Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	358,096	C→T	10.9%	intergenic (+64/‑66)	tdcG‑I → / → PP_5441	L‑serine dehydratase/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	358,096	0	C	T	10.9%	116.8 / 4.4	48	intergenic (+64/‑66)	tdcG‑I/PP_5441	L‑serine dehydratase/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (21/20);  new base T (2/3);  total (25/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.85e-01

CGCGATACCGGCGCCGATATGCACGACAAGTACAAAGAGACCTCGCGCGGCGGCCTGGCGGTCAGCGCTATCGAGTGCTGATTTTCTGAGCTGACCTTCTGGGCCTCTTCGCGGGCAAGCCCGCTCCTACAGGAACTGTGCAATCCCTGTAGGAGCGGGCTTGCCCGCGAAGAGGCCCTTGAGGCTGATGCAGGTGCAACACAACCGCCTATGCCTCTTTATGGTGCGGTGATGGGCGCCCCGCCTACCGATCGTCGGATGTCGCGATCAGTGTGGGCGTTGTCGGTGACAC  >  NC_002947/357952‑358243                                                                                                                                                 |                                                                                                                                                    cgcgATACCGGCGCCGATATGCACGACAAGTACAAAGAGACCTCGCGCGGCGGCCTGGCGGTCAGCGCTATCGAGTGCTGATTTTCTGAGCTGACCTTCTGGGCCTCTTCGCGGGCAAGCCCGCTCCTACAGGAACTGTGCAATCCCt                                                                                                                                                  <  7:161917/148‑1 (MQ=255) cgcgATACCGGCGCCGATATGCACGACAAGTACAAAGAGACCTCGCGCGGCGGCCTGGCGGTCAGCGCTATCGAGTGCTGATTTTCTGAGCTGACCTTCTGGGCCTCTTCGCGGGCAAGCCCGCTCCTACAGGAACTGTGCAATCCCTg                                                                                                                                                 <  7:19392/149‑1 (MQ=255)      tACCGGCGCCGATATGCACGACAAGTACAAAGAGACCTCGCGCGGCGGCCTGGCGGTCAGCGCTATCGAGTGCTGATTTTCTGAGCTGACCTTCTGGGCCTCTTCGCGGGCAAGCCCGCTCCTACAGGGATTGCACAGTTCCTGTAGGa                                                                                                                                            <  8:72467/149‑1 (MQ=37)        ccGGCGCCGATATGCACGACAAGTACAAAGAGACCTCGCGCGGCGGCCTGGCGGTCAGCGCTATCGAGTGCTGATTTTCTGAGCTGACCTTCTGGGCCTCTTCGCGGGCAAGCCCGCTCCTACAGGAACTGTGCAATCCCTGTAGGAg                                                                                                                                           <  6:149257/148‑1 (MQ=255)                     gCACGACAAGTACAAAGAGACCTCGCGCGGCGGCCTGGCGGTCAGCGCTATCGAGTGCTGATTTTCTGAGCTGACCTTCTGGGCCTCTTCGCGGGCAAGCCCGCTCCTACAGGAACTGTGCAATCCCTGt                                                                                                                                                >  8:94969/1‑130 (MQ=255)                              gTACAACGCCACCTCGCGCGGCGGCCTGGCGGTCCGCGCTAGCGCGTGCTGATTTTCTGCGCTGACCTTCTGGGCCTCTTCGCGGGCAAGCCCGCTCCTCCAGGGATTGCACAGTTCCTGTAGGAGCGGGCTTGCCCGCGAAGAGGccc                                                                                                                    <  6:273919/149‑1 (MQ=17)                               tACAAAGAGACCTCGCGCGGCGGCCTGGCGGTCAGCGCTATCGAGTGCTGATTTTCTGAGCTGACCTTCTGGGCCTCTTCGCGGGCAAGCCCGCTCCTACAGGAACTGTGCAATCCCTGTAGGAGCgg                                                                                                                                        <  5:308691/128‑1 (MQ=255)                               tACAAAGAGACCTCGCGCGGCGGCCTGGCGGTCAGCGCTATCGAGTGCTGATTTTCTGAGCTGACCTTCTGGGCCTCTTCGCGGGCAAGCCCGCTCCTACAGGAACTGTGCAATCCCTGTAGGAGCgg                                                                                                                                        >  6:308691/1‑128 (MQ=255)                                  aaaGAGACCTCGCGCGGCGGCCTGGCGGTCAGCGCTATCGAGTGCTGATTTTCTGAGCTGACCTTCTGGGCCTCTTCGCGGGCAAGCCCGCTCCTACAGGGACTGTGCAATCCCTGGTGGAGCGGGGTTGCCCGGGAAGAGGGCCtt                                                                                                                  >  1:109299/1‑147 (MQ=38)                                  aaaGAGACCTCGCGCGGCGGCCTGGCGGTCAGCGCTATCGAGTGCTGATTTTCTGAGCTGACCTTCTGGGCCTCTTCGCGGGCAAGCCCGCTCCTACAGGAACTGTGCAATCCCTGTAGGAGCGGGCTTGCCCGCGAAGAGGCCCtt                                                                                                                  >  1:55643/1‑147 (MQ=255)                                   aaGAGACCTCGCGCGGCGGCCTGGCGGTCAGCGCTATCGAGTGCTGATTTTCTGAGCTGACCTTCTGGGCCTCTTCGCGGGCAAGCCCGCTCCTACAGGAACTGTGCAATcc                                                                                                                                                    >  2:95653/1‑112 (MQ=255)                                   aaGAGACCTCGCGCGGCGGCCTGGCGGTCAGCGCTATCGAGTGCTGATTTTCTGAGCTGACCTTCTGGGCCTCTTCGCGGGCAAGCCCGCTCCTACAGGAACTGTGCAATcc                                                                                                                                                    <  1:95653/112‑1 (MQ=255)                                    cgccaCCCCGCGCGCCGGCCGGGCGGCCCCCGCTACCGCGCGCTGATTTCCGGCCCTCACCTTCTGGCCCTCTCCCCGGGCACGCCCGCCCCACCAGCACCTGTCCAATCCCTGACGGCGCGGGCTTGCCCGCGAAGAGGCCCTTGAgg                                                                                                              <  8:274526/145‑1 (MQ=255)                                     ccgatcgcgcgcgGCGGCAGGGCGGTCACCGCTTTCCAGTGCTGATTTCCTGTGCTCACCTTCTGGCCCTCTTCGCGGGCAAGCCCGCCCCTACAGCAACTGTCCAACCCCTGTCGCAGCGGGCTTGCCCGCGAAGAGGCCCTTGAg                                                                                                               <  4:269932/140‑1 (MQ=21)                                           tCGCGCGGCGGCCTGGCGGTCAGCGCTATCGAGTGCTGATTTTCTGAGCTGACCTTCTGGGCCTCTTCGCGGGCAAGCCCGCTCCTACAGGAACTGTGCAATCCCTGTAGGAGCGGGCtt                                                                                                                                    <  2:150157/120‑1 (MQ=255)                                           tCGCGCGGCGGCCTGGCGGTCAGCGCTATCGAGTGCTGATTTTCTGAGCTGACCTTCTGGGCCTCTTCGCGGGCAAGCCCGCTCCTACAGGAACTGTGCAATCCCTGTAGGAGCGGGCtt                                                                                                                                    >  1:150157/1‑120 (MQ=255)                                             gcgcgGCGGCCTGGCGGTCAGCGCTATCGAGTGCTGATTTTCTGAGCTGACCTTCTGGGCCTCTTCGCGGGCAAGCCCGCTCCTACAGGAACTGTGCAATCCCGGTAGGAGCGGGCTTGCCCGCGGAGAGGCCCGTGAg                                                                                                               >  3:269932/1‑139 (MQ=255)                                                                     tATCGAGTGCTGATTTTCTGAGCTGACCTTCTGGGCCTCTTCGCGGGCAACCCCCCAACAACACGAACAGTGCAAAACCAGTACGACCGGCGGTGCCCGAGAACACGCCCATGAGGCGGATGCAGGGTCCACACCAACGccgaatccg                                                                              >  4:221359/1‑141 (MQ=255)                                                                          agggCTGATTTTCTGAGCGCCCCTTCTGGGCCGCTCCGCGGGCAAGCCCGCTCCTCCCGCAACTGTGCAATCCCTGTAGGAGCGGGCTTGCCCGCGAAGAGGCCCTTGAGGCTGATGCAGGTGCAACACAACCGCCTATGCCTCTTTAt                                                                        <  5:183410/146‑1 (MQ=37)                                                                            tGCTGATTTTCTGAGCTGACCTTCTGGGCCTCTTCGCGGGCAAGCCCGCTCCTACAGGAACTGTGCAATCCCTGTAGGAGCGGGCTTGCCCGCGAAGAGGCCCTTGAGGCTGATGCAGGTGCAACACAACCGCCTATGCCTCTTTATgg                                                                      >  3:37552/1‑149 (MQ=255)                                                                              cTGATTTTCTGAGCTGACCTTCTGGGCCTCTTCGCGGGCAAGCCCGCTCCTACAGGTACTGTGCAATCCCAGTAGGACCGGGCTTTCGCGCGCAGAGGCCCGTGAGGCTGGAGGCGGTGGAACACCACCGCCTATGCCTCTTTATCGTg                                                                    >  6:237384/1‑149 (MQ=25)                                                                               tGATTTTCTGAGCTGACCTTCTGGGCCTCTTCGCGGGCAAGCCCGCTCCTACAGGAACTGTGCAATCCCTGTAGGAGCGGGCTTGCCCGCGAAGAGGCCCTTGAGGCTGATGCAGGTGCAACACAACCGCCTATGCCTCTTTATGGTGc                                                                   >  1:246052/1‑149 (MQ=255)                                                                                 aTTTTCTGAGCTGACCTTCTGGGCCTCTTCGCGGGCAAGCCCGCTCCTACAGGAACTGTCCAATCCCTGTCGGTGCGGGCTTGCCCGCGAAGAGGCCCTTGAGGCTGATGCAGGTGCAACACAACCGCCTATGCCTCTTTATGGTGCg                                                                  <  6:173840/148‑1 (MQ=255)                                                                                  ttttCTGCGCGGACCTGCTGGCCCTCTTCGCGGGCAACCCCGCCCCAACAGCAACTGTCCAACCCCTGTCGCAGCGGGCTCCCCCGCGAAGAGGCCCTTGAGGCTGATGCAGGTGCAACACAACCGCCTATGCCTCTTTATGGTGCgg                                                                 <  2:109299/148‑1 (MQ=255)                                                                                  ttttCTGAGCTGACCTTCTGGGCCTCTTCGCGGGCAAGCCCGCTCCTACAGGAACTGTGGAATGCCTGTAGGAGCGGGCTTGCCCGCGAAGAGGCCCTTGAGGCTGATGAAGGTGCAACACAACCGCCTATGCCTCTTTATGGTTCGGt                                                                >  7:53858/1‑149 (MQ=255)                                                                                              aCCTTCTGGGCCTCTTCGCGGGCAAGCCCGCTCCTACAGGAACTGTGCAATCCCTGTAGGAGCGGGCTTGCCCGCGAAGAGGCCCTTGAGGCTGATGCAGGTGCAACACAACCGCCTATGCCTCTTTATGGTGCGGTGATGGGCGcccc                                                    >  1:70887/1‑149 (MQ=255)                                                                                                   acgggCCTCTGCGCGGCCACGCCCGCGCCTCCCGGCTTTGCACCGTCCCTGTCGGTGCGGGCTTGCCCGCGAAGAGGCCCTTGAGGCTGATGCAGGTGCAACACAACCGCCTATGCCTCTTTATGGTGCGGTGATGGGCGCCCCGCCTa                                               <  1:114294/147‑1 (MQ=25)                                                                                                        ccTCTTCGCGGGCAAGCCCGCTCCTACAGGAACTGTGCAATccc                                                                                                                                                   <  5:315783/44‑1 (MQ=255)                                                                                                        ccTCTTCGCGGGCAAGCCCGCTCCTACAGGAACTGTGCAATccc                                                                                                                                                   >  6:315783/1‑44 (MQ=255)                                                                                                            ttCGCGGGCAAGCCCGCTCCTACAGGAACTGTGCAATCCCTGTAGGAGCGGGCTTGCCCGCGAAGAGGCCCTTGAGGCTGATGCAGGTGCAACACAACCGCCTATGCCTCTTTATGGTGCGGTGATGGGCGCCCCGCCTACCGAtcgtc                                      >  5:131496/1‑149 (MQ=255)                                                                                                                 gggCAAGCCCGCTCCTACAGGAACTGTGCAATCCCTGTAGGAGCGGGCTTGCCCGCGAAGAGGCCCTTGAGGCTGATGCAGGTGCAACACAACCGCCTATGCCTCTTTATGGTGCGGTGATGGGCGCCCCGCCTACCGATCGTCGGATg                                 >  4:236708/1‑149 (MQ=255)                                                                                                                  ggCAAGCCCGCTCCTACAGGAACTGTGCAATCCCTGTAGGAGCGGGCTTGCCCGCGAAGAGGCCCTTGAGGCTGATGCAGGTGCAACACAACCGCCTATGCCTCTTTATGGTGCGGTGATGGGCGCCCCGCCTACCGATCGTCGGATGt                                >  1:73136/1‑149 (MQ=255)                                                                                                                        cccGCTCCTACAGGAACTGTGCAATCCCTGTAGGAGCGGGCTTGCCCGCGAAGAGGCCCTTGAGGTTGATGCAGGTGCAACACAACCGCCTATGCCTCTTTATGGTGCGGTGATGGGCGCCCCGCCTACCGATCGTCGGATGTCGCGAt                          >  1:289590/1‑149 (MQ=255)                                                                                                                        cccGCTCCTACAGGAACTGTGCAATCCCTGTAGGAGCGGGCTTGCCCGCGAAGAGGCCCTTGAGGCTGATGCAGGTGCAACACAACCGCCTATGCCTCTTTATGGTGCGGTGATGGGCGCCCCGCCTACCGATCGTCGGATGTCGCGAt                          <  3:236708/149‑1 (MQ=255)                                                                                                                        ccagCTCCTACAGGAACTGTGCAATCCCTGTAGGAGCGGGCTTGCCCGCGAAGAGGCCCTTGAGGCTGATGCAGGTGCAACACAACCGCCTATGCCTCTTTATGGTGCGGTGATGGGCGCCCCGCCTACCGATCGTCGGATGTCGCGAt                          <  8:53858/146‑1 (MQ=255)                                                                                                                           gCTCCTACAGGAACTGTGCAATCCCTGTAGGAGCGGGCTTGCCCGCGAAGAGGCCCTTGAGGCTGATGCAGGTGCAACACAACCGCCTATGCCTCTTTATGGTGAGGTGATGGGCGCCCCGCCTACCGATCCTCGGATGTCGCGATCac                       >  7:250117/1‑148 (MQ=255)                                                                                                                             tCCTACAGGGATTGCACAGTTCCTGTAGGAGCGGGCTTGCCCGCGAAGAGGCCCTTGAGGCTGATGCAGGTGCAACACAACCGCCTATGCCTCTTTATGGTGCGGTGATGGGCGCCCCGCCTACCGATCGTCGGAt                                  >  6:257058/1‑136 (MQ=37)                                                                                                                             tCCTACAGGGATTGCACAGTTCCTGTAGGAGCGGGCTTGCCCGCGAAGAGGCCCTTGAGGCTGATGCAGGTGCAACACAACCGCCTATGCCTCTTTATGGTGCGGTGATGGGCGCCCCGCCTACCGATCGTCGGAt                                  <  5:257058/136‑1 (MQ=37)                                                                                                                               cTACAGGGATTGCACAGTTCCTGTAGGAGCGGGCTTGCCCGCGAAGAGGCCCTTGAGGCTGATGCAGGTGCAACACAACCGCCTATGCCTCTTTATGGTGCGGTGATGGGCGCCCCGCCTACCGATCGTCGGATGTCGCGATCAGtgtg                   >  2:281027/1‑149 (MQ=37)                                                                                                                                tACAGGAACTGTGCAATCCCTGTAGGAGCGGGCTTGCCCGCGAAGAGGCCCTTGAGGCTGATGCAGGTGCAACACAACCGCCTATGCCTCTTTATGGTGCGGTGATGGGCGCCCCGCCTACCGATCGTCGGATGTCGCGATCAGTGTgg                  >  4:304407/1‑149 (MQ=255)                                                                                                                                tACAGGAACTGTGCAATCCCTGTAGGAGCGGGCTTGCCCGCGAAGAGGCCCTTGAGGCTGATGCAGGTGCAACACAACCGCCTATGCCTCTTTATGGTGCGGTGATGGGCGCCCCGCCTACCGATCGTCGGATGTCGCGATCAGTGTgg                  >  3:158130/1‑149 (MQ=255)                                                                                                                                  ccgctaCTGTGCAATCCCTGTCGGAGCGGGCTTGCCCGCGAAGAGGCCCTTGAGGCTGATGCAGGTGCAACACAACCGCCTATGCCTCTTTATGGTGCGGTGATGGGCGCCCCGCCTACCGATCGTCGGATGTCGCGATCAGTGTgg                  <  5:237384/142‑1 (MQ=255)                                                                                                                                  cAGGAACTGTGCAATCCCTGTAGGAGCGGGCTTGCCCGCGAAGAGGCCCTTGAGGCTGATGCAGGTGCAACACAACCg                                                                                       >  6:255103/1‑78 (MQ=255)                                                                                                                                  cAGGAACTGTGCAATCCCTGTAGGAGCGGGCTTGCCCGCGAAGAGGCCCTTGAGGCTGATGCAGGTGCAACACAACCg                                                                                       <  5:255103/78‑1 (MQ=255)                                                                                                                                           tgaaaTCCCTGCAGGAGCGGGCTGGCCCGCGAAGAGGCCCTTGAGGCTGATGCAGGTGCAACACAACCGCCTATGCCTCTTTATGGTGCGGTGATGGGCGCCCCGCCTACCGATCGTCGGATGTCGCGATCAGTGTGGGCGTTGTCGGt       <  3:221359/146‑1 (MQ=255)                                                                                                                                           tgCAATCCCTGTAGGAGCGGGCTTGCCCGCGAAGAGGCCCTTGAGGCTGATGCAGGTGCAACACAACCGCCTATGCCTCTTTATGGTGCGGTGATGGGCGCCCCGCCTACCGATCGTCGGATGTCGCGATCAGTGTGGGc                <  6:244042/140‑1 (MQ=255)                                                                                                                                           tgCAATCCCTGTAGGAGCGGGCTTGCCCGCGAAGAGGCCCTTGAGGCTGATGCAGGTGCAACACAACCGCCTATGCCTCTTTATGGTGCGGTGATGGGCGCCCCGCCTACCGATCGTCGGATGTCGCGATCAGTGTGGGc                >  5:244042/1‑140 (MQ=255)                                                                                                                                           tgCAATCCCTGTAGGAGCGGGCTTGCCCGCGAAGAGGCCCTTGAGGCTGATGCAGGTGCAACACAACCGCCTATGCCTCTTTATGGTGCGGTGATGGGCGCCCCGCCTACCGATCGTCGGATGTCGCGATCAGTGTGGGCGTTGTCGGt       >  6:151134/1‑149 (MQ=255)                                                                                                                                           tgCAATCCCTGTAGGAGCGGGCTTGCCCGCGAAGAGGCCCTTGAGGCTGATGCAGGTGCAACACAACCGCCTATGCCTCTTTATGGTGCGGTGATGGGCGCCCCGCCTACCGATCGTCGGATGTCGCGATCAGTGTGGGCGTTGTCGGt       <  5:151134/149‑1 (MQ=255)                                                                                                                                           tgCAATCCCTGTAGGAGCGGGCTTGCCCGCGAAGAGGCCCTTGAGGCTGATGCAGGTGCAACACAACCGCCTATGCCTCTTTATGGTGCGGTGATGGGCGCCCCGCCTACCGATCGTCGGATGTCGCGATCAGTGTGGGCGTTGGCGGt       >  8:290553/1‑149 (MQ=255)                                                                                                                                               aTCCCTGTAGGAGCGGGCTTGCCCGCGAAGAGGCCCTTGAGGCTGATGCAGGTGCAACACAACCGCCTATGCCTCTTTATGGTGCGGTGATGGGCGCCCCGCCTACCGATCGTCGGATGTCGCGATCAGTGTGGGCGTTGTCGGTGaca   <  2:73136/149‑1 (MQ=255)                                                                                                                                                tCCCTGTAGGAGCGGGCTTGCCCGCGAAGAGGCCCTTGAGGCTGATGCAGGTGCAACACAACCGCCTATGCCTCTTTATGGTGCGGTGATGGGCGCCCCGCCTACCGATCGTCGGATGTCGCGATCAGTGTGGGCGTTGTCGGTGacac  <  5:319403/149‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                    CGCGATACCGGCGCCGATATGCACGACAAGTACAAAGAGACCTCGCGCGGCGGCCTGGCGGTCAGCGCTATCGAGTGCTGATTTTCTGAGCTGACCTTCTGGGCCTCTTCGCGGGCAAGCCCGCTCCTACAGGAACTGTGCAATCCCTGTAGGAGCGGGCTTGCCCGCGAAGAGGCCCTTGAGGCTGATGCAGGTGCAACACAACCGCCTATGCCTCTTTATGGTGCGGTGATGGGCGCCCCGCCTACCGATCGTCGGATGTCGCGATCAGTGTGGGCGTTGTCGGTGACAC  >  NC_002947/357952‑358243

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: ‑