Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,466,841	T→G	22.8%	intergenic (‑16/+108)	PP_3081 ← / ← PP_5560	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,466,841	0	T	G	22.8%	86.4 / 6.0	50	intergenic (‑16/+108)	PP_3081/PP_5560	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (11/26);  new base G (7/4);  total (20/30)
Fisher's exact test for biased strand distribution p-value = 7.38e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTGCGGGCAGGTTGTCCCAGCTCAGTTGCGGGGTCCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGC‑GGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAGGGCGTCACGGCTCAGTCTAGCCCAGGTCTGCTTCAGCGGCTGTCCTGGTCCTCGGCAGT  >  NC_002947/3466699‑3466975                                                                                                                                               |                                                                                                                                        cTGCGTGCAGGTTGTCCCAGCTCAGTTGCGGGGTCCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTgc‑ggcg                                                                                                                                  <  1:235622/149‑1 (MQ=255)    cGGGCAGGTTGTCCCAGCTCAGTTGCGGGGTCCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGGCCCCCGc‑ggcgggc                                                                                                                               >  3:150851/1‑147 (MQ=255)    cGGGCAGGTTGTCCCAGCTCAGTTGCGGGGTCCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGC‑ggcggc                                                                                                                                >  7:228759/1‑148 (MQ=255)       gCAGGTTGTCCCAGCTCAGTTGCGGGGTCCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCGCA‑GGCGGCCaag                                                                                                                            <  2:40905/149‑2 (MQ=255)       gCAGGTTGTCCCAGCTCAGTTGCGGGGTCCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCCCCAGCGGGCGGCCac                                                                                                                             >  5:45548/1‑148 (MQ=255)        cAGGTTGTCCCAGCTCAGTTGCGGGGTCCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGC‑GGCGGCCAACg                                                                                                                           >  6:177963/1‑149 (MQ=255)              gTCCCAGCTCAGTTGCGGGGTCCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGC‑GGCGGCCAACGCtgtg                                                                                                                      >  1:22740/1‑148 (MQ=255)               tCCCAGCTCAGTTGCGGGGTCCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGC‑GGCGGCCAACGCTGTGCa                                                                                                                    <  5:82570/149‑1 (MQ=255)                 ccAGCTCAGTTGCGGGGTCCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGC‑GGCGGCCAACGCTGTGCAgg                                                                                                                  >  3:256827/1‑149 (MQ=255)                    gCTCAGTTGCGGGGTCCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCCGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGC‑GGCGGCCAACGCTGTGCAGGgca                                                                                                               <  8:228759/149‑1 (MQ=255)                    gCTCAGTTGCGGGGTCCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCCCCGTC‑AGCCGCCAACACAGTGAAgggac                                                                                                               >  4:14620/1‑147 (MQ=255)                     cTCAGTTGCGGGGTCCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGGGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGC‑GGCGGCCAACGCTGTGCAGGgcag                                                                                                              <  5:168886/149‑1 (MQ=255)                             cGGGGTCCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGC‑GGCGGCCAACGCTGTGCAGGGCAGCAAagca                                                                                                       <  2:268002/148‑1 (MQ=255)                               gggTCCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGC‑GGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCg                                                                                                    <  2:22740/149‑1 (MQ=255)                               gggTCCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGC‑GGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCg                                                                                                    <  4:26635/149‑1 (MQ=255)                                ggTCCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGGCGCCGGC‑GGCGGCCCACGCGGTGGAgggga                                                                                                               >  3:171945/1‑135 (MQ=255)                                    cGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGC‑ggcggc                                                                                                                                <  6:310524/116‑1 (MQ=255)                                    cGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGC‑GGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACa                                                                                                <  5:87459/148‑1 (MQ=255)                                    cGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCGGC‑GGCGGCCAACGCTGTGCATGGCCGCAAAGCACCGAACAg                                                                                               >  4:113266/1‑149 (MQ=255)                                            aCCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGC‑GGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGCACAGCCAGTGTc                                                                                       >  2:33717/1‑149 (MQ=255)                                              cGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGC‑GGCGGCCAACGCTGTGCAGGGCAGCAAagca                                                                                                       <  6:197555/131‑1 (MQ=255)                                              cGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGC‑GGCGGCCAACGCTGTGCAGGGCAGCAAagca                                                                                                       >  5:197555/1‑131 (MQ=255)                                                gCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGC‑GGCGGCCAACGCTGTGCa                                                                                                                    >  4:264888/1‑116 (MQ=255)                                                gCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGC‑GGCGGCCAACGCTGTGCa                                                                                                                    <  3:264888/116‑1 (MQ=255)                                                    cGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCCCCTGC‑GGCGGCCCACCCTGTGCAGGGCACCAAAACCGCGAACAGCCACTGTCTGAgggg                                                                                >  6:205054/1‑146 (MQ=255)                                                      aaTGCCGGGTCCTGGCCGACCTGTTGCAGGGAATTGACGCCGCAATCAGTCAAAGACGAGGAACTGACCGACATCGCGCATTGGCCGCCTGC‑GGGGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCAt                                                                             <  3:14620/148‑1 (MQ=255)                                                                 cTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGC‑GGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCtt                                                                  <  5:177963/149‑1 (MQ=255)                                                                 cTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGC‑GGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCtt                                                                  <  4:256827/149‑1 (MQ=255)                                                                 cTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGC‑GGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCAAGTGTCTGAGGTGCATGGTCAATCCtt                                                                  <  8:163436/149‑1 (MQ=255)                                                                  tGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGC‑GGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTg                                                                 >  6:172833/1‑149 (MQ=255)                                                                  tGGACGACCTGTTCCTGGCCAATGACGCCGCCATCTTTGAAAGACGATTAACTGCCCGACATCGGGCGTTGGGCGCGGGG‑GGGGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTg                                                                 <  2:339887/149‑1 (MQ=255)                                                                    gCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGC‑GGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTgg                                                                <  1:208279/148‑1 (MQ=255)                                                                    gCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGC‑GGCGGCCAACGATGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTgg                                                                >  7:90566/1‑148 (MQ=255)                                                                       gACCTGTTGCAGTGCATTGACGCCGCCATCTGTTATAGACCCGTAACTGACGCACATCGGGCGTTGGCCGCCGGG‑GGGGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAgg                                                            <  6:45548/149‑1 (MQ=255)                                                                       gACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGC‑GGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAgg                                                            <  5:205054/149‑1 (MQ=255)                                                                            gTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCGGC‑GGCGGCCCACGCTGTGCAGGGGCGCCAAGCAGCGCACAGGCAGTGTGTGGGGGGGCTGGTCCATCCGTGGCAGGGCGTc                                                       >  5:11868/1‑149 (MQ=255)                                                                             ttGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGC‑GGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAGGGCGTCa                                                      <  3:113266/149‑1 (MQ=255)                                                                                          aCGCCGCCATCAGTTAAAGACGAGTAACTGACCGACATCGCGCCTGGGCCGCCTGC‑GGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAg                                                                                   <  4:176330/107‑1 (MQ=255)                                                                                          aCGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCGGC‑GGCGGGCAACCCGGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCGGAg                                                                                   >  3:176330/1‑107 (MQ=255)                                                                                                 aaTCAGTGAAAGCCGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGG‑GGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAGGGCGTCACGGCTCAGTCTAGCCCAGGt                                  <  1:317353/148‑1 (MQ=255)                                                                                                       tGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGC‑GGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAgt                                                                                          <  8:249682/87‑1 (MQ=255)                                                                                                       tGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCGGC‑GGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAgt                                                                                          >  7:249682/1‑87 (MQ=255)                                                                                                           aGACGAGGAACTGACCGACATCGCGCCTTGGCCCCCGGC‑GGCGGCCAAAGCGGTGCAGGGGAGCAAAACAGCGAACAGCCAGTGTGGGAGGTGGATGGTGAATCCTTTGGAGGGCGTCACGGCGCAGGCTAGACCACGTGAGCATCAGc                        >  4:293883/1‑149 (MQ=255)                                                                                                            gACGAGGAACTGACCGACATCGCGCCTTGGCCGACTGC‑GGCGGACACAGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATACTTGGCAGGGCGTCAAGGCTCAGTCTAGCCCAGGTCTGCTTAAGCg                       >  3:207561/1‑149 (MQ=255)                                                                                                                  gAACTGACCGACATCGCGCCTTGGCCGCCTGC‑GGCGGCCAACGTTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAGGGCGTCACGGCTCAGTCTAGCCCAGGTCTGCTTCAGCGGCTGTc                 <  8:90566/149‑1 (MQ=255)                                                                                                                  caccTGCCCGACATCGCGCCTGGGCCGCCTGC‑GGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAGGGCGTCACGGCTCAGTCTAGCCCAGGTCTGCTTCAGCGGCTGTc                 <  8:135997/146‑1 (MQ=255)                                                                                                                     cTGACCGACATCGCGCCTTGGCCGCCTGC‑GGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAGGGCGTCACGGCTCAGTCTAGCCCAGGTCTGCTTCAGCGGCTGTCCTg              <  3:293883/149‑1 (MQ=255)                                                                                                                            aCATGGCGCCTTCGCCGCCTGC‑GGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAGGGCGTCACGGCTCAGTCTGGCCCAGGTCTGCTTCAGCGGCTGTCCTGGTCCTCg       <  4:345668/149‑1 (MQ=255)                                                                                                                                 gcgcCTTGGCCGCCTGC‑GGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAGGGCGTCACGGCTCAGTCTAGCCCAGGTCTGCTTCAGCGGCTGTc                 <  7:287048/134‑1 (MQ=255)                                                                                                                                 gcgcCTTGGCCGCCGGC‑GGCGGCCAACGGTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCGTTGGCAGGGCGTCACGGCTCAGTCTAGCCCAGGTCTGCTTCAGCGGCTGTCCTGGTCCTCGGCAGt  <  1:249395/149‑1 (MQ=255)                                                                                                                                               |                                                                                                                                        CTGCGGGCAGGTTGTCCCAGCTCAGTTGCGGGGTCCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGC‑GGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAGGGCGTCACGGCTCAGTCTAGCCCAGGTCTGCTTCAGCGGCTGTCCTGGTCCTCGGCAGT  >  NC_002947/3466699‑3466975

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: ‑