Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,376,485:1	+T	12.8%	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	3,376,485	1	.	T	12.8%	127.5 / 16.2	39	intergenic (+17/‑131)	PP_2975/PP_2976	insertion element ISR1 protein A3/transposase
Reads supporting (aligned to +/- strand):  ref base . (18/16);  new base T (2/3);  total (20/19)
Fisher's exact test for biased strand distribution p-value = 6.61e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.28e-01

GGATGCATCATTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTGAGAGAATGGAGCCCATATGAGCAAGCACACCAAAT  >  NC_002947/3376345‑3376634                                                                                                                                              |                                                                                                                                                      ggATGCATCATTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTC‑GCGCCGCTGAGATGgct                                                                                                                                              <  2:828614/150‑2 (MQ=255)                gaCCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGCGgttcgt                                                                                                                               >  2:809809/1‑150 (MQ=255)                   cAGGCTGCGTGAACTTGAAGAGGAGAACCGTCGGCTCAAGAAGATCTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCa                                                                                                                            <  1:360371/150‑1 (MQ=255)                   cAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCa                                                                                                                            >  2:567911/1‑150 (MQ=255)                         gCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCAGGCaaa                                                                                                                      <  1:55963/150‑1 (MQ=255)                             gAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCa                                                                                                                  >  1:439717/1‑150 (MQ=255)                             gAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCAAGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCa                                                                                                                  <  1:808001/150‑1 (MQ=255)                                 tGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTC‑GCGCCGCTGAGATGgct                                                                                                                                              <  1:182419/118‑2 (MQ=255)                                 tGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTC‑GCGCCGCTGAGATGgct                                                                                                                                              >  2:182419/1‑117 (MQ=255)                                     agagGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCaaa                                                                                                          >  2:624648/1‑150 (MQ=255)                                                 tCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATgg                                                                                                                                                >  1:302868/1‑100 (MQ=255)                                                 tCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATgg                                                                                                                                                <  2:302868/100‑1 (MQ=255)                                                        aagaagATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTg                                                                                       <  1:809809/150‑1 (MQ=255)                                                        aagaagATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTg                                                                                       >  1:84074/1‑150 (MQ=255)                                                          gaagaTGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGt                                                                                     >  1:507667/1‑150 (MQ=255)                                                          gaagaTGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTC‑GCGCCGCTGAGATGgctt                                                                                                                                             >  2:704938/1‑92 (MQ=38)                                                          gaagaTGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTC‑GCGCCGCTGAGATGgctt                                                                                                                                             <  1:704938/94‑3 (MQ=38)                                                                            gcacatCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTTCCTGTCGTTTGGTATCAGCACGACTGAACCg                                                                   >  2:32714/6‑150 (MQ=255)                                                                                cTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTg                                                                                              <  1:624538/119‑1 (MQ=255)                                                                                cTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTg                                                                                              >  2:624538/1‑119 (MQ=255)                                                                                         gagaTCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTcgc                                                      >  1:119311/1‑150 (MQ=255)                                                                                                tcCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCt                                               >  2:515572/1‑150 (MQ=255)                                                                                                   aggaggCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCa                                            <  2:575318/150‑1 (MQ=255)                                                                                                         ccATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCttt                                      <  1:75214/150‑1 (MQ=255)                                                                                                         ccATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCttt                                      <  2:439717/150‑1 (MQ=255)                                                                                                          cATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTg                                     >  1:611602/1‑150 (MQ=255)                                                                                                           aTGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTga                                    <  1:624648/150‑1 (MQ=255)                                                                                                               cAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCa                                            <  2:531225/138‑1 (MQ=255)                                                                                                               cAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCa                                            >  1:531225/1‑138 (MQ=255)                                                                                                                 aaaaaGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTGAGAGAAt                              >  1:73244/1‑150 (MQ=255)                                                                                                                      gTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTGAGAGAATGGAGc                         <  2:119311/150‑1 (MQ=255)                                                                                                                        ggTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAAc                                                                     <  2:72824/104‑1 (MQ=255)                                                                                                                        ggTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAAc                                                                     >  1:72824/1‑104 (MQ=255)                                                                                                                            aaGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTGAGATAATGGAGCCCatat                   <  1:567911/150‑1 (MQ=255)                                                                                                                            aaGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTGAGAGAATGGAGCCCatat                   <  2:507667/150‑1 (MQ=255)                                                                                                                             aGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTGAGAGAATGGAGCCCATATg                  >  1:159758/1‑150 (MQ=255)                                                                                                                                  tctcAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTGAGAGaa                               <  2:837310/132‑1 (MQ=255)                                                                                                                                  tctcAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTGAGAGaa                               >  1:837310/1‑132 (MQ=255)                                                                                                                                  tctcAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTGAGAGAATGGAGCCCATATGagcaa             >  1:740940/1‑150 (MQ=255)                                                                                                                                             c‑gAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGTCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTGAGAGAATGGAGCCCATATGAGCAAGCACACCAAAt  >  2:633526/1‑150 (MQ=255)                                                                                                                                              |                                                                                                                                                      GGATGCATCATTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTGAGAGAATGGAGCCCATATGAGCAAGCACACCAAAT  >  NC_002947/3376345‑3376634

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: ‑