Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	727,315	C→T	11.9%	W6* (TGG→TAG) ‡	PP_0621 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	727,315	0	C	T	11.9%	126.3 / 6.1	50	W6* (TGG→TAG) ‡	PP_0621	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (20/24);  new base T (4/2);  total (24/26)
Fisher's exact test for biased strand distribution p-value = 4.09e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.62e-01

GACTGCTGGCTGACTTTGTATTTGCGCCACAGCCAGAACGCGGCGGCGATCAGGGCGATCCAGAAAAGTAGGCGAACCATGGTGTCCAGCTTGTCGATTGAAGAAGCCAACAGTCTAGGACGCGGCCAATAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCACCGCTGAAGGTCAGTCGAACAGACCAAAGGTCATGTAGCTGAACCAGGAACGGTCTTTCTCGGCTTCTTTCGGGCCTTCCGGCACGATTGGGTCGCCGTTCTCGTCTTTAGGCAGCAGCTCTCGCGG  >  NC_002947/727171‑727461                                                                                                                                                 |                                                                                                                                                   gACTGCTGGCTGACTTTGTATTTGCGCCACAGCCAGAACGCGGCGGCGATCAGGGCGATCCAGAAAAGTAGGCGAACCATGGTGTCCAGCTTGTCGATTGAAGAAGCCAACAGTCTAGGACGCGGCCAATAAAAAAGGGAGGCCCAAgg                                                                                                                                                >  1:173405/1‑149 (MQ=255)   ctgctgGCTGACTTTGTATTTGCGCCCCAGCCAGACCGCGGCGCCGAGAAGGGCGAGCCAGAAAAGTTGGCGAACAATGGTGTCCTGCTTGACGATTGATCAAGCCACAAGTCAAGGACGCGCCAAATAAAAAAGGGAGGCCCAAGGcc                                                                                                                                              >  4:111767/1‑149 (MQ=255)      ctggctgACTTTGTATTTGCGCCACAGCCAGAACGCGGCGGCGATCAGGGCGATCCAGAAAAGTAGGCGAACCATGGTGTCCAGCTTGTCGATTGAAGAAGCCAACAGTCTAGGACGCGGCCAATAAAAAAGGGAGGCCCAAg                                                                                                                                                 <  5:173864/143‑1 (MQ=255)      ctggctgACTTTGTATTTGCGCCACAGCCAGAACGCGGCGGCGATCAGGGCGATCCAGAAAAGTAGGCGAACCATGGTGTCCAGCTTGTCGATTGAAGAAGCCAACAGTCTAGGACGCGGCCAATAAAAAAGGGAGGCCCAAg                                                                                                                                                 >  6:173864/1‑143 (MQ=255)         gctgACTTTGTATTTGCGCCACAGCCAGAACGCGGCGGCGATCAGGGCGATCCAGAAAAGTAGGCGAACCATGGTGTCCAGCTTGTCGATTGAAGAAGCCAACAGTCTAGGACGCGGCCAATAAAAAAGGGAGGCCCAAGGCCTCCCtt                                                                                                                                        >  4:137112/1‑149 (MQ=255)         gctgACTTTGATTTTGCGCCACAGCCAGAACGCGGCGGCGATCAGGGCGATCCAGAAAAGTAGGCGAACCATGGTGTCCAGCTTGTCGATTGAAGAAGCCAACAGTCTAGGACGCGGCCAATAAAAAAGGGAGGCCCAAGGCCTCCCt                                                                                                                                         <  1:276441/148‑1 (MQ=255)           tgACTTTGTATTTGCGCCACAGCCAGAACGCGGCGGCGATCAGGGCGATCCAGAAAAGTAGGCGAACCATGGTGTCCAGCTTGTCGATTGAAGAAGCCAACAGTCTAGGACGCGGCCAATAAAAAAGGGAGGCCCAAGGCCTCCCttt                                                                                                                                       >  2:46416/1‑148 (MQ=255)                  gTATTTGCGCCACAGCCAGAACGCGGCGGCGATCAGGGCGATCCAGAAAAGTAGGCGAACCATGGTGTCCAGCTTGTCGATTGAAGAAGCCAACAGTCTAGGACGCGGCCAATAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCAc                                                                                                                                <  8:265255/148‑1 (MQ=255)                   tATTTGCGCCACAGCCAGAACGCGGCGGCGATCAGGGCGATCCAGAAAAGTAGGCGAACCATGGTGTCCAGCTTGTCGATTGAAGAAGCCAACAGTCTAGGACGCGGCCAATAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCACCg                                                                                                                              <  1:215803/149‑1 (MQ=255)                     tttGCGCCACAGCCAGAACGCGGCGGCGATCAGGGCGATCCAGAAAAGTAGGCGAACCATGGTGTCCAGCTTGTCGATTGAAGAAGCCAACAGTCTAGGACGCGGCCAATAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCACCGCt                                                                                                                            >  3:80294/1‑149 (MQ=255)                     tttGCGCCACAGCCAGAACGCGGCGGCGATCAGGGCGATCCAGAAAAGTAGGCGAACCATGGTGTCCAGCTTGTCGATTGAAGAAGCCAACAGTCTAGGACGCGGCCAATAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCACCGCt                                                                                                                            >  1:287813/1‑149 (MQ=255)                     tttGCGCCACAGACAGAACGCGGCGGCGATCAGGGCGATCCAGAAAAGTAGGCGAAACATGGTGTCCAGCTTGTCGATTGAAGAAGCCACCAGTCTAGGACGCGGCCAATAAAAAAGGGATGCCCAAGCCCTCCCATTCATTCACCGCt                                                                                                                            >  2:273840/1‑149 (MQ=255)                        gcgcCACAGCCAGAACGCGGCGGCGATCAGGGCGATCCAGAAAAGTAGGCGAACCATGGTGTCCAGCTTGTCGATTGAAGAAGCCAACAGTCTAGGACGCGGCCAATAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCACCGCTg                                                                                                                           >  2:309319/1‑147 (MQ=255)                         cgcCACAGCCAGAACGCGGCGGCGATCAGGGCGATCCAGAAAAGTAGGCGAACCATGGTGTCCAGCTTGTCGATTGAAGAAGCCAACAGTCTAGGACGCGGCCAATAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCACCGCTGaa                                                                                                                         <  2:173405/148‑1 (MQ=255)                          gcCACAGCCAGAACGCGGCGGCGATCAGGGCGATCCAGAAAAGTAGGCGAACCATGGTGTCCAGCTTGTCGATTGAAGAAGCCAACAGTCTAGGACGCGGCCAATAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCACCGCTGAAgg                                                                                                                       <  1:46416/149‑1 (MQ=255)                            cacaGCCAGAACGCGGCGGCGATCAGGGCGATCCAGAAAAGTAGGCGAACCATGGTGTCCAGCTTGTCGATTGAAGAAGCCAACAGTCTAGGACGCGGCCAATAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCACCGCTGAAGGt                                                                                                                      >  8:197771/1‑148 (MQ=255)                             acaGCCAGAACGCGGCGGCGATCAGGGCGATCCAGAAAAGTAGGCGAACCAAGGTGTCCAGCTTGTCGATTGAAGAAGCCAACAGTCTAGGACGCGGCCAATAAAAAAGGGAGGCACAAGGCCTCCCTTTCATTAACCGCAGAAgga                                                                                                                      >  2:322857/1‑146 (MQ=255)                                 ccAGAACGCGGCGGCGTTCAGGGCGATCCAGAAAAGTAGGCGAACCATGGTGTCCAGCTTGTCGATTGAAGAAGCCAACAGTCTAGGACGCGGCCAATAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCACCGCTGAAGGTCAGTc                                                                                                                 >  7:139641/1‑148 (MQ=255)                                    gtaCGCGGCGGCGATCAGGGCGATCCAGAAAAGTAGGCGAACCATGGTGTCCAGCTTGTCGATTGAAGAAGCCAACAGTCTAGGACGCGGCCAATAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCACCGCTGAAGGTCAGTCGAAc                                                                                                             <  3:111767/147‑1 (MQ=255)                                         cggcggcgATCAGGGCGATCCAGAAAAGTAGGCGAACCATGGTGTCCAGCTTGTCGATTGAAGAAGCCAACAGTCTAGGACGCGGCCAATAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCACCGCTGAAGGTCAGTCGAACAGAc                                                                                                         >  3:304778/1‑148 (MQ=255)                                            cggcgATCAGGGCGATCCAGAAAAGTAGGCGAACCATGGTGTCCAGCTTGTCGATTGAAGAAGCCAACAGTCTAGGACGCGGCCAATAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCACCGCTGAAGGTCAGTCGAACAGACCaaa                                                                                                     <  4:80294/149‑1 (MQ=255)                                            cggcgATCAGGGCGATCCAGAAAAGTAGGCGAACCATGGTGTCCAGCTTGTCGATTGAAGAAGCCAACAGTCTAGGACGCGGCCAATAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCACCGCTGAAGGTCAGTCGAACAGACCaaa                                                                                                     <  3:137112/149‑1 (MQ=255)                                                    aGGGCGATCCAGAAAAGTAGGCGAACCATGGTGTCCAGCTTGTCGATTGAAGAAGCCAACAGTCTAGGACGCGGCCAATAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCACCGCTGAAGGTCAGTCGAACAGACCAAAGGTCATg                                                                                              <  2:287813/148‑1 (MQ=255)                                                          aTCAAGAAAAGTATGGGAACCATGGTGTCCAGCTTGTAGATTGAAGAAGCCAAAAGTCTAGTACGCGGCCAATAAAAAAGGGAGTCCCAAGGACTCCCTTTCATTCACCGCTGAAGGTCAGTCGAACAGACCAAATGTCATGTAGCTGa                                                                                       <  5:252496/149‑1 (MQ=255)                                                              aGAAAAGTAGGCGAACCATGGTGTCCAGCTTGTCGATTGAAGAAGCCAACAGTCTAGGACGCGGCCAATAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCCCCGCTGAAGGTCAGTCGAACAGACCAAAGGTAATGTAGCTGAAc                                                                                     >  4:309407/1‑147 (MQ=255)                                                                              cATGGTGTCCAGCTTGTCGATTGAAGAAGCCAACAGTCTAGGACGCGGCCAATAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCACCGCTGAAGGTCAGTCGAACAGACCAAAGGTCATGTAGCTGAACCAGGAACGGTCTTTCTCg                                                                   >  3:32651/1‑149 (MQ=255)                                                                                     tCCAGCTTGTCGATTGAAGAAGCCAACAGTCTAGGACGCGGCCAATAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCACCGCTGAAGGTCAGTCGAACAGACCAAAGGTCATGTAGCTGAACCAGGAACGGTCttt                                                                       >  6:89565/1‑138 (MQ=255)                                                                                     tCCAGCTTGTCGATTGAAGAAGCCAACAGTCTAGGACGCGGCCAATAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCACCGCTGAAGGTCAGTCGAACAGACCAAAGGTCATGTAGCTGAACCAGGAACGGTCttt                                                                       <  5:89565/138‑1 (MQ=255)                                                                                       cAGCTTGTCGATTGAAGAAGCCAACAGTCTAGGACGCGGCCAATAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCACCGCTGAAGGTCAGTCGAACAGACCAAAGGTCATGTAGCTGAACCAGGAACGGTCTTTCTCGGCTTCTTTc                                                          <  4:304778/149‑1 (MQ=255)                                                                                       cAGCTTGTCGATTGAAGAAGCCAACAGTCTAGGACGCGGCCAATAAAAAAGGGAGGCCCAAGGCCTCCCTATCATTCACCGCTGAAGGTCAGTCGAACAGACCAAAGGTCATGTAGCGGAACCAGGAACGGTCTTTCTCGGCTTCTTTc                                                          >  2:290140/1‑149 (MQ=255)                                                                                                 aTTGAAGAAGCCAACAGTCTAGGACGCGGCCAATAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCACCGCTGAAGGTCAGTCGAACAGACCAAAGGTCATGTAGCTGAACCAGGAACGGTCTTTCTCGGCTTCTTTCGGGCCTTCCg                                                <  3:265508/149‑1 (MQ=255)                                                                                                 aTTGAAGAAGCCAACAGTCTAGGACGCGGCCAATAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCACCGCTGAAGGTCAGTCGAACAGACCAAAGGTCATGTAGCTGAACCAGGAACGGTCTTTCTCGGCTTCTTTCGGGCCTTCCg                                                <  4:32651/149‑1 (MQ=255)                                                                                                          gCCAACAGTCTAGGACGCGGCCAAAAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCACCGCTGAAGGTCAGTCGAACAGACCAAAGGTCATGTAGCTGAACCAGGAACGGTCTTTCTCGGCTTCTTTCGGGCCTTCCGGCACGATTg                                       <  1:273840/149‑1 (MQ=255)                                                                                                             aaCAGTCTAGGACGCGGCCAATAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCACCGCTGAAGGTCAGTCGAACAGACCAAAGGTCATGTAGCTGAACCAGGAACGGTCTTTCTCGGCTTCTTTCGGGCCTTCCGGCACGATTGGGt                                    >  3:184983/1‑149 (MQ=255)                                                                                                                  tCTAGGACGCGGCCAATAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCACCGCTGAAGGTCAGTCGAACAGACCAAAGGTCATGTAGCTGAACCAGGAACGGTCTTTCTCGGCTTCTTTCGGGCCTTCCGGCACGATTGGGTCGCCg                               >  2:269625/1‑149 (MQ=255)                                                                                                                      ggACGCGGCCAATAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCACCGCTGAAGGTCAGTCGAACAGACCAAAGGTCATGTAGCTGAACCAGGAACGGTCTTTCTCGGCTTCTTTCGGGCCTTCCGGCACGATTGGGTCGCCGTtc                            <  6:16069/148‑1 (MQ=255)                                                                                                                       gACGCGGCCAATAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCACCGCTGAAGGTCAGTCGAACAGACCAAAGGTCATGTAGCTGAACCAGGAACGGTCTTTCTCGGCTTCTTTCGGGCCTTCCGGCACGATTGGGTCGCCGTtctc                          <  1:309319/149‑1 (MQ=255)                                                                                                                            ggCCAATAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCACCGCTGAAGGTCAGTCGAACAGACCAAAGGTCATGTAGCTGAACCAGGAACGGTCTTTCTCGGCTTCTTTCGGGCCTTCCGGCACGATTGGGTCGCCGTTCTCGTCtt                     <  4:184983/149‑1 (MQ=255)                                                                                                                              ccAATAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCACCGCTGAAGGTCAGTCGAACAGACCAAAGGTCATGTAGCTGAACCAGGAACGGTCTTTCTCGGCTTCTTTCGGGCCTTCCGGCACGATTGGGTCGCCGTTCTCGTCTTTa                   <  2:197145/149‑1 (MQ=255)                                                                                                                               cAATAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCACCGCTGAAGGTCAGTCGAACAGACCAAAGGTCATGTAGCTGAACCAGGAACGGTCTTTCTCGGCTTCTTTCGGGCCTTCCGGCACGATTGGGTCGCCGTTCTCGTCTTTAg                  <  8:139641/149‑1 (MQ=255)                                                                                                                                aaTAAAAAAGGGAGGCCCAAGGCCTACCTTTCATTCACCGCTGAAGGTCAGTCGAACAGACCAAAGGTCATGTAGCTGAACCAGGAACGGTCTTTCTCGGCTTCTTTCTGGCCTTCCGGCACGATTGGGTCGCCGTTCTCGTCTTTAgg                 <  7:22350/149‑1 (MQ=255)                                                                                                                                 aTAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCACCGCTGAAGGTCAGTCGAACAGACCAAAGGTCATGTAGCTGAACCAGGAACGGTCTTTCTCGGCTTCTTTCGGGCCTTCCGGCACGATTGGGTCGCCGTTCTCGTCTTTAGgc                <  8:95684/149‑1 (MQ=255)                                                                                                                                  tAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCACCGCTGAAGGTCATTCGAACAGACCAAAGGTCATGTAGCTGAACCAGGAACGGTCTTTCTCGGCTTCTTTCGGGCCTTCCGGCACGATTGGGTCGCCGTTCTCGTCTTTAgg                 >  5:38116/1‑147 (MQ=255)                                                                                                                                    tgaaaGGGAGGCCTTGGGCCTCCCTTTCATTCACCGCTGAAGGTCAGTCGAACAGACCAAAGGTCATGTAGCTGAACCAGGAACGGTCTTTCTCGGCTTCTTTCGGGCCTTCCGGCACGATTGGGTCGCCGTTCTCGTCTTTAg                  >  1:124796/3‑144 (MQ=255)                                                                                                                                    tgaaaGGGAGGCCTTGGGCCTCCCTTTCATTCACCGCTGAAGGTCAGTCGAACAGACCAAAGGTCATGTAGCTGAACCAGGAACGGTCTTTCTCGGCTTCTTTCGGGCCTTCCGGCACGATTGGGTCGCCGTTCTCGTCTTTAg                  <  2:124796/142‑1 (MQ=255)                                                                                                                                     gaaaGGGAGGCCTTGGGCCTCCCTTTCATTCACCGCTGAAGGTCAGTCGAACAGACCAAAGGTCATGTAGCTGAACCAGGAACGGTCTTTCTCGGCTTCTTTCGGGCCTTCCGGCACGATTGGGTCGCCGTTCTCGTCTTTAGgcag              >  8:254062/2‑147 (MQ=255)                                                                                                                                      aaaGGGAGGCCTTGGGCCTCCCTTTCATTCACCGCTGAAGGTCAGTCGAACAGACCAAAGGTCATGTAGCTGAACCAGGAACGGTCTTTCTCGGCTTCTTTCGGGCCTTCCGGCACGATTGGGTCGc                                 <  7:13564/127‑1 (MQ=255)                                                                                                                                      aaaGGGAGGCCTTGGGCCTCCCTTTCATTCACCGCTGAAGGTCAGTCGAACAGACCAAAGGTCATGTAGCTGAACCAGGAACGGTCTTTCTCGGCTTCTTTCGGGCCTTCCGGCACGATTGGGTCGc                                 >  8:13564/1‑127 (MQ=255)                                                                                                                                        aGGGAGGCCTTGGGCCTCCCTTTCATTCACCGCTGAAGGTCAGTCGAACAGACCAAAGGTCATGTAGCTGAACCAGGAACGGTCTTTCTCGGCTTCTTTCGGGCCTTCCGGCACGATTGGGTCGCCGTTCTCGTCTTTAGGCAGCAGct         >  4:13622/1‑149 (MQ=255)                                                                                                                                             ggCCCAAGGCCTCCCTTTCATTCACCGCTGAAGGTCAGTCGAACAGACCAAAGGTCATGTAGCTGAACCAGGAACGGTCTTTCTCGGCTTCTTTCGGGCCTTCCGGCACGATTGGGTCGCCGTTCTCGTCTTTAGGCAGCAGCTCTggc    <  1:322857/149‑1 (MQ=255)                                                                                                                                                ccAAGGCCTCCCTTTCATTCACCGCTGAAGGTCAGTCGAACAGACCAAAGGTCATGTAGCTGAACCAGGAACGGTCTTTCTCGGCTTCTTTCGGGCCTTCCGGCACGATTGGGTCGCCGTTCTCGTCTTTAGGCAGCAGCTCTCGCgg  >  2:175260/1‑148 (MQ=255)                                                                                                                                                 |                                                                                                                                                   GACTGCTGGCTGACTTTGTATTTGCGCCACAGCCAGAACGCGGCGGCGATCAGGGCGATCCAGAAAAGTAGGCGAACCATGGTGTCCAGCTTGTCGATTGAAGAAGCCAACAGTCTAGGACGCGGCCAATAAAAAAGGGAGGCCCAAGGCCTCCCTTTCATTCACCGCTGAAGGTCAGTCGAACAGACCAAAGGTCATGTAGCTGAACCAGGAACGGTCTTTCTCGGCTTCTTTCGGGCCTTCCGGCACGATTGGGTCGCCGTTCTCGTCTTTAGGCAGCAGCTCTCGCGG  >  NC_002947/727171‑727461

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: ‑