Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,869,100	C→A	11.1%	intergenic (+639/‑292)	PP_2520 → / → PP_2522	hypothetical protein/transposase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,869,100	0	C	A	11.1%	142.0 / 7.9	52	intergenic (+639/‑292)	PP_2520/PP_2522	hypothetical protein/transposase
Reads supporting (aligned to +/- strand):  ref base C (20/26);  new base A (2/4);  total (22/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.85e-01

GCTTTCAGGCAACCCTCACATCTCGATCAATACCCGGGTCGCTGATTCGGAATATCAGTTTCGCGCGCGCAACGCT‑‑GCCATGGCGTA‑‑CCTGATGCAGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGCGCGGGCA‑TTCTGCTTCCTGGCCAATGATGGGTTCTGCAAGCACAGCGGTGAGCAGATCCTGACGCGGCGCCAGACCCAACAAGTGAACTCGATCATGGCCACCAGCGGG  >  NC_002947/2868953‑2869247                                                                                                                                                         |                                                                                                                                                     gCTTTCAGGCAACCCTCACATCTCGATCAATACCCGGGTCGCTGATTCGGAATATCAGTTTCGCGCGCGCAACGCT‑‑GCCATGGCGTA‑‑CCTGATGCAGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCa                                                                                                                                                     <  1:37591/149‑1 (MQ=255)  cTTTCAGGCAACCCTCACATCTCGATCAATACCCGGGTCGCTGATTCGGAATATCAGTTTCGCGCGCGCAACGCT‑‑GCCATGGCGTA‑‑CCTGATGCAGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAg                                                                                                                                                    <  7:146086/149‑1 (MQ=255)        ggCAACCCTCACATCTCGATCAATACCCGGGTCGCTGATTCGGAATATCAGTTTCGCGCGCGCAACGCT‑‑GCCATGGCGTA‑‑CCTGATGCAGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTAACTGAAGTAACTg                                                                                                                                              <  1:92945/149‑1 (MQ=255)         gCAACCCTCACATCTCGATCAATACCCGGGTCGCTGATTCGGAATATCAGTTTCGCGCGCGCAACGCT‑‑GCCATGGCGTA‑‑CCTGATGCAGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTAACTGAAGTAACTgc                                                                                                                                             <  1:208449/149‑1 (MQ=255)            aCCCTCACATCTCGATCAATACCCGGGTCGCTGATTCGGAATATCAGTTTCGCGCGCGCAACGCT‑‑GCCATGGCGTA‑‑CCTGATGCAGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCa                                                                                                                                          <  8:294140/149‑1 (MQ=255)            aCCCTCACATCTCGATCAATACCCGGGTCGCTGATTCGGAATATCAGTTTCGCGCGCGCAACGCT‑‑GCCATGGCGTA‑‑CCTGATGCAGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTAACTGAAGTAACTGCGCa                                                                                                                                          <  1:167015/149‑1 (MQ=255)             cccTCACATCTCGATCAATACCCGGGTCGCTGATTCGGAATATCAGTTTCGCGCGCGCAACGCT‑‑GCCATGGCGTA‑‑CCTGATGCAGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCAc                                                                                                                                         <  1:140166/149‑1 (MQ=255)             cccTCACATCTCGATCAATACCCGGGTCGCTGATTCGGAATATCAGTTTCGCGCGCGCAACGCT‑‑GCCATGGCGTA‑‑CCTGATGCAGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTAACTGAAGTAACTGCGCag                                                                                                                                         <  3:252349/149‑2 (MQ=255)                  acaTCTCGATCAATACCCGGGTCGCTGATTCGGAATATCAGTTTCGCGCGCGCAACGCT‑‑GCCATGGCGTA‑‑CCTGATGCAGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGc                                                                                                                                      <  6:64224/147‑1 (MQ=255)                   caTCTCGATCAATACCCGGGTCGCTGATTCGGAATATCAGTTTCGCGCGCGCAACGCT‑‑GCCATGGCGTA‑‑CCTGATGCAGTCATTTGGCAACTATCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCaa                                                                                                                                    <  1:294018/149‑1 (MQ=255)                   caTCTCGATCAATACACGGGTCGCTGATTAGGTAAATCAGTTTATCGCGCGCAAAGCTCCGCCATGGCGTACCCCCCTTGCAGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTg                                                                                                                                       <  1:117635/149‑1 (MQ=255)                         gATCAATACCCGGGTCGCTGATAAGGAATATCAGTTTCGCGCGCGCAACGCT‑‑GCCATGGCGTA‑‑CCTGATGCAGTCATTTGGCAACT‑TACATAACGAGGTCGAGAAGGTGCTGCGCAGTTACTTAAGTTACTGCGCACTGCAAATGaaat                                                                                                                             >  7:57162/1‑147 (MQ=255)                           tCAATACCCGGGTCGCTGATTCGGAATATCAGTTTCGCGCGCGCAACGCT‑‑GCCATGGCGTA‑‑CCTGATGCAGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGc                                                                                                                           <  8:174301/149‑1 (MQ=255)                              aTACCCGGGTCGCTGATTCGGAATATCAGTTTCGCGCGCGCAACGCT‑‑GCCATGGCGTA‑‑CCTGATGCAGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTg                                                                                                                        >  7:40764/1‑149 (MQ=255)                                 cccGGGTCGCTGATTCGGAATATCAGTTTCGCGCGCGCAACGCT‑‑GCCATGGCGTA‑‑CCTGATGCAGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGAc                                                                                                                     <  5:257454/149‑1 (MQ=255)                                  ccGGGTCGCTGATTCGGAATATCAGTTTCGCGCGCGCAACGCT‑‑GCCATGGCGTA‑‑CCTGATGCAGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGATGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGaac                                                                                                                    >  7:308450/1‑147 (MQ=255)                                          cTGATTCGGAATATCAGTTTCGCGCGCGCAACGCT‑‑GCCATGGCGTA‑‑CCTGATGCAGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGCGCgg                                                                                                            >  5:301265/1‑149 (MQ=255)                                          cTGATTCGGAATATCAGTTTCGCGCGCGCAACGCT‑‑GCCATGGCGTA‑‑CCTGATGCAGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGCGCgg                                                                                                            >  7:75753/1‑149 (MQ=255)                                             aTTCGGAATATCAGTTTCGCGCGCGCAACGCT‑‑GCCATGGCGTA‑‑CCTGATGCAGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACt                                                                                                                                               <  8:334381/111‑1 (MQ=255)                                             aTTCGGAATATCAGTTTCGCGCGCGCAACGCT‑‑GCCATGGCGTA‑‑CCTGATGCAGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACt                                                                                                                                               >  7:334381/1‑111 (MQ=255)                                                   aaTATCAGTTTCGCGCGCGCAACGCT‑‑GCCATGGCGTA‑‑CCTGATGCAGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGCGCGGGCA‑TTCTGc                                                                                                  >  1:46999/1‑149 (MQ=255)                                                     tatCAGTTTCGCGCGCGCAACGCT‑‑GCCATGGCGTA‑‑CCTGATGCAGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGCGCGGGCA‑TTCTGCtt                                                                                                <  2:46999/149‑1 (MQ=255)                                                      atCAGTTTCGCGCGCGCAACGCT‑‑GCCATGGCGTA‑‑CCTGATGCAGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGCGCGGGCA‑TTCTg                                                                                                   <  4:179120/145‑1 (MQ=255)                                                      atCAGTTTCGCGCGCGCAACGCT‑‑GCCATGGCGTA‑‑CCTGATGCAGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGCGCGGGCA‑TTCTg                                                                                                   >  3:179120/1‑145 (MQ=255)                                                          gTTTCTCGCGCGCAACGCT‑‑GCCATGGCGTA‑‑CCTGATGCAGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGCGCGGGCA‑TTCTGCTTCCTgg                                                                                           <  8:308450/149‑1 (MQ=255)                                                           tttCGCGCGCGCAACGCT‑‑GCCATGGCGTA‑‑CCTGATGCAGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGCGCGGGCA‑TTCTGCTTCCTGGc                                                                                          >  4:258090/1‑149 (MQ=255)                                                             tCGCGCGCGCAACGCT‑‑GCCATGGCGTA‑‑CCTGATGCAGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGCGCGGGCA‑TTCTGCTTCCTGGcc                                                                                         <  3:258090/148‑1 (MQ=255)                                                                    cgcAACGCT‑‑GCCATGGCGTA‑‑CCTGATGCAGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGCGCGGGCA‑TTCTGCTTCCTGGCCAATGATgg                                                                                 <  3:316664/149‑1 (MQ=255)                                                                       aaCGCT‑‑GCCATGGCGTA‑‑CCTGATGCAGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGCGCGGGCA‑TTCTGCTTCCTGGCCAATGATGGGt                                                                               >  6:335249/1‑148 (MQ=255)                                                                                       gTA‑‑CCTGATGCAGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGCGCGGGCA‑TTCTGCTTCCTGGCCAATGATGGGTTCTGCAAGCACAGCg                                                                <  5:335249/149‑1 (MQ=255)                                                                                            ccTGATGCATTTATTTGGCAAAT‑TCCATAACGATGTCGATACGGTTCTGCGCATTTACTTCAGTTACTGCGCACTGTAAATGAACTGCCTGGATCTGGCGCGGGTA‑TTCTGTTTTCTGGCTAATGATGGGTTCTGCAAGCACAGCGGt                                                              <  8:57162/148‑1 (MQ=255)                                                                                             cTGATGCAGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAAt                                                                                                                                  <  8:196679/80‑1 (MQ=255)                                                                                             cTGATGCAGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAAt                                                                                                                                  >  7:196679/1‑80 (MQ=255)                                                                                                    aGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGCGCGGGCA‑TTCTGCTTCCTGGCCAATGATGGGTTCTGCAAGCACAGCGGTGAGCAGATc                                                     >  6:63257/1‑149 (MQ=255)                                                                                                       cATTAGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGCGCGGGCA‑TTCTGCTTCCTGGCCAATGATGGGTTCTGCAAGCACAGCGGTGAGCAGATCCt                                                   >  2:125098/1‑148 (MQ=255)                                                                                                         tttGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGCGCGGGCA‑TTCTGCTTCCTGGCCAATGATGGGTTCTGCAAGCACAGCGGTGAGCAGATCCTGAc                                                <  8:40764/149‑1 (MQ=255)                                                                                                               aaCT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGcgcg                                                                                                             <  5:91904/83‑1 (MQ=255)                                                                                                               aaCT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGcgcg                                                                                                             >  6:91904/1‑83 (MQ=255)                                                                                                                aCT‑TCCATAACGAGGGCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGCGCGGGCA‑TTCTGCTTCCTGGCCAATGATGGGTGCTGCAAGCACAGCGGTGAGCAGATCCTGACGCGgcgc                                         <  6:265938/149‑1 (MQ=255)                                                                                                                 cT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGCGCGGGCA‑TTCTGCTTCCTGGCCAATGATGGGTTCTGCAAGCACAGCGGTGAGCAGATCCTGACGCGgcgc                                         >  7:249389/1‑148 (MQ=255)                                                                                                                  t‑tCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGCGCGGGCA‑TTCTGCTTCCTGGCCAATGATGGGTTCTGCAAGCACAGCGGTGAGCAGATCCTGACGCGgcgc                                         >  1:59327/1‑147 (MQ=255)                                                                                                                      cATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGCGCGGGCA‑TTCTGCTTCCTGGCCAATGATGGGTTCTGCAAGCACAGCGGTGAGCAGATCCTGACGCGGCGCCAGAc                                    >  6:76486/1‑149 (MQ=255)                                                                                                                      cATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGCGCGGGCA‑TTCTGCTTCCTGGCCAATGATGGGTTCTGCAAGCACAGCGGTGAGCAGATCCTGACGCGGCGCCAGAc                                    <  8:204905/149‑1 (MQ=255)                                                                                                                            gAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGCGCGGGCA‑TTCTGCTTCCTGGCCAATGATGGGTTCTGCAAGCACAGCGGTGAGCAGATCCTGACGCGGCGCCAGACCcaac                               >  3:373734/1‑148 (MQ=255)                                                                                                                             aGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGCGCGGGCA‑TTCTGCTTCCTGGCCAATGATGGGTTCTGCAAGCACAGCGGTGAGCAGATCCTGACGCGGCGCCAGACCcaacaa                             <  5:63257/149‑1 (MQ=255)                                                                                                                               gTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGCGCGGGCA‑TTCTGCTTCCTGGCCAATGATGGGTTCTGCAAGCACAGCGGTGAGCAGATCCTGACGCGGCGCCAGACCCAACAAGt                           <  6:301265/149‑1 (MQ=255)                                                                                                                               gTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGCGCGGGCA‑ATCTGCTTCCTGGCAAATGATGGGTTCTGCAAGCAGAGCGGTGAGCAGATCCTGACGCGGCGCCAGACCCAACAAGt                           <  8:75753/149‑1 (MQ=255)                                                                                                                                       ggTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGCGCGGGCA‑TTCTGCTTCCTGGCCAATGATGGGTTCTGCAAGCACAGCGGTGAGCAGATCCTGACGCGGCGCCAGACCCAACAAGTGAACTCGa                   <  5:76486/149‑1 (MQ=255)                                                                                                                                           gtgcGCAGTAACTGAAG‑TACTGCGCACTGCAAATGAACTGCCTGGACCTGGCGCGGGCA‑TTCTGCTTCCTGGCCAATGATGGGTTCTGCAAGCACAGCGGTGAGCAGATCCTGACGCGGCGCCAGACCCAACAAGTGAACTCGATCATg              >  2:186821/2‑149 (MQ=255)                                                                                                                                             gcgcAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGCGCGGGCA‑TTCTGCTTCCTGGCCAATGATGCGTTCTGCAAGCACAGCGGTGAGCAGATCCTGACGCGGCGCCAGACCCAACAAGTGAACTCGATCATgg             >  4:84668/1‑149 (MQ=255)                                                                                                                                                     aCTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGCGCGGGCATTTCTGCTTCCTGGCCAATGATGGGTTCTGCAAGCACAGCGGTGAGCAGATCCTGACGCGGCGCCAGACCCAACAAGTGAACTCGATCATGGCCACCAg      >  1:93904/1‑149 (MQ=255)                                                                                                                                                       ttCAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGCGCGGGCA‑TTCTGCTTCCTGGCCAATGATGGGTTCTGCAAGCACAGCGGTGAGCAGATCCTGACGCGGCGCCAGACCCAACAAGTGAACTCGATCATGGCCACCAGCgg   >  7:176232/1‑149 (MQ=255)                                                                                                                                                         cAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGCGCGGGCA‑TTCTGCTTCCTGGCCAATGATGGGTTCTGCAAGCACAGCGGTGAGCAGATCCTGACGCGGCGCCAGACCCAACAAGTGAACTCGATCATGGCCACCAGCggg  <  8:249389/148‑1 (MQ=255)                                                                                                                                                         |                                                                                                                                                     GCTTTCAGGCAACCCTCACATCTCGATCAATACCCGGGTCGCTGATTCGGAATATCAGTTTCGCGCGCGCAACGCT‑‑GCCATGGCGTA‑‑CCTGATGCAGTCATTTGGCAACT‑TCCATAACGAGGTCGAGACGGTGCTGCGCAGTTACTTCAGTTACTGCGCACTGCAAATGAACTGCCTGGACCTGGCGCGGGCA‑TTCTGCTTCCTGGCCAATGATGGGTTCTGCAAGCACAGCGGTGAGCAGATCCTGACGCGGCGCCAGACCCAACAAGTGAACTCGATCATGGCCACCAGCGGG  >  NC_002947/2868953‑2869247

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: ‑