Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,944,719	G→A	10.4%	A80A (GCC→GCT)	PP_3480 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,944,719	0	G	A	10.4%	126.7 / 4.9	48	A80A (GCC→GCT)	PP_3480	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (21/22);  new base A (2/3);  total (23/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.08e-01

GCCAGCTGGGTCTTGGGGTCGATACCCAACGCGTATTCACCGCGGGCCAGGCTGATGCGCTCGGCGCTGGCCAGACGGTACAGACGCTCGATCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAGCTCACCCCGCTTGACACGCCCTACCTGTTCGCTGGCCTGCGCTTCGGTGACACGCAGTTCGCGTACGCTTTGCCATTGCGGCAGCACGCCGGCACACCCAACGCCAATGGCGAG  >  NC_002947/3944576‑3944865                                                                                                                                                |                                                                                                                                                    gCCAGCTGGGTCTTGGGGTCGATACCCAACGCGTATTCACCGCGGGCCAGGCTGATGCGCTCGGCGCTGGCCAGACGGTACAGACGCTCGATCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCctg                                                                                                                                                <  7:171422/149‑1 (MQ=255) gCCAGCTGGGTCTTGGGGTCGATACCCAACGCGTATTCACCGCGGGCCAGGCTGATGCGCTCGGCGCTGGCCAGACGGTACAGACGCTCGATCAACTCGCTGGCCAGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCctg                                                                                                                                                >  5:51856/1‑149 (MQ=255)  ccAGCTGGGTCTTGGGGTCGATACCCAACGCGTATTCACCGCGGGCCAGGCTGATGCGCTCGGCGCTGGCCAGACGGTACAGACGCTCGATCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCCCTCGACAGCctgc                                                                                                                                               <  5:187327/149‑1 (MQ=255)                     gATACCCAACGCGTATTCACCGCGGGCCAGGCTGATGCGCTCGGCGCTGGCCAGACGGTACAGACGCTCGATCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCGCaa                                                                                                                           >  1:370383/1‑149 (MQ=255)                      aTACCCAACGCGTATTCACCGCGGGCCAGGCAGATGCGCTCGGCGCTGGCCAGACGGTACAGACGCTCGATCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCGCAAt                                                                                                                          >  1:228064/1‑149 (MQ=255)                       tACCCAACGCGTATTCACCGCGGGCCAGGCTGATGCGCTCGGCGCTGGCCAGACGGTACAGACGCTCGATCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCGCAATc                                                                                                                         <  1:79001/149‑1 (MQ=255)                       tACCCAACGCGTATTCACCGCGGGCCAGGCTGATGCGCTCGGCGCTGGCCAGACGGTACAGACGCTCGATCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCACAATc                                                                                                                         <  3:187314/149‑1 (MQ=255)                          ccAACGCGTATTCACCGCGGGCCAGGCTGATGCGCTCGTCGCTGGCCAGACGGTACAGACGCTCGATCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTg                                                                                                                                   >  6:345381/1‑136 (MQ=255)                          ccAACGCGTATTCACCGCGGGCCAGGCTGATGCGCTCGGCGCTGGCCAGACGGTACAGACGCTCGATCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGGGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTg                                                                                                                                   <  5:345381/136‑1 (MQ=255)                           cAACGCGTATTCACCGCGGGCCAGGCTGATGCGCTCGGCGCTGGCCAGACGGTACAGACGCTCGATCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCCCTCGACAGCctgcgcca                                                                                                                                           <  4:170064/128‑5 (MQ=255)                           cAACGCGTATTCACCGCGGGCCAGGCTGATGCGCTCGGCGCTGGCCAGACGGTACAGACGCTCGATCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCCCTCGACAGCctgcgcca                                                                                                                                           >  3:170064/1‑124 (MQ=255)                            aaCGCGTATTCACCGCGGGCCAGGCTGATGCGCTCGGCGCTGGCCAGACGGTACAGACGCTCGATCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAg                                                                                                                    <  3:333368/149‑1 (MQ=255)                             aCGCGTATTCACCGCGGGCCAGGCTGATGCGCTCGGCGCTGGCCAGACGGTACAGACGCTCGATCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAGc                                                                                                                   >  7:345744/1‑149 (MQ=255)                               gcgTATTCACCGCGGGCCAGGCTGATGCGCTCGGCGCTGGCCAGACGGTACAGACGCTCGATCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑Tc                                                                                                                                         <  8:346046/125‑1 (MQ=255)                               gcgTATTCACCGCGGGCCAGGCTGATGCGCTCGGCGCTGGCCAGACGGTACAGACGCTCGATCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑Tc                                                                                                                                         >  7:346046/1‑125 (MQ=255)                                    ttCACCGCGGGCCAGGCTGATGCGCTCGGCGCTGGCCAGACGGTACAGACGCTCGATCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCCCTCGACAGCctgcgcca                                                                                                                                           <  1:148165/119‑5 (MQ=255)                                    ttCACCGCGGGCCAGGCTGATGCGCTCGGCGCTGGCCAGACGGTACAGACGCTCGATCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCCCTCGACAGCctgcgcca                                                                                                                                           >  2:148165/1‑115 (MQ=255)                                     tCACCGCGGGCCAGGCTGATGCGCTCGGCGCTGGCCAGACGGTACAGACGCTCGATCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAGCTCACCCCg                                                                                                           >  6:325678/1‑149 (MQ=255)                                      cACCGCGGGCCAGGCTGATACGCTCGGCGCTGGCCAGACGGTACAGACGCTCGATCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TAGGGCTGGACCGCAATCTTCAGCTCACCCCGc                                                                                                          >  4:95730/1‑149 (MQ=255)                                                cAGGCTGATGCGCTCGGCGCTGGCCAGACGGTACAGACGCTCGATCTACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCACGCTGTCGAGGGCCTGCTGC‑TCGGGCTGGCACGGAATCTTCAGCTCACCCCGCTAGACACGcc                                                                                                >  6:287220/1‑149 (MQ=255)                                                 aGGCTGATGCGCTCGGCGCTGGCCAGACGGTACAGACGCTCGATCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAGCTCACCCCGCTTGACACGccc                                                                                               >  5:133728/1‑149 (MQ=255)                                                     tGATGCGCTCGGCGCTGGCCAGACGGTACAGACGCTCGATCAACTCGCTGGCATGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAGCTCACCCCGCTTGACACGCCCTAcc                                                                                           >  3:72742/1‑149 (MQ=255)                                                      gATGCGCTCGGCGCTGGCCAGACGGTACAGACGCTCGATCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAgg                                                                                                                                                     <  2:67317/91‑1 (MQ=255)                                                      gATGCGCTCGGCGCTGGCCAGACGGTACAGACGCTCGATCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAgg                                                                                                                                                     >  1:67317/1‑91 (MQ=255)                                                       aTGCGCTCGGCGCTGGCCAGACGGTACAGACGCTCGATCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAGCTCACCCCGCTTGACACGCCCTACCTg                                                                                         >  1:351757/1‑149 (MQ=255)                                                         gcgcTCGGCGCTGGCCAGACGGTACAGACGCTCGATCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAGCTCACCCCGCTTGACACGCCCTACCTGtt                                                                                       >  1:54063/1‑149 (MQ=255)                                                               ggCGCTGGCCAGACGGTACAGACGCTCGATCAACTCGCTGGCCAGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAGCTCACCCCGCTTGACACGCCCTACCTGTTCGCTg                                                                                  <  6:51856/148‑1 (MQ=255)                                                                gcgcTGGCCAGACGGTACAGACGCTCGATCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAGCTCACCCCGCTTGACACGCCCTACCTGTTCGCTGGc                                                                                >  6:145526/1‑149 (MQ=255)                                                                        cAGACGGTACAGACGCTCGATCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAGCTCACCCCGCTTGACACGCCCTACCTGTTCGCTGGCCTGCGCtt                                                                        >  7:309270/1‑149 (MQ=255)                                                                         aGACGGTACAGACGCTCGATCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAGCTCACCCCGCTTGACACGCCCTACCTGTTCGCTGGCCTGCGCTTc                                                                       <  1:13556/149‑1 (MQ=255)                                                                             ggTACAGACGCTCGATCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAGCTCACCCCGCTTGACACGCCCTACCTGTTCGCTGGCCTGCGCTTCGGTg                                                                   <  2:351757/149‑1 (MQ=255)                                                                               tACAGACGCTCGATCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAGCTCACCCCGCTTGACACGCCCTACCTGTTCGCTGGCCTGCGCTTCGGTGac                                                                 <  2:370383/149‑1 (MQ=255)                                                                                      gCTCGATCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAGCTCACCCCGCTTGACACGCCCTACCTGTTCGCTGGCCTGCGCTTCGGTGACACGCAGt                                                          >  2:59129/1‑149 (MQ=255)                                                                                          gATCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAGCTCACCCCGCTTGACACGCCCTACCTGTTCGCTGGCCTGCGCTTCGGTGACACGCAGTTcgc                                                      >  4:152881/1‑149 (MQ=255)                                                                                           aTCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTAGAGGGCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAGCTCACCCCGCTTGACACGCCCTACCTGTTCGCTGGCCTGCGCTTCGGTGACACGCAGTTcgcg                                                     <  2:228064/149‑1 (MQ=255)                                                                                            tCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAGCTCACCCCGCTTGACACGCCCTACCTGTTCGCTGGCCTGCGCTTCGGTGACACGCAGTTCGCGt                                                    <  8:345744/149‑1 (MQ=255)                                                                                               aCTCGCTCGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAGCTCACCCCGCTTGACACGCCCTACCTGTACGCTGGCCTCCGCTTCGGTGACACGAAGATCGCGTACg                                                 >  4:322320/1‑149 (MQ=255)                                                                                                    cTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAGCTCACCCCGCTTGACACGCCCTACCTGTTCGCTTTCCTGCGCTTCGGTGACACGCAGTTCGCGTACGCTTTg                                            <  3:95730/149‑1 (MQ=255)                                                                                                     tGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGCGTCGGGCTGGACCGCAATCTTCAGCTCCCCCCGCTTGACACGCCCTACCTGTTCGCTGGCCTGCGCTTCGGTGACACGCAGTTCGCGTACGCTTTg                                            >  1:283562/1‑149 (MQ=255)                                                                                                     tGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAGCTCACCCCGCTTGACACGCCCTACCTGTTCGCTGGCCTGCGCTTCGGTGACACGCAGTTCGCGTACGCTTTGc                                           >  7:351676/1‑149 (MQ=255)                                                                                                       gCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAGCTCACCCCGCTTGACACGCCCTACCTGTTCGCTGGCCTGCGCTTCGGTGACACGCAGTTCGCGTACGCTTTGCCa                                         <  5:325678/149‑1 (MQ=255)                                                                                                            gggCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAGCTCACCCCGCTTGACACGCCCTACCTGTTCGCTGGCCTGCGCTTCGGTGACACGCAGTTCGCGTACGCTTTGCCATTg                                      <  1:59129/147‑1 (MQ=255)                                                                                                            gggCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAGCTCACCCCGCTTGACACGCCCTACCTGTTCGCTGGCCTGCGCTTCGGTGACACGCAGTTCGCGTACGCTTTGCCATTGc                                     <  5:145526/148‑1 (MQ=255)                                                                                                                      ggCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAGCTCACCCCGCTTGACACGCCCTACCTGTTCGCTGGCCTGCGCTTCGGTGACACGCAGTTCGCGTACGCTTTGCCATTGCGGCAGCACGcc                          <  8:309270/149‑1 (MQ=255)                                                                                                                       gCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAGCTCACCCCGCTTGACACGCCCTACCTGTTCGCTGGCCTGCGCTTCGGTGACACGCAGTTCGCGTACGCTTTGCCATTGCGGCAGCACGCCg                         <  2:54063/149‑1 (MQ=255)                                                                                                                           ttGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAGCTCACCCCGCTTGACACGCCCTACCTGTTCGCTGGCCTGCGCTTCGGTGACACGCAGTTCGCGTACGCTTTGCCATTGCGGCAGCACGCCGGca                      >  2:241806/1‑148 (MQ=255)                                                                                                                                        cTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAGCTCACCCCGCTTGACACGCCCTACCTGTTCGCTGGCCTGCGCTTCGGTGACACGCAGTTCGCGTACGCTTTGCCATTGCGGCAGCACGCCGGCACACCCAACGCCAAt        <  1:241806/149‑1 (MQ=255)                                                                                                                                        cTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAGCTCACCCCGCTTGACACGCCCTACCTGTTCGCTGGCCTGCGCTTCGGTGACACGCAGTTCGCGTACGCTTTGCCATTGCGGCAGCACGCCGGCACACCCAACGCCAAt        <  3:152881/149‑1 (MQ=255)                                                                                                                                           tCGTGGGCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAGCTCACCCCGCTTGACACGCCCTACCTGTTCGCTGGCCTGCGCTTCGGTGACACGCAGTTCGCGTACGCTTTGCCATTGCGGCAGCACGCCGGCACTCCCAACGCCAATGGc     <  3:322320/149‑1 (MQ=255)                                                                                                                                           tCGAGGGCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAGCTCACCCCGCTTGACACGCCCTACCTGTTCGCTGGCCTGCGCTTCGGTGACACGCAGTTCGCGTACGCTTTGCCATTGCGGCAGCACGCCGGCACACCCAACGCCAATg       <  6:133728/147‑1 (MQ=255)                                                                                                                                                ggCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAGCTCACCCCGCTTGACACGCCCTACCTGTTCGCTGGCCTGCGCTTCGGTGACACGCAGTTCGCGTACGCTTTGCCATTGCGGCAGCACGCCGGCACACCCAACGCCAATGGCGAg  >  2:150165/1‑147 (MQ=255)                                                                                                                                                |                                                                                                                                                    GCCAGCTGGGTCTTGGGGTCGATACCCAACGCGTATTCACCGCGGGCCAGGCTGATGCGCTCGGCGCTGGCCAGACGGTACAGACGCTCGATCAACTCGCTGGCCTGGGGCTGACCGGGCAGTTGCTGGCGCAGGCTGTCGAGGGCCTGCTGC‑TCGGGCTGGACCGCAATCTTCAGCTCACCCCGCTTGACACGCCCTACCTGTTCGCTGGCCTGCGCTTCGGTGACACGCAGTTCGCGTACGCTTTGCCATTGCGGCAGCACGCCGGCACACCCAACGCCAATGGCGAG  >  NC_002947/3944576‑3944865

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: ‑