Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	AE015451	197,248	G→A	12.6%	Q918Q (CAG→CAA)	PP_0168 →	putative surface adhesion protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AE015451	197,248	0	G	A	12.6%	118.7 / 2.4	46	Q918Q (CAG→CAA)	PP_0168	putative surface adhesion protein
Reads supporting (aligned to +/- strand):  ref base G (21/19);  new base A (4/2);  total (25/21)
Fisher's exact test for biased strand distribution p-value = 6.73e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.43e-01

CCGTCAGCGTCACCATCGAGAACGCCACAGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACCCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTAATCACCTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGTCATCACTGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGTTCGACCGTCAGCGTCACCATCGAGAACGCCACCGGCGGCAACTTCGAACAGCTGACCCCGAACCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGC  >  AE015451/197031‑197476                                                                                                                                                                                                                          |                                                                                                                                                                                                                                     ccGTCAGCGTCACCATCGAGAACGCCACAGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACCCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTAATCACCTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGTCATCACTGTTTAAGcc                                                                                                                                                                                                                    >  1:62905/1‑236 (MQ=255)                                             cagcTGACCCCGAACCCGACCCCGGCTCAGACCACGATCAACGACTCGGTCGACACCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTAATCACCTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGTCATCACTGTTGAAGCCg                                                                                                                                                                                                                   <  2:653368/190‑1 (MQ=255)                                                                       tCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTAATCACCTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGTCATCACTGTTGAAGc                                                                                                                                                                                                                     <  2:907727/165‑1 (MQ=255)                                                                                            ggTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACCTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGTCATCACTGTTGa                                                                                                                                                                                                                        >  2:761090/1‑141 (MQ=255)                                                                                            ggTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTAATCACCTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGTCATCACTGTTGa                                                                                                                                                                                                                        <  1:761093/141‑1 (MQ=255)                                                                                              tcgacaccaccaCCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACCTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGCCATCACTGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAg                                                                                                                                                                                      <  2:757577/167‑1 (MQ=255)                                                                                               cGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTAATCACCTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGTCATCACTGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTacaa                                                                                                                                                               >  1:375264/1‑195 (MQ=255)                                                                                               cGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTAATCACCTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGTCATCACTGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGTTCGACCGTCAGCGTCACCATCGAGAACGCCAc                                                                                                                        >  1:70238/1‑234 (MQ=255)                                                                                                    ccaccaCCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTAATCACCTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGTCATCACTGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCa                                                                                                                                                                            <  2:375261/177‑1 (MQ=255)                                                                                                           cgcgACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACCTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGTCATCACTGTTGAAGCCg                                                                                                                                                                                                                   <  1:539406/131‑1 (MQ=255)                                                                                                           cgcgACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACCTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGTCATCACTGTTGAAGCCg                                                                                                                                                                                                                   >  2:539403/1‑131 (MQ=255)                                                                                                               aCCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTAATCACCTACACCGTGCCCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAAGTCATCACTGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTa                                                                                                                                                                  >  2:718678/1‑176 (MQ=255)                                                                                                                       ggCGAGCCCGTCGGTCACCGAAGGCGGCGTAATCACCTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGTCCAg                                                                                                                                                                                                                                      >  1:224077/1‑100 (MQ=255)                                                                                                                               cGTCGGTCACCGAAGGCGGCGTAATCACCTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGCCATAACTGTTGAAGCAGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGATCGACCGTCAGCGTCACCATCgagag                                                                                                                              >  2:586187/1‑195 (MQ=255)                                                                                                                                        ccGAAGGCGGCGTGATCACCTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGTCATCACTGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAg                                                                                                                                                                                      <  2:819401/131‑1 (MQ=25)                                                                                                                                          gAATGCGGCGTAATCACCTTCACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGTTCATCACTGTTGAAGCCTGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCa                                                                                                                                                                            <  2:541601/139‑1 (MQ=255)                                                                                                                                          gAAGGCGGCGTAATCACCTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGTCATCACTGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGTTCGACCGTCAGCGTCACCATCGAGAACGCCACCGGCGGCAACTTCGAACAGCTGACCCCGAACCCGACGCCGGCTCa                                                                           <  1:698569/236‑1 (MQ=255)                                                                                                                                                     aaTCACCTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGTCATCACTGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGTTCGACCGTCAGCGTCACCATCGAGAACGCCACcggcg                                                                                                                   >  2:698566/1‑185 (MQ=35)                                                                                                                                                             atacCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGTCATCACTGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGATCCCGGCCAATGACGTCTACAACTACGGTTCGACCGTCAGCGTCACCATCGAGAACGCCACcggcg                                                                                                                   <  2:878375/175‑1 (MQ=21)                                                                                                                                                                   tGACCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGt                                                                                                                                                                                                                                    <  1:42087/58‑1 (MQ=255)                                                                                                                                                                    gACCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGTCATCACTGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGTTCGACCGTCAGCGTCACCATCGAGAACGCCACAGGCGGCAACTTCGAGCAACTGACCCCGAACCCGACCCCGGCCCAGGCCa                                                                      >  2:618726/1‑215 (MQ=255)                                                                                                                                                                      cccTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAAGTCATCAc                                                                                                                                                                                                                              >  2:9705/1‑61 (MQ=255)                                                                                                                                                                      cccTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAAGCCATCACTGTTGAAGCCg                                                                                                                                                                                                                   >  1:691972/1‑72 (MQ=255)                                                                                                                                                                        cTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGTCATTACTGTTGAAGCCg                                                                                                                                                                                                                   >  2:384557/1‑70 (MQ=255)                                                                                                                                                                        cTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGTCATCACTGTTGAAGCCg                                                                                                                                                                                                                   >  2:56325/1‑70 (MQ=40)                                                                                                                                                                        cTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGTCATCACTGTTGAAGCCg                                                                                                                                                                                                                   <  1:56325/70‑1 (MQ=40)                                                                                                                                                                        cTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGTCATCACTGTTGAAGCCg                                                                                                                                                                                                                   <  1:384560/70‑1 (MQ=40)                                                                                                                                                                          gAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGTCATCACTGTTGAAGCCg                                                                                                                                                                                                                   <  2:790121/68‑1 (MQ=40)                                                                                                                                                                           aGCCATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGTCATCACTGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGTTCGACCGTCAGCGTCACCATCGAGAACGCCACCGGCGGCAACTTCGAACAGCTGACCCCGAACCCg                                                                                      <  2:70238/192‑1 (MQ=255)                                                                                                                                                                            gCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGTCATCACTGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGTTCGACCGTCAGCGTCACCATCGAGAACGCCACCGGCGGCAACTTCGAACAGCTGACCCCGaa                                                                                          <  2:780362/187‑1 (MQ=255)                                                                                                                                                                            gCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGTCATCACTGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGTTCGACCGTCAGCGTCACCATCGAGAACGCCACCGGCGGCAACTTCGAACAGCTGACCCCGaa                                                                                          >  1:780365/1‑187 (MQ=255)                                                                                                                                                                              aaTCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGt                                                                                                                                                                                                                                    <  2:911516/47‑1 (MQ=38)                                                                                                                                                                                  cTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGTCATCACTGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAg                                                                                                                                                                                      <  2:600051/89‑1 (MQ=33)                                                                                                                                                                                   tGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGTCATCACTGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGa                                                                                                                                                                        >  2:916368/1‑102 (MQ=32)                                                                                                                                                                                        aGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGTCATCACTGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGTTCGACCGTCAGCGTCACCATCGAGAACGCCACCGGCGGCAACTTCGaa                                                                                                        >  2:207203/1‑161 (MQ=37)                                                                                                                                                                                        aGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGTCATCACTGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGTTCGACCGTCAGCGTCACCATCGAGAACGCCACCGGCGGCAACTTCGAACAGCTGACCCCGAACCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACg                             >  1:122094/1‑236 (MQ=255)                                                                                                                                                                                        aGACGCCGGTAACCGTGACCCTGTCCAACGGCCAAATCATCACTGTTGAAGCCGGAAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGcc                                                                                                                                                                             <  1:485143/92‑1 (MQ=255)                                                                                                                                                                                        aGACGCCGGTAACCGTGAACCTGTCCAACGGCCAAACCATCACTGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGcc                                                                                                                                                                             >  2:485140/1‑92 (MQ=11)                                                                                                                                                                                             ccGGTAACCGTGACCCTGTCCAACGGCCAGGTCATCACTGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTCcaacaaacatt                                                                                                                                                       >  1:545896/1‑104 (MQ=255)                                                                                                                                                                                             ccGGTAACCGTGACCCTGTCCAACGGCCAGGCCATCACTGTTGAAGCCGGCAAAACCCa                                                                                                                                                                                                         >  1:121950/1‑59 (MQ=255)                                                                                                                                                                                               ggTAACCGTGACCCTGTCCAACGGCCAGGTCATCACTGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGTTCGACCGTCAGCGTCACCATCGAGAACGCCACCGGCGGTAACTTCGACCAGCTGACCCCGAACCCGa                                                                                     >  2:631967/1‑173 (MQ=25)                                                                                                                                                                                                        gACCCTGTCCAACCGCCAACTCATCACCGTTGAAGCCGGCAACACCCACAGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACTGTTCGACCGTCAGCGTCACCATCGACAACGCCACCGGCGGCAACTTCGAACa                                                                                                      <  2:171112/147‑1 (MQ=11)                                                                                                                                                                                                             tGTCCAACGGCCAGGTCATCACTGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGTTCGACCGTCAGCGTCACCATCGAGAACGCCACCGGCGGCAACTTCGAACAGCTGACCCCGAACCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTc                  >  2:454985/1‑226 (MQ=255)                                                                                                                                                                                                                 cAACGGCCAGGTCATCACTGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGTTCGACCGTCAGCGTCACCATCGAGAACGCCACCGGCGGCAACTTCGAACAGCTGACCCCGAACCCGACGCCGGCt                                                                             >  2:153639/1‑163 (MQ=255)                                                                                                                                                                                                                  aaCGGCCAGGTCATCACTGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGTTCGACCGTCAGCGTCACCATCGAGAACGCCACCGGCGGCAACTTCGa                                                                                                         >  1:164591/1‑134 (MQ=34)                                                                                                                                                                                                                  aaCGGCCAGCTCATCACTGTCGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGTACGACCGTCAGCGTCACCATCGAGAACGCCACCGGCGGGAACTTCGAACAGCTGACCCCGAACCCg                                                                                      >  2:492164/1‑153 (MQ=255)                                                                                                                                                                                                                   aCGGCCAGGTCATCACTGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGTTCGACCGTCAGCGTCACCATCGAGAACGCCACCGGCGGCAACTTCGAACAGCTGACCCCGAACCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAggcggc  <  1:454988/236‑1 (MQ=255)                                                                                                                                                                                                                          |                                                                                                                                                                                                                                     CCGTCAGCGTCACCATCGAGAACGCCACAGGCGGTAATTTCGAGCAACTGACCCCGAATCCGACCCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTAATCACCTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAGGTCATCACTGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGTTCGACCGTCAGCGTCACCATCGAGAACGCCACCGGCGGCAACTTCGAACAGCTGACCCCGAACCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGC  >  AE015451/197031‑197476

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑