Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	AE015451	196,390	T→C	20.6%	D632D (GAT→GAC)	PP_0168 →	putative surface adhesion protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AE015451	196,390	0	T	C	20.6%	89.6 / 16.6	48	D632D (GAT→GAC)	PP_0168	putative surface adhesion protein
Reads supporting (aligned to +/- strand):  ref base T (22/15);  new base C (5/5);  total (27/21)
Fisher's exact test for biased strand distribution p-value = 7.23e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGGCGGTAATTTCGAGCAACTGACCCCGAACCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGACACCACTACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACTTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTGACAGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGC  >  AE015451/196159‑196576                                                                                                                                                                                                                                        |                                                                                                                                                                                           gggCGGTAATTTCGAGCAACTGACCCCGAACCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGACACCACTACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACTTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTGACAGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAGACCCAGGGCAGCGTCGATTTc                                                                                                                                                                                         >  1:506999/1‑235 (MQ=37)               aGCAACTGACCCCGAACCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGACACCACTACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACTTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTGACAGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAAt                                                                                                                                                                          >  1:860350/1‑236 (MQ=39)                  aaCTGACCCCGAACCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGACACCACTACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACTTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTGACAGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAAt                                                                                                                                                                          <  2:860347/233‑1 (MQ=38)                                                  aCGATCAACGACTCGGTCGACACCACTACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACTTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTGACAGTGACCCTGTCCAACGGCCAAACGATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGACTTCCAGACCCCGGCGaa                                                                                                                                                                           >  1:1088799/1‑200 (MQ=255)                                                                     acacCACTACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACTTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTGACAGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAGACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTacaaca                                                                                                                                                             >  2:71580/1‑195 (MQ=18)                                                                               cacagcccTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACTTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTAACAGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCgaga                                                                                                                               <  1:596343/210‑1 (MQ=25)                                                                                    cccTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACTTACACCGTGACCCTGAGCAACCCTGCCCAGACGCCGGTGACCGTGACCCTGTCCAACGGCCAAACGATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGACTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCGGTAATTTCGAGCa                                                                                                      <  1:481864/235‑1 (MQ=255)                                                                                           ggCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACTTACACCGTGACCCTGAGCAACCCTGCCCAGACGCCGGTGACCGTGACCCTGTCCAACGGCCAAACGATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGACTTCCAGACCCCGGCGAATGACGTc                                                                                                                                                                    >  1:896756/1‑166 (MQ=255)                                                                                                 cccGTCGGTCACCGAAGGCGGCGTAATCACCTACACCGTGACCCTGAGCAACCCTGCCCAGACGCCGGTGACAGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGACTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGt                                                                                                                                                <  2:768645/180‑1 (MQ=9)                                                                                                         ttaCCGAAGCCGGCGTGATCACTTACCCCTGGACCCTGAGCAACCCTGCCCAGACGCCGGTGACCGTGACCCTGTCCAACGGCCAAACGATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGACTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGCGTCACCATCGAGaa                                                                                                                              <  2:896753/188‑1 (MQ=11)                                                                                                                              cTTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTGACAGTGACCCTGTACAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACcggcggca                                                                                                                >  1:608315/1‑181 (MQ=37)                                                                                                                                     cGTGACCCTGAGCAATCCTGCCCAGACGCCGGTGACCGTGACCCTGTCCAACGGCCAAACGATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGACTTCCAGACCCCGGCGAATg                                                                                                                                                                         <  2:366396/119‑1 (MQ=255)                                                                                                                                        gACCCTGAGCAATCCTGCCCAGACGCCGGTGACAGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGAc                                                                                                                                                   <  2:488011/138‑1 (MQ=32)                                                                                                                                        gACCCTGAGCAATCCTGCCCAGACGCCGGTGACAGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGAc                                                                                                                                                   >  1:488014/1‑138 (MQ=32)                                                                                                                                          cccTGAGCAATCCTGCCCAGACGCCGGTGACAGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATg                                                                                                                                                                         >  2:558984/1‑114 (MQ=32)                                                                                                                                          cccTGAGCAACCCTGCCCAGACGCCGGTGACCGTGACCCTGTCCAACGGCCAAACGATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGACTTCCAg                                                                                                                                                                                      >  1:149464/1‑101 (MQ=11)                                                                                                                                            cTGAGCAATCCTGCCCAGACGCCGGTGACAGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGccac                                             >  1:713213/1‑236 (MQ=38)                                                                                                                                            cTGAGCAACCCTGCCCAGACGCCGGTGACCGTGACCCTGTCCAACGGCCAAACGATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGACTTCCAGACCCCGGCGAATGACGTCTacaa                                                                                                                                                               >  1:169669/1‑122 (MQ=255)                                                                                                                                                gCAATCCTGCCCAGACGCCGGTGACAGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTacaa                                                                                                                                                               >  1:903533/1‑118 (MQ=18)                                                                                                                                                  aaTCCTGCCCAGACGCCGGTGACAGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACCCCGGCTCAGACCACGATCAACGACTCGGTCGCTGcct                                              >  1:1013311/1‑228 (MQ=18)                                                                                                                                                      cTGCCCAGACGCCGGTGACAGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGa                                                                   >  2:456603/1‑204 (MQ=40)                                                                                                                                                       tGCCCAGACGCCGGTGACAGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGa                                                                                                                                                                            >  1:511511/1‑98 (MQ=33)                                                                                                                                                        gCCCAGACGCCGGTGACAGTGACCCTGTCCAACGGCCAAGCCATCACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCgg                                                                                                                                                                               <  2:966809/94‑1 (MQ=16)                                                                                                                                                              gcGCCGGTGACCGTGCCCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGaa                                                                                          <  2:204943/172‑1 (MQ=25)                                                                                                                                                                 ccGGTGACCGTGACCCTGTCCAACGGCCAAACGATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGACTTCCAGACCCCGGCCAATGACGTCTAcaacaa                                                                                                                                                            >  1:357397/1‑104 (MQ=11)                                                                                                                                                                 ccGGTGACAGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCg                                                                                                                                                     >  2:945547/1‑111 (MQ=32)                                                                                                                                                                 ccGGTGACAGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCg                                                                                      >  1:1012417/1‑174 (MQ=38)                                                                                                                                                                 ccGGTGACAGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGa                         >  1:657389/1‑235 (MQ=37)                                                                                                                                                                  cGGTGACAGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCg                          <  2:713210/233‑1 (MQ=38)                                                                                                                                                                        ccgTGACCCTGTCCAACGGCCAAACGATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGa                                                                                                                                                                                     >  1:873326/3‑72 (MQ=255)                                                                                                                                                                         tgTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGAc                                                                                                                                                   <  2:590157/104‑1 (MQ=17)                                                                                                                                                                         cgTGACCCTGTCCAACGGCCAAACGATTACCGTTGAAGCGGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGaa                                                                                          <  2:237441/161‑1 (MQ=9)                                                                                                                                                                         aGTGACCCTGTCCAACGGCCACACCACTACCGGTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACCCCGGCTCa                                                                           <  2:201676/177‑1 (MQ=255)                                                                                                                                                                                   tCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCAACGACTCg                                                        <  1:880773/186‑1 (MQ=39)                                                                                                                                                                                      aaCGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACcggcgg                                                                                                                  >  1:167003/1‑125 (MQ=38)                                                                                                                                                                                      aaCGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAAt                                                                                         >  1:201678/1‑150 (MQ=38)                                                                                                                                                                                      aaCGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACCCCGGCTCa                                                                           >  1:848148/1‑164 (MQ=25)                                                                                                                                                                                       aCGGCCAAACGATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGACTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAggcgac  <  1:408367/236‑3 (MQ=255)                                                                                                                                                                                        cGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAggcggc  <  1:456606/235‑1 (MQ=38)                                                                                                                                                                                                   ttACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGACTTCCAGACCCCGGCGAAt                                                                                                                                                                          <  2:75587/56‑1 (MQ=255)                                                                                                                                                                                                            aaGCCGGTAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCg                                                                                                                                                     <  1:387825/68‑1 (MQ=25)                                                                                                                                                                                                              gCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCAACGACTCGGt                                                      >  1:167917/1‑161 (MQ=38)                                                                                                                                                                                                                    aaaaCCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAAt                                                                                                                                                                          >  1:568197/1‑39 (MQ=40)                                                                                                                                                                                                                    aaaaCCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAAt                                                                                                                                                                          <  2:568194/39‑1 (MQ=40)                                                                                                                                                                                                                     aaaCCCAGGGCAGCGTCGAGTTCCAGACCCCGGCGAAt                                                                                                                                                                          <  2:339322/38‑1 (MQ=255)                                                                                                                                                                                                                         ccAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCgaga                                                                                                                               <  2:408065/77‑1 (MQ=34)                                                                                                                                                                                                                                     cGATTTCCAGACCCCGGCGAATGACGTCTGCAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGCAATTTCGAGCAACTGACCCCGAATCCGACGCCGGGTCAGACCa                                                                      >  1:107446/1‑122 (MQ=255)                                                                                                                                                                                                                                     cGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGACACCATCGAGAACGCCACTGGCGGTa                                                                                                                >  1:278624/1‑80 (MQ=255)                                                                                                                                                                                                                                        |                                                                                                                                                                                           GGGCGGTAATTTCGAGCAACTGACCCCGAACCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGACACCACTACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACTTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTGACAGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGTGTCACCATCGAGAACGCCACCGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGC  >  AE015451/196159‑196576

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑