCGCAGTGAGGAAT‑AAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTcgcg                                                                                                             >  5:267177/1‑149 (MQ=255)                               tGACTAATGGCACAATGATTTCTACGATTTGGTTATAACTCCAATCGCAGTGAGGAAT‑AAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCCCCCAGCCAACACAGCGGGGGGTGGCACCCGCGTTTGGGGTGTTggcg                                                                                                             >  4:213414/1‑149 (MQ=255)                                     aTGGCACAATGATTTCTACGATTTGGTTATAACTCCAATCGCAGTGAGGAAT‑AAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGt                                                                                                        <  3:213414/148‑1 (MQ=255)                                      tGGCACAATGATTTCTACGATTTGGTTATAACTCCAATCGCAGTGAGGAAT‑AAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGgt                                                                                                                    >  5:291258/1‑135 (MQ=255)                                      tGGCACAATGATTTCTACGATTTGGTTATAACTCCAATCGCAGTGAGGAAT‑AAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGgt                                                                                                                    <  6:291258/135‑1 (MQ=255)                                      tGGCACAATGATTTCTACGATTTGGTTATAACTCCAATCGCAGTGAGGAAT‑AAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCCCGCAGCCTACACAGCGGGGGGTGGCACCCGCgttggcggggttggcgggggggc                                                                                                      >  6:181687/1‑144 (MQ=255)                                       ggCACAATGATTTCTACGATTTGGTTATAACTCCAATCGCAGTGAGGAAT‑AAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATACACAGCGGTGGGTGCCACCCGCGTTTGCGGTGTTGGCGGGCGTGcc                                                                                                     >  4:66226/1‑149 (MQ=255)                                                    cTACGATGTGGTTATAACTCCAATCGCAGTGAGCAAT‑AAATTGGGCGCCCTAATGCCTTCCTGGGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACAAg                                                                                        <  7:45812/148‑1 (MQ=37)                                                             ggTTAAAACTCCAATCGCAGTGCGGAAT‑AAATTTGGGGCCCTAATCCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACAAGGGGCGCggg                                                                               <  5:181687/148‑1 (MQ=255)                                                              gTTATAACTCCAATCGCAGTGAGGAAT‑AAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACAAGGGGCGCGGGGc                                                                             <  6:310969/149‑1 (MQ=255)                                                               ttATAACTCCAATCGCAGTGAGGAAT‑AAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACCGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACaa                                                                                         <  8:63106/136‑1 (MQ=255)                                                               ttATAACTCCAATCGCAGTGAGGAAT‑AAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACCGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACaa                                                                                         >  7:63106/1‑136 (MQ=255)                                                                  taACTCCAATCGCAGTGAGGAAT‑AAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACAAGGGGCGCGGGGCCTgc                                                                         <  5:24775/149‑1 (MQ=255)                                                                  taACTCCAATCGCAGTGAGGAAT‑AAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACAAGGGGCGCGGGGCCTgc                                                                         <  6:258091/149‑1 (MQ=255)                                                                   aaCTCCAATCGCAGTGAGGAAT‑AAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACAAGGGGCGCGGGGCCTgcg                                                                        >  5:316826/1‑149 (MQ=255)                                                                      tCCAATCGCAGTGAGGAAT‑AAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACAAGGGGCGCggg                                                                               <  7:41322/139‑1 (MQ=255)                                                                      tCCAATCGCAGTGAGGAAT‑AAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACAAGGGGCGCGGGGCCTgcgc                                                                       >  5:161837/1‑147 (MQ=255)                                                                       ccAATCGCAGTGAGGAAT‑AAATTTGGGGCCCTAATGCCTTCCTGGGGGAGCGGGCGCCCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGCTTCCCACAAGGGGCGCGGGGCCTGCGCTa                                                                     <  1:178650/149‑1 (MQ=38)                                                                         aaTCGCAGTGAGGAAT‑AAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACAAGGGGCGCGGGGCCTGCGCTagcc                                                                  <  6:267177/149‑1 (MQ=255)                                                                          aTCGCAGTGAGGAAT‑AAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACAAGGGGCGCGGGGCCTGCGCTagcca                                                                 <  5:61937/149‑1 (MQ=255)                                                                              cAGTGAGGAAT‑AAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACAAGGGGCGCGGGGCCTGCGCTagccagcc                                                              <  6:161837/148‑1 (MQ=255)                                                                                            aTTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAAt                                                <  5:43227/149‑1 (MQ=255)                                                                                                ggggCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGc                                             <  2:294721/148‑1 (MQ=255)                                                                                                                   gggggAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACAAGGGGCGCGGGGCCTGCGCTagccagc                                                               <  1:38379/109‑1 (MQ=255)                                                                                                                     gggAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTtc                       <  3:66226/149‑1 (MQ=255)                                                                                                                      ggAGGGTGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGggcg                             <  3:301864/142‑1 (MQ=255)                                                                                                                       gAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTtctc                     <  3:67387/149‑1 (MQ=255)                                                                                                                         gCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCa                   <  7:9918/149‑1 (MQ=255)                                                                                                                           gggCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGc                 <  4:307127/149‑1 (MQ=255)                                                                                                                            ggCGAGCCCGCGAAGCATCCACAGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCa                >  8:246383/1‑149 (MQ=255)                                                                                                                                 gCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCATTGc            >  4:235489/1‑148 (MQ=255)                                                                                                                                  cccGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCATTGCCa          <  8:26355/149‑1 (MQ=255)                                                                                                                                      ggtggCATCCACCGCAGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACAAGGGGCGCGGGGCCTGCGCTAGCCCGCCACCAGCACGCGAATGGCATCCAGGCGCAGGGCGGCCTTCTCCAGCATTGCCAGGcc      >  6:267429/5‑149 (MQ=38)                                                                                                                                      cgAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACAAGGGGCGCGGGGCCTGCGCTATCTAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGTCTTCTCCAGCATTGCCAGGcc      <  1:45967/149‑1 (MQ=255)                                                                                                                                         aGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCATTGCCAGGCCATc   >  2:214164/1‑149 (MQ=255)                                                                                                                                          gCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCATTGCCAGGCCATCt  >  2:55598/1‑149 (MQ=255)                                                                                                                                          gCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAACCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCATTGCCAGGCCATCt  >  7:223322/1‑149 (MQ=255)                                                                                                                                            aTCCACCGCAGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGggcggc                           >  3:199263/1‑122 (MQ=255)                                                                                                                                            aTCCACCGCAGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGggcggc                           <  4:199263/122‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                           GCAGTATAGGAAGGAGTACTTAAGCCTTCCTGACTAATGGCACAATGATTTCTACGATTTGGTTATAACTCCAATCGCAGTGAGGAAT‑AAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGC‑TCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCATTGCCAGGCCATCT  >  NC_002947/1311595‑1311879

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑