Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,376,442:1	+T	13.7%	intergenic (+17/‑131)	PP_2975 → / → PP_2976	insertion element ISR1 protein A3/transposase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,376,442	1	.	T	13.7%	162.7 / 25.2	51	intergenic (+17/‑131)	PP_2975/PP_2976	insertion element ISR1 protein A3/transposase
Reads supporting (aligned to +/- strand):  ref base . (23/21);  new base T (2/5);  total (25/26)
Fisher's exact test for biased strand distribution p-value = 4.19e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.99e-01

CGGCATGGATGCATCATTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTGAGAGAATGGAGCCCATATGAGCAAGCACAC  >  NC_002947/3376296‑3376586                                                                                                                                                    |                                                                                                                                                  cggcATGGATGCATCATTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGgcgc                                                                                                                                                    >  3:37853/1‑147 (MQ=255)     aTGGATGCATCATTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTC‑GCGCCGCTGAGATg                                                                                                                                             <  6:24279/149‑1 (MQ=255)         aTGCATCATTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTC‑GCGCCGCTGAGATGgctt                                                                                                                                         <  3:308259/149‑3 (MQ=255)            catcatTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTC‑GCGCCGCTGAGATGgctttac                                                                                                                                      <  5:221819/149‑6 (MQ=255)             atcatTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCgca                                                                                                                                        <  4:200361/146‑1 (MQ=255)             atcatTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCgca                                                                                                                                        >  3:200361/1‑146 (MQ=255)                atTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑Agg                                                                                                                                  <  8:46047/148‑1 (MQ=255)                     tgaCCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCAGCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGgttc                                                                                                                            <  3:17028/149‑1 (MQ=255)                               gCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTC‑GCGCCGCTGAGATg                                                                                                                                             <  1:38805/123‑1 (MQ=255)                               gCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTC‑GCGCCGCTGAGATg                                                                                                                                             >  2:38805/1‑123 (MQ=255)                                 gTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑Agg                                                                                                                                  <  4:230703/131‑1 (MQ=255)                                 gTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑Agg                                                                                                                                  >  3:230703/1‑131 (MQ=255)                                      cTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAg                                                                                                            >  4:321345/1‑148 (MQ=255)                                       tGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTa                                                                                                          >  1:289410/1‑149 (MQ=255)                                       tGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTa                                                                                                          >  4:307408/1‑149 (MQ=255)                                        ggAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTAt                                                                                                         >  4:97897/1‑149 (MQ=255)                                         gAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTAt                                                                                                         <  2:289410/148‑1 (MQ=255)                                               gagaACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAgg                                                                                                                     >  7:212329/1‑130 (MQ=255)                                               gagaACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAgg                                                                                                                     <  8:212329/130‑1 (MQ=255)                                                 gaACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGc                                                                                                <  4:37853/149‑1 (MQ=255)                                                          gCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTc                                                                                       <  8:233042/149‑1 (MQ=255)                                                          gCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCATGtg                                                                                       >  5:1076/1‑148 (MQ=255)                                                            tCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCTCCGAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCg                                                                                      >  1:110397/1‑149 (MQ=255)                                                                gaagaTGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTgg                                                                                 >  6:30719/1‑149 (MQ=255)                                                                        aCGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGc                                                                          <  1:174341/148‑1 (MQ=255)                                                                           ccGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGa                                                                      >  2:184416/1‑149 (MQ=255)                                                                                     ccTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGgtt                                                                                                                             >  6:31986/1‑84 (MQ=255)                                                                                     ccTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGgtt                                                                                                                             <  5:31986/84‑1 (MQ=255)                                                                                      cTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGc                                                                                            >  6:280647/1‑116 (MQ=255)                                                                                         aaGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCgg                                                        >  2:277499/1‑149 (MQ=255)                                                                                            gCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGtt                                                     >  7:220767/1‑149 (MQ=255)                                                                                              cGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTg                                                                                  >  3:65895/1‑118 (MQ=255)                                                                                              cGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTg                                                                                  <  4:65895/118‑1 (MQ=255)                                                                                              cGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTc                                                   <  3:307408/149‑1 (MQ=255)                                                                                              cGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTc                                                   >  5:148601/1‑149 (MQ=255)                                                                                                   tcatcCAGGAGGCCATGGCAAAAAAGTTGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGa                                              <  7:280138/149‑1 (MQ=255)                                                                                                      tcCTGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTGAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTGGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTcgcg                                                <  3:209690/144‑1 (MQ=255)                                                                                                      tcCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGAGGCGA‑GAGATGTCGCAGC‑AGGCGCTTCGTTCAGGCAAAGCCAGAATCAAAATAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGCGGTTCGCGGAga                                            >  4:209690/1‑147 (MQ=255)                                                                                                           gaggCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGc                                                                                                >  8:13493/1‑91 (MQ=255)                                                                                                           gaggCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGc                                                                                                <  7:13493/91‑1 (MQ=255)                                                                                                                  tGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTga                               <  5:30719/149‑1 (MQ=255)                                                                                                                  tGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTga                               <  3:97897/149‑1 (MQ=255)                                                                                                                           aGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCCCGGAGGCTCCACCCTTTGAGAGAATGGa                      <  1:184416/149‑1 (MQ=255)                                                                                                                                 tgcgCCATCTC‑GCGCCGCTGAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTgaga                             >  3:122143/4‑136 (MQ=255)                                                                                                                                 tgcgCCATCTC‑GCGCCGCTGAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTgaga                             <  4:122143/133‑1 (MQ=255)                                                                                                                                     ccATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTGAGAGAATGGAGCCCatat              >  3:233981/1‑147 (MQ=255)                                                                                                                                      cATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCa                                                                            >  2:293103/1‑84 (MQ=255)                                                                                                                                      cATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCa                                                                            <  1:293103/84‑1 (MQ=255)                                                                                                                                        tctcAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTGAGAGAATGGAGCCCATATGagc          >  7:259144/1‑148 (MQ=255)                                                                                                                                          tcAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGCCACAGCCAGTATCAAATTAGCGTGCCGGTCGTTTGGTATCAGCACGCCTGAGGCGCCCCGGGGGTCGCGGCGGCTCGCGCCTGTGCGAGAATGGAGCCGATATGagcgag       >  8:153457/1‑149 (MQ=255)                                                                                                                                            aGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTGAGAGAATGGAGCCCATATGagcaa        <  3:321345/146‑1 (MQ=255)                                                                                                                                               ggcgC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCACGGAGGCTCCACCCTTTGAGAGAATGGAGCCCATATGAGCAAGCacac  <  2:110397/149‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                  CGGCATGGATGCATCATTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGC‑AGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTGAGAGAATGGAGCCCATATGAGCAAGCACAC  >  NC_002947/3376296‑3376586

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑