Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	AE015451	197,551	C→G	19.2%	T1019T (ACC→ACG)	PP_0168 →	putative surface adhesion protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AE015451	197,551	0	C	G	19.2%	93.3 / 15.6	51	T1019T (ACC→ACG)	PP_0168	putative surface adhesion protein
Reads supporting (aligned to +/- strand):  ref base C (20/21);  new base G (7/3);  total (27/24)
Fisher's exact test for biased strand distribution p-value = 3.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.62e-01

CCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACCTACACCGTGATCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAGACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCGGTAATTTCGAGCAACTGACCCCGAACCCGACGCCGGCTCAGACCACGATCACCGACTCGGTCGACACCACTACTGCGACCCTGACCGCCTCGCCAAGCGTGACCGAAGGCGGCGT  >  AE015451/197389‑197778                                                                                                                                                                   |                                                                                                                                                                                                                                    cccGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTAATCACCTACACCGTGATCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAGACCCAGGGCAGCGTCGATTTCCAGACCCCGGCg                                                                                                                                                                               <  2:182346/217‑1 (MQ=21)   cGACCCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACCTACACCGTGATCCTGAGCAACCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCg                                                                                                                                                                                                                     <  2:422339/177‑1 (MQ=25)                                          ccaccaCCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACCTACACCGTGATCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAGACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCgg                                                                                                                    >  1:225088/1‑235 (MQ=35)                                                     aCCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACCTACACCGTGATCCTGAGCAATCCTGCCCAGACGCCGGTATCCGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAGACCCAGGGCAGCGTCGAATTCCAGACCCCgg                                                                                                                                                                                 >  2:36581/1‑163 (MQ=25)                                                        cTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACCTACACCGTGATCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAGACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAAt                                                                                                                                                                            >  2:259007/1‑165 (MQ=37)                                                        cTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACCTACACCGTGATCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACg                                                                                                                                                            >  2:408190/1‑181 (MQ=25)                                                              gCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACCCACACCGCGATCCTGAGCCATCCTGCCCAGACGCCGGTACCCGTGACCCTGTCCCACGGCAAAACCATTAc                                                                                                                                                                                                                                >  2:107914/1‑107 (MQ=14)                                                                      gTCGGTCACCGAAGGCGGCGTGATCACCTACACCGTGACCCTGAGCAACCCTGCCCAGACGCCGGTGACCGTGACCCTGTCCAACGGCCAAACGATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGACTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGGCAGCGTCACCATCGAGAACGCCACAGGCGGTAATTTCGAGCAACTGACCCCGAACCCGa                                                                                       <  1:448286/236‑1 (MQ=255)                                                                                  aGGCGGCGTAATCACCTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAGACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGa                                                                                                                                                                              <  2:183943/137‑1 (MQ=12)                                                                                       gcgTGATCACCTACACCGTGATCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAGACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACCGTCAGCg                                                                                                                                             <  1:259011/165‑1 (MQ=18)                                                                                        cgTGATCACCTACACCGTGATCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAGACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACCGTCAGCGTCACCATCGAGAACGCCACAGGCGGTAATTTCGAGCAACTGACCCCGAATCCGa                                                                                       >  2:299226/1‑218 (MQ=14)                                                                                             ccgccTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAGACCCAGGGCAGCGTCGAttt                                                                                                                                                                                            <  1:517752/109‑1 (MQ=9)                                                                                                     acCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTGACCGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAGACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCGGTAATTTCGAGCAACTGACCCCGAACCCGACGCCGGCTCAGACCACGATCACCGACTCGGt                                                        <  1:292033/236‑1 (MQ=21)                                                                                                       cGTGACCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAAACCATCACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCGGTAATTTCGAGCAACTGa                                                                                                   <  2:222626/191‑1 (MQ=18)                                                                                                          gacccTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCACACCATTACCGTTGAAGCCg                                                                                                                                                                                                                     >  2:213463/4‑74 (MQ=255)                                                                                                          gATCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCg                                                                                                                                                                                                                     <  1:213467/74‑1 (MQ=255)                                                                                                            tCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAGACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTTCAACAACGGTTCGACCGTCAGCGTCACCATCGAGAACGCCACAGGCGGTaa                                                                                                                 >  2:351441/1‑172 (MQ=17)                                                                                                            tCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAGACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGATCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCGGCAAttt                                                                                                              >  1:501903/1‑175 (MQ=25)                                                                                                            cccTGAGCAATCCTGCCCAGACGCCGGTGACCGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCGGTAATTTCGAGCAACTGACCCCGAACCCGa                                                                                       >  1:150613/2‑198 (MQ=17)                                                                                                            cccTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAAACGATTACCGTTGAAGCCGGCAAAACCCAggg                                                                                                                                                                                                        >  2:405759/2‑85 (MQ=255)                                                                                                            cccTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCg                                                                                                                                                                                                                     <  1:340863/71‑1 (MQ=25)                                                                                                            cccTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAGACCCAGGGCAGc                                                                                                                                                                                                    >  2:62674/2‑89 (MQ=37)                                                                                                            cccTGAGCAACCCTGCCCAGACGCCGGTGACCGTGACCCTGTCCGACGGCCAAACGATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGACTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCGGTAATTTCGAGCAACTGACCACGAACCCGAccc                                                                                    >  1:316627/2‑199 (MQ=11)                                                                                                            cccTGAGCAACCCTGCCCAGACGCCGGTGACCGTGACCCTGTCCAACGGCCAAACGATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGACTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCGGt                                                                                                                   >  1:205827/2‑170 (MQ=255)                                                                                                              cTGAGCAATCCTGCCCAGACGCCGGTAACTGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCg                                                                                                                                                                                                                     >  2:517748/1‑70 (MQ=18)                                                                                                              cTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAAACCATCACCGtg                                                                                                                                                                                                                            >  2:45733/1‑62 (MQ=255)                                                                                                              cTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGGCCAACTGTCAAAACCTTACCGTTCAAGCCGGCaaccc                                                                                                                                                                                                              >  2:243461/1‑74 (MQ=14)                                                                                                              cTGAGCAACCCTGCCCAGACGCCGGTGACCGTGACCCTGTCCAACGGCCAAACGATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGACTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCGGTAAtt                                                                                                               >  1:97532/1‑172 (MQ=255)                                                                                                              cTGAGCAACCCTGCCCAGACGCCGGTGACCGTGACCCTGTCCAACGGCCAAACGATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGACTTCCAGACCCCGGCGAATGACGTCTACAACAACGGATCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCGGGAAt                                                                                                                >  1:1510/1‑171 (MQ=11)                                                                                                              cTGAGCAACCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCg                                                                                                                                                                                                                     >  1:361951/1‑70 (MQ=255)                                                                                                                  gCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCg                                                                                                                                                                                                                     >  1:342226/1‑66 (MQ=39)                                                                                                                  gCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCg                                                                                                                                                                                                                     <  2:342222/66‑1 (MQ=40)                                                                                                                      tCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAAACGATGACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGcca                                                                                                                                                                              <  1:384465/101‑3 (MQ=11)                                                                                                                      cccTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGa                                                                                                                                                                              >  1:363250/2‑101 (MQ=17)                                                                                                                         tGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAGACCCAGGGCAGc                                                                                                                                                                                                    <  1:320596/76‑1 (MQ=39)                                                                                                                         tGCCCAGACGCCGGTAACCGTGAACCTGTCCAACGGCCAAACGATTACCGTTGAAGCCGGCAAGACCCAGGGCAGc                                                                                                                                                                                                    >  2:320592/1‑76 (MQ=255)                                                                                                                           cccAGACGCCGGTAACCGTGAACCTGTCCAACGGCCAAACGATTACCGTTGAAGCCGGCAAGACGCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACCGTCAg                                                                                                                                               <  2:486690/127‑1 (MQ=11)                                                                                                                              aGACGCCGGTAACCGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCg                                                                                                                                                                                                                     <  1:382603/54‑1 (MQ=255)                                                                                                                              aGACGCCGGTAACCGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAGACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATg                                                                                                                                                                           <  2:245845/96‑1 (MQ=37)                                                                                                                                acgacgGTAACCGTGACCCTGTCCAACGGCCAAACCATTACCGtt                                                                                                                                                                                                                            <  2:53635/45‑1 (MQ=255)                                                                                                                                   ccGGTAACCGTGACCCTGTCCAACTGCCAACCGATTACGGTTGAAGc                                                                                                                                                                                                                       >  2:492702/1‑47 (MQ=17)                                                                                                                                   ccGGTAACCGTGACCCTGTCCAACGGCCAAAcc                                                                                                                                                                                                                                     >  2:99018/1‑33 (MQ=40)                                                                                                                                   ccGGTAACCGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAGACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGCTCGACCGTCAGCGTCACCATCGAGAACGCCACAGGCg                                                                                                                     >  2:184539/1‑145 (MQ=12)                                                                                                                                     ggTAACCGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCg                                                                                                                                                                                                                     <  1:285459/47‑1 (MQ=255)                                                                                                                                      gTAGCCGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCg                                                                                                                                                                                                                     <  1:189517/46‑1 (MQ=255)                                                                                                                                          ccGTGAACCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAGACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGa                                                                                                                                                                              <  2:226099/81‑1 (MQ=17)                                                                                                                                          cagTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAGACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACCGTCAGCGTCACCATCGAGAACGCCACAGGCGGTAATTTCGAGCAACTGACCCCGAACCCGACGCCg                                                                                  <  2:139672/171‑1 (MQ=14)                                                                                                                                           cGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCg                                                                                                                                                                                                                     <  2:448722/41‑1 (MQ=32)                                                                                                                                                        aaCGGCCAAACCATTACCGTTGAAGCCGGCAAGACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCGGTAATTTCGAGCAACTGACCCCGAACCCGACGCCGGCTCCGACCa                                                                        >  1:461318/1‑169 (MQ=25)                                                                                                                                                        aaCGGCCAAACCATTACCGTTGAAGCCGGCAAGACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCGGTAATTTCGAGCAACTGACCCCGAACCCGACGCCGGCTCAGACCACGATCACCGACTCGGTCGACACCACTACTGCGACCCTGACCGCCTCGCCAAGCGTGACCGAAggcg      >  1:254070/1‑235 (MQ=255)                                                                                                                                                           ggCCAAACCATTACCGTTGAAGCCGGCAAGACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCGGTAATTTCGAGCAACTGACCCCGAACCCGACGCCGGCTCAGACCACGATCACCGACTCGGTCGACACCACTACTGCGACCCTGACCGCCTCGCCAAGCGTGACCGAAggcggc    <  2:254066/234‑1 (MQ=255)                                                                                                                                                            gCCAAACCATTACCGTTGAAGCCGGCAAGACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCGGTAATTTCGAGCAACTGACCCCGAACCCGACGCCGGCTCAGACCACGATCACCGACTCGGTCGACACCACTACTGCGACCCTGACCGCCTCGCCAAGCGTGACCGAAGGCGGCGt  <  1:397147/235‑1 (MQ=255)                                                                                                                                                                  ccATTACCGTTGAAGCCGGCAAGACCCCTGGCAGTGTCGCTCTCCAGACCCTGGCGAATGACCTCCACGACAACGTTTCGACTGTCAGCGTCACCATCGAGAACGcc                                                                                                                            >  2:413571/1‑107 (MQ=11)                                                                                                                                                                   |                                                                                                                                                                                                                                    CCCGACGCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACCTACACCGTGATCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCCGGCAAGACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCGGTAATTTCGAGCAACTGACCCCGAACCCGACGCCGGCTCAGACCACGATCACCGACTCGGTCGACACCACTACTGCGACCCTGACCGCCTCGCCAAGCGTGACCGAAGGCGGCGT  >  AE015451/197389‑197778

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑