Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	790,957	T→A	9.8%	Q46L (CAG→CTG)	PP_0677 ←	lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	790,957	0	T	A	9.8%	132.7 / 5.1	51	Q46L (CAG→CTG)	PP_0677	lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (18/28);  new base A (2/3);  total (20/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.34e-01

AGCGCTCGTGGTATTGGCGCTGTTCTTCGCTGTTCTGCATGGCGTGACACTGGCGGAAGCCATCGTCCCAGCCGGTTTCGTACT‑‑‑GACGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAACCGTGGTTGACCATCTGCTCGTGGGTGGTTTCGCAACCCGACAGCAACAACGCAATGCACACGCCGAACCAGTACCGCGACATAGCCACAAAGC  >  NC_002947/790811‑791104                                                                                                                                                      |                                                                                                                                                    aGCGCTCGTGGTATTGGCGCTGTTCTTCGCTGTTCTGCATGGCGTGACACTGGCGGAAGCCATCGTCCCAGCCGGTTTCGTACT‑‑‑GACGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTgg                                                                                                                                                   <  2:51240/149‑1 (MQ=255)   cgcTCGTGGTATTGGCGCTGTTCTTCGCTGTTCTGCATGGCGTGACACTGGCGGAAGCCATCGTCCCAGCCGGTTTCGTACT‑‑‑GACGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTggcg                                                                                                                                                 <  4:44003/149‑1 (MQ=255)        gTGGTATTGGCGCTGTTCTTCGCTGTTCTGCATGGCGTGACACTGGCGGAAGCCATCGTCCCAGCCGGTTTCGTACT‑‑‑GACGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGTAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCa                                                                                                                                             <  1:55353/148‑1 (MQ=255)        gTGGTATTGGCGCTGTTCTTCGCTGTTCTGCATGGCGTGACACTGGCGGAAGCCATCGTCCCAGCCGGTTTCGTACT‑‑‑GACGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCAGGCGGccgg                                                                                                                                            <  3:86327/149‑3 (MQ=255)        gTGGTATTGGCGCTGGTCTTCGCTTGTCTGCATGGCGTTTCACTGGCGGAAGCCATCGTCCCAGCCGGTTTCGTACTTCCCCCGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTggcggc                                                                                                                                               <  1:107557/149‑1 (MQ=255)             aTTGGCGCTGTTCTTCGCTGTTCTGCATGGCGTGACACTGGCGGAAGCCATCGTCCCAGCCGGTTTCGTACT‑‑‑GACGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCActgctg                                                                                                                                       >  8:875/1‑149 (MQ=255)                          ttcGCTGTTCTGCATGGCGTGACACTGGCGGAAGCCATCGTCCCAGCCGGTTTCGTACT‑‑‑GACGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCAGGCGGccggg                                                                                                                                           >  5:203402/1‑129 (MQ=255)                          ttcGCTGTTCTGCATGGCGTGACACTGGCGGAAGCCATCGTCCCAGCCGGTTTCGTACT‑‑‑GACGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCAGGCGGccggg                                                                                                                                           <  6:203402/132‑4 (MQ=255)                                   cTGCATGGCGTGGCACTGGCGGAAGCCATCGTCCCAGCCGGTTTCGTACT‑‑‑GACGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATcc                                                                                                                  <  4:60770/148‑1 (MQ=255)                                      cATGGCGTGACACTGGCGGAAGCCATCGTCCCAGCCGGTTTCGTACT‑‑‑GACGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCa                                                                                                               >  4:172692/1‑148 (MQ=255)                                       aTGGCGTGACACTGGCGGAAGCCATCGTCCCAGCCGGTTTCGTACT‑‑‑GACGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATa                                                                                                             <  8:43403/149‑1 (MQ=255)                                          gCGTGACACTGGCGGAAGCCATCGTCCCAGCCGGTTTCGTACT‑‑‑GACGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAgg                                                                                                           <  5:271938/148‑1 (MQ=255)                                           cGTGACACTGGCGGAAGCCATCGTCCCAGCCGGTTTCGTACT‑‑‑GACGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAgg                                                                                                           >  8:319395/1‑147 (MQ=255)                                            gTGACACTGGCGGAAGCCATCGTCCCAGCCGGTTTCGTACT‑‑‑GACGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCAGGCGGccggg                                                                                                                                           <  6:80908/114‑4 (MQ=255)                                            gTGACACTGGCGGAAGCCATCGTCCCAGCCGGTTTCGTACT‑‑‑GACGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCAGGCGGccggg                                                                                                                                           >  5:80908/1‑111 (MQ=255)                                                cacTGGCGGAAGCCATCGTCCCAGCCGGTTTCGTACT‑‑‑GACGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCaggagg                                                                                                    <  2:271593/149‑1 (MQ=255)                                                cacTGGCGGAAGCCATCGTCCCAGCCGGTTTCGTACT‑‑‑GACGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCaggagg                                                                                                    <  3:97278/149‑1 (MQ=255)                                                 acTGGCGGAAGCCATCGTCCCAGCCGGTTTCGTACT‑‑‑GACGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAggg                                                                                                   >  6:284075/1‑149 (MQ=255)                                                            ccATCGTCCCAGCCGGTTTCGTACT‑‑‑GACGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCGTGGAAGCTATCCGCATAGGCAGGAGGGTAACCGTGGtt                                                                                        <  1:30155/149‑1 (MQ=255)                                                            ccATCGTCCCAGCCGGTTTCGTACT‑‑‑GACGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAACCGTGGtt                                                                                        <  4:12677/149‑1 (MQ=255)                                                              aTCGTCCCAGCCGGTTTCGTACT‑‑‑GACGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAACCGTGGTTGa                                                                                      >  5:325946/1‑149 (MQ=255)                                                                  tCCCAGCCGGTTTCGTACT‑‑‑GACGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAACCGTGGTTGACCa                                                                                   >  8:200469/1‑148 (MQ=255)                                                                         cGGTTTCGTACT‑‑‑GACGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAACCGTGGTTGACCATCTGCTCg                                                                           >  4:26712/1‑149 (MQ=255)                                                                           gTTTCGTACT‑‑‑GACGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAACCGTGGTTGACCATCTGCTCgtg                                                                         >  2:140030/1‑149 (MQ=255)                                                                            tttCGTACT‑‑‑GACGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAACCGTGGTTGa                                                                                      <  5:95962/135‑1 (MQ=255)                                                                            tttCGTACT‑‑‑GACGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAACCGTGGTTGa                                                                                      >  6:95962/1‑135 (MQ=255)                                                                               cGTACT‑‑‑GACGCTCGTGCAGGTAGCTCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAACCGTGGTTGACCATCTGCTCgtgggtg                                                                     >  1:112692/1‑149 (MQ=255)                                                                                gTACT‑‑‑GACGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAAc                                                                                               >  1:78938/1‑122 (MQ=255)                                                                                gTACT‑‑‑GACGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAAc                                                                                               <  2:78938/122‑1 (MQ=255)                                                                                 tACT‑‑‑GACGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAACCGTGGTTGACCATCTGCTCGTGggtggt                                                                   >  6:23245/1‑149 (MQ=255)                                                                                   cT‑‑‑GACGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAACCGTGGTTGACCATCTGCTCGTGGGTGGttt                                                                 <  3:263933/149‑1 (MQ=255)                                                                                   cT‑‑‑GACGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATAAGCATAGGCAGGAGGGTAACCGTGGTTGACCATCTGCTCGTGGGTGGttt                                                                 >  1:287048/1‑149 (MQ=255)                                                                                          cGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAACCGTGGTTGACCATCTGCTCGTGGGTGGTTTCGCa                                                             <  7:319395/149‑1 (MQ=255)                                                                                            cTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAACCGTGGTTGACCATCTGCTCGTGGGTGGTTTCGCAAc                                                           <  3:172692/149‑1 (MQ=255)                                                                                                  cAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAACCGTGGTTGACCATCTGCTCGTGGGTGGTTTCGCAACCCGAc                                                      <  3:26712/148‑1 (MQ=255)                                                                                                  cAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAACCGTGGTTGACCATCTGCTCGTGGGTGGTTTCGCAACCCGACa                                                     <  7:200469/149‑1 (MQ=255)                                                                                                  cAGGTACCGCGGCACGTGCTTGCGGAAGTGCCCCACCATCCGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAACCGTGGTTGACCATCTGCTCGTGGGTGGTTTCGCAACCCGACa                                                     <  8:91922/149‑1 (MQ=255)                                                                                                       aGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAACCGTGGTTGACCATCTGCTCGTGGGTGGTTTCGCAACCCGACAGcaa                                                 >  2:113011/1‑148 (MQ=255)                                                                                                          gcgGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAACCGTGGTTGACCATCTGCTCGTGGGTGGTTTCGCAACCCGACAGCaacaac                                             <  3:81099/149‑1 (MQ=255)                                                                                                            ggTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAACCGTGGTTGACCATCTGCTCGTGGGTGGTTTCGCAACCCGACAGCAACAACGc                                           <  1:155288/149‑1 (MQ=255)                                                                                                            ggTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAACCGTGGTTGACCATCTGCTCGTGGGTGGTTTCGCAACCCGACAGCAACAACGc                                           <  5:23245/149‑1 (MQ=255)                                                                                                                cGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAACCGTGGTTGACCATCTGCTCGTGGGTGGTTTCGCAACCCGACAGCAACAACGCAAt                                        <  1:140030/148‑1 (MQ=255)                                                                                                                       gCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAACCGTGGTTGACCATCTGCTCGTGGGTGGTTTc                                                                >  7:171993/1‑117 (MQ=255)                                                                                                                       gCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAACCGTGGTTGACCATCTGCTCGTGGGTGGTTTc                                                                <  8:171993/117‑1 (MQ=255)                                                                                                                       gCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAACCGTGGTTGACCATCTGCTCGTGGGTGGTTTCGCAACCCGACAGCAACAACGCAATGcaca                                   <  7:875/146‑1 (MQ=255)                                                                                                                        cGGAAGTTGCCCACCATCAGCCCGTCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAACCGTGGTTGACCATCTGCTCGTGGGTGGTTTCGCAACCCGACAGCAACAACGCAATGCACACGc                                <  3:77882/148‑1 (MQ=255)                                                                                                                                  ccaccaTCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAACCGTGGTTGACCATCTGCTCGTGGGTGGTTTCGCAACCCGACAGCAACAACGCAATGCACACGCCGAACCAGTAc                     >  7:316359/1‑149 (MQ=255)                                                                                                                                  ccaccaTCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAACCGTGGTTGACCATCTGCTCGTGGGTGGTTTCGCAACCCGACAGCAACAACGCAATGCACACGCCGAACCAGTAc                     <  3:250602/149‑1 (MQ=255)                                                                                                                                             ccGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAACCGTGGTTGACCATCTGCTCGTGGGTGGTTTCGCAACCCGACAGCAACAACGCAATGCACACGCCGAACCAGTACCGCGACATAGc          <  5:284075/149‑1 (MQ=255)                                                                                                                                                    ccTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAACCGTGGTTGACCATCTGCTCGTGGGTGGTTTCGCAACCCGACAGCAACAACGCAATGCACACGCCGAACCAGTACCGCGACATAGCCACAAAg   >  2:215596/1‑149 (MQ=255)                                                                                                                                                     cTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAACCGTGGTTGACCATCTGCTCGTGGGTGGTTTCGCAACCCGACAGCAACAACGCAATGCACACGCCGAACCAGTACCGCGACATAGCCACAAAGc  >  1:83665/1‑149 (MQ=255)                                                                                                                                                      |                                                                                                                                                    AGCGCTCGTGGTATTGGCGCTGTTCTTCGCTGTTCTGCATGGCGTGACACTGGCGGAAGCCATCGTCCCAGCCGGTTTCGTACT‑‑‑GACGCTCGTGCAGGTAGCGCGGTACGTTCTTGCGGAAGTTGCCCACCATCAGCCCGGCCGCCTGGCGGCCACTGCTGCAGCCGTCCTGGAAGCCATCCGCATAGGCAGGAGGGTAACCGTGGTTGACCATCTGCTCGTGGGTGGTTTCGCAACCCGACAGCAACAACGCAATGCACACGCCGAACCAGTACCGCGACATAGCCACAAAGC  >  NC_002947/790811‑791104

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: ‑