Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,741,952	G→A	8.7%	intergenic (‑20/+393)	PP_3305 ← / ← PP_3306	TerC family membrane protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,741,952	0	G	A	8.7%	157.7 / 4.4	57	intergenic (‑20/+393)	PP_3305/PP_3306	TerC family membrane protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (26/26);  new base A (2/3);  total (28/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.02e-01

CCCGCGGTGGAGCACACCTAAGTCAAGCGCCAACAGTGTTAGCACAACAGCGAAAAAGGAAAGCCAAAGCCAGAGGTCAGTACCAAGAACGTCTTGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCGGCGTCACGAATAAAGAATTTATCGAGCGCGAGTAGGCTGCAAGTAGAAAACATTTACAAATCTTGTCCATGACAAGCTAAAACGCTTGCAGTG  >  NC_002947/3741810‑3742097                                                                                                                                                |                                                                                                                                                  cccGCGGTGGAGCACACCTAAGTCAAGCGCCAACAGTGTTAGCACAACAGCGAAAAAGGAAAGCCAAAGCCAGAGGTCAGTACCAAGAACGTCTTGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGtt                                                                                                                                              <  1:225041/148‑1 (MQ=255)  ccGCGGTGGAGCACACCTAAGTCAAGCGCCAACAGTGTTAGCACAACAGCGAAAAAGGAAAGCCAAAGCCAGAGGTCAGTACCAAGAACGTCTTGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTg                                                                                                                                             >  1:105674/1‑148 (MQ=255)    gcgGTGGAGCACACCTAAGTCAAGCGCCAACAGTGTTAGCACAACAGCGAAAATGGAAAGCCAAAGCCAGAGGTCAGTACCAAGAGCGTCTTGGTAGAGATACGGACGAAGGGCAGACATGCGCCCCGCCT‑GTATAGTCGTCGTTGag                                                                                                                                           >  8:381619/1‑147 (MQ=255)            gCACACCTAAGTCAAGCGCCAACAGTGTTAGCACAACAGCGAAAAAGGAAAGCCAAAGCCAGAGGTCAGTACCAAGAACGTCTTGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCATAGTTGTTCAACTACGa                                                                                                                                  <  3:179842/149‑1 (MQ=255)                acCTAAGTCAAGCGCCAACAGTGTTAGCACAACAGCGAAAAAGGAAAGCCAAAGCCAGAGGTCAGTACCAAGAACGTCTTGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTcc                                                                                                                              <  4:127001/149‑1 (MQ=255)                     aGTCAAGCGCCAACAGTGTTAGCACAACAGCGAAAAAGGAAAGCCAAAGCCAGAGGTCAGTACCAAGAACGTCTTGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGAc                                                                                                                           <  8:287572/147‑1 (MQ=255)                         aaGCGCCAACAGTGTTAGCACAACAGCGAAAAAGGAAAGCCAAAGCCAGAGGTCAGTACCAAGAACGTCTTTGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCg                                                                                                                     >  2:219919/1‑149 (MQ=255)                         aaGCGCCAACAGTGTTAGCACAACAGCGAAAAAGGAAAGCCAAAGCCAGAGGTCAGTACCAAGAACGTCTTGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGc                                                                                                                      <  6:394681/148‑1 (MQ=255)                         aaGCGCCAACAGTGTTAGCACAACAGCGAAAAAGGAAAGCCAAAGCCAGAGGTCAGTACCAAGAACGTCTTGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCg                                                                                                                     >  7:151408/1‑149 (MQ=255)                          aGCGCCAACAGTGTTAGCACAACAGCGAAAAAGGAAAGCCAAAGCCAGAGCTCAGTACCAAGAACGTCTTGGTAGAGATACGTACTAAGGGCAGACATGATCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTAAGACATGGCgg                                                                                                                    >  5:407099/1‑149 (MQ=255)                            cgcCAACAGTGTTAGCACAACAGCGAAAAAGGAAAGCCAAAGCCAGAGGTCAGTACCAAGAACGTCTTGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGAGGta                                                                                                                  >  8:293577/1‑149 (MQ=255)                                           cacaACAGCGAAAAAGGAAAGCCAAAGCCAGAGGTCAGTACCAAGAACGTCTTGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAgggg                                                                                                   >  7:304253/1‑149 (MQ=255)                                               acaGCGAAAAAGGAAAGCCAAAGCCAGAGGTCAGTACCAAGAACGTCTTGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCg                                                                                               >  2:165429/1‑149 (MQ=255)                                               acaGCGAAAAAGGAAAGCCAAAGCCAGAGGTCAGTACCAAGAACGTCTTGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCg                                                                                               <  2:105674/149‑1 (MQ=255)                                                 aGCGAAAAAGGAAAGCCAAAGCCAGAGGTCAGTACCAAGAACGTCTTGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGaacaa                                                                                                                                        <  8:11181/106‑1 (MQ=255)                                                 aGCGAAAAAGGAAAGCCAAAGCCAGAGGTCAGTACCAAGAACGTCTTGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGaacaa                                                                                                                                        >  7:11181/1‑106 (MQ=255)                                                    gAAAAAGGAAAGCCAAAGCCAGAGGTCAGTACCAAGAACGTCTTGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCGGCGt                                                                                           <  8:151408/148‑1 (MQ=255)                                                         aGGAAAGCCAAAGCCAGAGGTCAGTACCAAGAACGTCTTGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCGGCGTCACGaa                                                                                     <  2:406440/149‑1 (MQ=255)                                                             aagccaaagccaGAGGTCAGTACCAAGAACGTCTTGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCGGCGTCACGAATaaa                                                                                 <  3:305646/149‑1 (MQ=255)                                                              agccaaagccaGAGGTCAGTACCAAGAACGTCTTGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCGGCGTc                                                                                          <  3:406854/139‑1 (MQ=255)                                                              agccaaagccaGAGGTCAGTACCAAGAACGTCTTGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCGGCGTc                                                                                          >  4:406854/1‑139 (MQ=255)                                                                ccaaagccaGAGGTCAGTACCAAGAACGTCTTGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCGGCGTCACGAATAAAGaa                                                                              <  8:304253/149‑1 (MQ=255)                                                                 caaagccaGAGGTCAGTACCAAGAACGTCTTGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACAGTCAGAGGGTCCCGGCGTCACGAATAAAGAAt                                                                             >  6:257411/1‑149 (MQ=255)                                                                  aaagccaGAGGTCAGTACCAAGAACGTCTTGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCGGCGTc                                                                                          <  2:235421/135‑1 (MQ=255)                                                                  aaagccaGAGGTCAGTACCAAGAACGTCTTGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCGGCGTc                                                                                          >  1:235421/1‑135 (MQ=255)                                                                  aaagccaGAGGTCAGTACCAAGAACGTCTTGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCATAGTTGTTCAACTACGACtatac                                                                                                                            <  6:195662/101‑5 (MQ=38)                                                                  aaagccaGAGGTCAGTACCAAGAACGTCTTGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCATAGTTGTTCAACTACGACtatac                                                                                                                            >  5:195662/1‑97 (MQ=38)                                                                       caGAGGTCAGTACCAAGAACGTCTTGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCTACATGGCGGTATAACCGTCAGAGGGGCCCGGAGTCACGAATAAACAATTTATc                                                                        >  5:349756/1‑148 (MQ=255)                                                                               aGTACCAAGAACGTCTTGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCGGCGTCACGAATAAAGAATTTATCGAGCGCGAg                                                               >  7:164144/1‑149 (MQ=255)                                                                                     aaGAACGTCTTGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCGGCGTCACGAATAAAGAATTTATCGAGCGCGAGTAGGCt                                                         >  8:112310/1‑149 (MQ=255)                                                                                       gAACGTCTTGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCGGCGTCACGAATAAAGAATTTATCGAGCGCGAGTAGGCTg                                                        >  6:176768/1‑148 (MQ=255)                                                                                       gAACGTCTTCGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCGGCGTCACGAATAAAGAATTTATCGAGCGCGAGTAGGCTGc                                                       <  1:219919/149‑1 (MQ=255)                                                                                            tCTTGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCGGCGTCACGAATAAAGAATTTATCGAGCGCGAGTAGGCTGCAAGTa                                                  >  8:274642/1‑149 (MQ=255)                                                                                            tCTTGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCGGCGTCACGAATAAAGAATTTATCGAGCGCGAGTAGGCTGCAAGTa                                                  <  1:165429/149‑1 (MQ=255)                                                                                              ttGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCGGCGTCACGAATAAAGAATTTATCGAGCGCGAGTAGGCTGCAAGTAGa                                                <  7:112310/149‑1 (MQ=255)                                                                                              ttGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTACGACATGGCGGTATAACCGTCAGAGGGGCACGGCGTAACGAATAAAGAATTTATCGAGCGCGAGTAGGCTGCAAGTAg                                                 >  7:337445/1‑148 (MQ=255)                                                                                              ttGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCATAGTTGTTCAACTACGACt                                                                                                                                <  1:237261/69‑1 (MQ=37)                                                                                              ttGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCATAGTTGTTCAACTACGACt                                                                                                                                >  2:237261/1‑69 (MQ=37)                                                                                                  tAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCGGCGTCACGAATAAAGAATTTATCGAGCGCGAGTAGGCTGCAAGTAGAAAAc                                            <  5:176768/149‑1 (MQ=255)                                                                                                     agaTACGTACTAAGGGCAGACATGAGCCCCTCCTAGTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCagag                                                                                                      >  1:263084/1‑89 (MQ=255)                                                                                                     agaTACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCagag                                                                                                      <  2:263084/88‑1 (MQ=255)                                                                                                           gTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCGGCGTCACGAATAAAGAATTTATCGAGCGCGAGTAGGCTGCAAGTAGAAAACATTTACaaa                                   >  7:37547/1‑149 (MQ=255)                                                                                                             aCTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCGGCGTCACGAATAAAGAATTTATCGAGCGCGAGTAGGCTGCAAGTAGAAAACATTTACAAATc                                 >  8:30133/1‑149 (MQ=255)                                                                                                              cTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGAGGTATAACCGTCAGAGGGGCCCGGCGTCACGAATAAAGAATTTATCGAGCGCGAGTAGGCTGCAAGTAGAAAACATTTACAAATc                                 <  7:293577/148‑1 (MQ=255)                                                                                                                 aGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCGGCGTCACTAATAAAGAATTTATCGAGCGCGAGTAGGCTGCAAGTAGAAAACATTTACAAATCTTGt                             <  5:257411/149‑1 (MQ=255)                                                                                                                     cAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTAAGACTCCGACATGGCTGTATAACCGTCAGAGGGGCCCGGCGTCACGAATAAAGAATTTATCGAGCGCGAGTAGGCTGCAAGTAGAAAACATTTACAAATCTTGTCCAt                         <  3:186/149‑1 (MQ=255)                                                                                                                      cgagaTGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCGGCGTCACGAATAAAGAATTTATCGAGCGCGAGTAGGCTGCAAGTAGAAAACATTTACAAATCTTGTCCAt                         <  5:361861/144‑1 (MQ=255)                                                                                                                        aCATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCGGCGTCACGAATAAAGAATTTATCGAGCGCGAGTAGGCTGCAAGTAGAAAACATTTACAAATc                                 >  3:82884/1‑138 (MQ=255)                                                                                                                        aCATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCGGCGTCACGAATAAAGAATTTATCGAGCGCGAGTAGGCTGCAAGTAGAAAACATTTACAAATc                                 <  4:82884/138‑1 (MQ=255)                                                                                                                            gAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCGGCGTCACGAATAAAGAATTTATCGAGCGCGAGTAGGCTGCAAGTAGa                                                <  3:336981/119‑1 (MQ=255)                                                                                                                            gAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCGGCGTCACGAATAAAGAATTTATCGAGCGCGAGTAGGCTGCAAGTAGa                                                >  4:336981/1‑119 (MQ=255)                                                                                                                               ccccTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCGGCGTCACGAATAAAGAATTTATCGAGCGCGAGTAGGCTGCAAGTAGAAAACATTTACAAATCTTGTCCATGACAAGCTa                >  7:219269/1‑148 (MQ=255)                                                                                                                                     ct‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCGGCGTCACGAATAAAGAATTTATCGAGCGCGAGTAGGCTGCAAGTAGAAAACATTTACAAATCTTGTCCATGACAAGCTAAAACGCt         >  3:146506/1‑149 (MQ=255)                                                                                                                                         tataGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCGGCGTCACGAATAAAGAATTTATCGAGCGCGAGTAGGCTGCAAGTAGAAAACATTTACAAATCTTGTCCATGACAAGCTAAAACGCTTg       <  8:164144/148‑1 (MQ=255)                                                                                                                                         tataGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCGGCGTCACGAATAAAGAATTTATCGAGCGCGAGTAGGCTGCAAGTAGAAAACATTTACAAATCTTGTCCATGACAAGCTAAAACGCTTg       <  2:406078/148‑1 (MQ=255)                                                                                                                                           taGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCGGCGTCAAGAATAAAGAATTTATCGAGCGCGAGTAGGCTGCAAGTAGAAAACATTTACAAATCTTGTCCATGACAAGCTAAAACGCTTGCAg    <  3:49283/149‑1 (MQ=255)                                                                                                                                              tCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCGGCGTCACGAATAAAGAATTTATCGAGCGCGAGTAGGCTGCAAGTAGAAAACATTTACAAATCTTGTCCATGACAAGCTAAAACGCTTGCAGTg  >  5:11229/1‑148 (MQ=255)                                                                                                                                                |                                                                                                                                                  CCCGCGGTGGAGCACACCTAAGTCAAGCGCCAACAGTGTTAGCACAACAGCGAAAAAGGAAAGCCAAAGCCAGAGGTCAGTACCAAGAACGTCTTGGTAGAGATACGTACTAAGGGCAGACATGAGCCCCTCCT‑GTATAGTCGTAGTTGAACAACTATGACTCCGACATGGCGGTATAACCGTCAGAGGGGCCCGGCGTCACGAATAAAGAATTTATCGAGCGCGAGTAGGCTGCAAGTAGAAAACATTTACAAATCTTGTCCATGACAAGCTAAAACGCTTGCAGTG  >  NC_002947/3741810‑3742097

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: ‑