Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,043,260	T→C	7.1%	F110F (TTT→TTC)	PP_4448 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,043,260	0	T	C	7.1%	161.6 / 2.6	56	F110F (TTT→TTC)	PP_4448	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (26/26);  new base C (2/2);  total (28/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.39e-01

GACGATAGAAAAAATCGCCGACACGTTATTGAGGCCCTGCCACTGGGCGTGATCAAGGATGATAAATTTATCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTGACATCAGGGTACCAGTTGACGGAAACAGATTCTTCAACAAGCATATTGCGGTAGTCGGATCAACAGGCGCCGGCAAATCCAACACAGT  >  NC_002947/5043114‑5043406                                                                                                                                                    |                                                                                                                                                   gACGATAGAAAAAATCGCCGACACGTTATTGAGGCCCTGCCACTGGGCGTGATCAAGGATGATAAATTTATCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTg                                                                                                                                                   <  4:173013/148‑1 (MQ=255) gACGATAGAAAAAATCGCCGACACGTTATTGAGGCACTGCCACTGGGCGTGATCAAGGATGATAAATTTATCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTg                                                                                                                                                   >  2:121832/1‑148 (MQ=255)        gAAAAAATCGCCGACACGTTATTGAGGCCCTGCCACTGGGCGTGATCAAGGATGATAAATTTATCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTc                                                                                                                                            <  1:167859/148‑1 (MQ=255)               tCGCCGACACGTTATTGAGGCCCTGCCACTGGGCGTGATCAAGGATGATAAATTTATCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCa                                                                                                                                    <  1:121832/149‑1 (MQ=255)               tCGCCGACACGTTATTGAGGCCCTGCCACTGGGCGTGATCAAGGATGATAAATTTATCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCa                                                                                                                                    >  1:19701/1‑149 (MQ=255)               tCGCCGACACGTTATTGAGGCCCTGCCACTGGGCGTGATCAAGGATGATAAATTTATCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCa                                                                                                                                    >  7:301457/1‑149 (MQ=255)                  ccGACACGTTATTGAGGCCCTGCCACTGGGCGTGATCAAGGATGATAAATTTATCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACt                                                                                                                                  >  2:103675/1‑148 (MQ=255)                     acacGTTATTGAGGCCCTGCCACTGGGCGTGATCAAGGATGATAAATTTATCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATa                                                                                                                              <  8:301528/149‑1 (MQ=255)                         gTTATTGAGGCCCTGCCACTGGGCGTGATCAAGGATGATAAATTTATCCGTGGAGCAGACGCCCTGACCATTCCTCCAACTGGCGTTGCCCCTGGCACTATTCATGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGa                                                                                                                           >  5:235878/1‑148 (MQ=255)                            aTTGAGGCCCTGCCACTGGGCGTGATCAAGGATGATAAATTTATCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAAt                                                                                                                               >  4:303193/1‑141 (MQ=255)                            aTTGAGGCCCTGCCACTGGGCGTGATCAAGGATGATAAATTTATCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAAt                                                                                                                               <  3:303193/141‑1 (MQ=255)                                aGGCCCTGCCACTGGGCGTGATCAAGGATGATAAATTTATCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAAt                                                                                                                        >  4:236319/1‑144 (MQ=255)                                aGGCCCTGCCACTGGGCGTGATCAAGGATGATAAATTTATCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAAt                                                                                                                        <  3:236319/144‑1 (MQ=255)                                aGGCCCTGCCACTGGGCGTGATCAAGGATGATAAATTTATCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGa                                                                                                                    <  1:88244/148‑1 (MQ=255)                                 ggCCCTGCCACTGGGCGTGATCAAGGATGATAAATTTATCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGt                                                                                                                  >  4:304988/1‑149 (MQ=255)                                    ccTGCCACTGGGCGTGATCAAGGATGATAAATTTATCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGtttt                                                                                                               >  8:81885/1‑149 (MQ=255)                                     cTGCCACTGGGCGTGATCAAGGATGATAAATTTATCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTc                                                                                                              <  2:30919/149‑1 (MQ=255)                                        ccACTGGGCGTTATCAAGGATGATAAATTTATCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCt                                                                                                            <  3:138500/148‑1 (MQ=255)                                         cACTGGGCGTGATAAAGGATGATAAATTTATCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCTCTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTAGCCACTAATAGGAAATTTGAGTTTTCCTc                                                                                                           <  5:90042/148‑1 (MQ=255)                                              ggCGTGATCAAGGATGATAAATTTATCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTc                                                                                                                                            >  8:209792/1‑110 (MQ=255)                                              ggCGTGATCAAGGATGATAAATTTATCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTc                                                                                                                                            <  7:209792/110‑1 (MQ=255)                                              ggCGTGATCAAGGATGATAAATTTATCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGt                                                                                                     >  6:299190/1‑149 (MQ=255)                                                          gatgatAAATTTATCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTg                                                                                          >  7:128109/1‑148 (MQ=255)                                                           atgatAAATTTATCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTGAc                                                                                        <  2:107107/149‑1 (MQ=255)                                                            tgatAAATTTATCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTCGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTGACa                                                                                       >  2:32098/1‑149 (MQ=255)                                                            tgatAAATTTATCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTCGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTGACa                                                                                       >  6:91752/1‑149 (MQ=255)                                                             gatAAATTTATCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCAtt                                                                                                        >  6:130451/1‑131 (MQ=255)                                                             gatAAATTTATCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCAtt                                                                                                        <  5:130451/131‑1 (MQ=255)                                                                 aaTTTATCCGTGGAGGAGACGCACTGACCATTCCTCCAAATGGCGTTGCCCCTGCCACTATTCAATACATTAAAAATCTTCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTGACATCAg                                                                                   <  1:103675/149‑1 (MQ=255)                                                                   tttATCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATa                                                                                                                              >  6:224601/1‑103 (MQ=255)                                                                   tttATCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATa                                                                                                                              <  5:224601/103‑1 (MQ=255)                                                                       tCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTGATGTCAGGGtcggt                                                                            <  8:301457/149‑5 (MQ=255)                                                                       tCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTGATGTCAGGGtcggt                                                                            <  2:19701/149‑5 (MQ=255)                                                                       tCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTCGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTGACATCAGGGTAcc                                                                             <  1:32098/148‑1 (MQ=255)                                                                       tCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTCGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTGACATCAGGGTAcc                                                                             <  5:91752/148‑1 (MQ=255)                                                                          gTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTGACATCAGGGTACCAGtt                                                                         >  1:135712/1‑149 (MQ=255)                                                                              aggagACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTGACATCAGGGTACCAGTTGACg                                                                     <  7:81885/149‑1 (MQ=255)                                                                               ggagACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTGACATCAGGGTACCAGTTGACg                                                                     >  3:28803/1‑148 (MQ=255)                                                                                gagaCGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTGACATCAGGGTACCAGTTGACgg                                                                    >  4:206732/1‑148 (MQ=255)                                                                                         tGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTGACATCAGGGTACCAGTTGACGGAAACAGAttc                                                          <  3:273286/149‑1 (MQ=255)                                                                                           aCCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTGACATCAGGGTAc                                                                              >  8:275295/1‑127 (MQ=255)                                                                                           aCCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTGACATCAGGGTAc                                                                              <  7:275295/127‑1 (MQ=255)                                                                                           aCCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTGACATCAGGGTACCAGTTGACGGAAACAGAttct                                                         >  3:274353/1‑148 (MQ=255)                                                                                           aCCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTGACATCAGGGTACCAGTTGACGGAAACAGAttc                                                          >  4:273286/1‑147 (MQ=255)                                                                                               ttCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTGACATCAGGGTACCAGTTGACGGAAACAGATTCTTcaa                                                     >  4:155766/1‑148 (MQ=255)                                                                                                  ctccAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTGACATCAGGGTACCAGTTGACGGAAACAGATTCTTcaacaa                                                  <  4:274353/148‑1 (MQ=255)                                                                                                  ctccAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTGACATCAGGGTACCAGTTGACGGAAACAGATTCTTCAACAAg                                                 <  4:28803/149‑1 (MQ=255)                                                                                                      aaCTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTGACATCAGGGTACCAGTTGACGGAAACAGATTCTTCAACAAGCata                                             >  5:115171/1‑149 (MQ=255)                                                                                                      aaCTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTGACATCAGGGTACCAGTTGACGGAAACAGATTCTTCAACAAGCata                                             <  8:128109/149‑1 (MQ=255)                                                                                                             gTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTGACATCAGGGTACCAGTTGACGGAAACAGATTCTTCAACAAGCATATTGCgg                                       >  2:292740/1‑148 (MQ=255)                                                                                                                   ccTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTGACATCAGGGTACCAGTTGACGGAAACAGATTCTTCAACAAGCATATTGCGGTAGTCg                                 >  3:70905/1‑148 (MQ=255)                                                                                                                    cTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTGACATCAGGGTACCAGTTGACGGAAACAGATTCTTCAACAAGCATATTGCGGTAGTCGGa                               <  2:135712/149‑1 (MQ=255)                                                                                                                       ccACTATTCAAGACATTAAAAA‑CATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTGACATCAGGGTACCAGTTGACGGAAACAGATTCTTCAACAAGCATATTGCGGTAGTCGGAt                              <  6:235878/147‑1 (MQ=255)                                                                                                                                     aTTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTGACATCAGGGTACCAGTTGACGGAAACAGATTCTTCAACAAGCATATTGCGGTAGTCGGATCAACAGGCGCCGGCa               >  7:158007/1‑148 (MQ=255)                                                                                                                                              gATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTGACATCAGGGTACCAGTTGACGGAAACAGATTCTTCAACAAGCATATTGCGGTAGTCGGATCAACAGgcgc                    >  6:153985/1‑135 (MQ=255)                                                                                                                                              gATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTGACATCAGGGTACCAGTTGACGGAAACAGATTCTTCAACAAGCATATTGCGGTAGTCGGATCAACAGgcgc                    <  5:153985/135‑1 (MQ=255)                                                                                                                                                   ttGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTGACATCAGGGTACCAGTTGACGGAAACAGATTCTTCAACAAGCATATTGCGGTAGTCGGATCAACAGGCGCCGGCAAATCCAACACAGt  >  1:317265/1‑148 (MQ=255)                                                                                                                                                    |                                                                                                                                                   GACGATAGAAAAAATCGCCGACACGTTATTGAGGCCCTGCCACTGGGCGTGATCAAGGATGATAAATTTATCCGTGGAGGAGACGCACTGACCATTCCTCCAACTGGCGTTGCCCCTGCCACTATTCAAGACATTAAAAA‑GATCTTTGAAGACTCCGTACCCACTAATAGGAAATTTGAGTTTTCCTCATTAGTTACCGACCCTGACATCAGGGTACCAGTTGACGGAAACAGATTCTTCAACAAGCATATTGCGGTAGTCGGATCAACAGGCGCCGGCAAATCCAACACAGT  >  NC_002947/5043114‑5043406

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: ‑