Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	198,367	G→C	8.5%	V1291V (GTG→GTC)	PP_0168 →	putative surface adhesion protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	198,367	0	G	C	8.5%	142.2 / 2.9	48	V1291V (GTG→GTC)	PP_0168	putative surface adhesion protein
Reads supporting (aligned to +/- strand):  ref base G (24/19);  new base C (2/2);  total (26/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.65e-01

CTTGATGCAGGCTCCATCACGCTCAGTGTTACCGACGCTACAGTTCCGGGTGCCACCTTCGAGAAGCTGGCCTTGGGTGGCCCGGCTACCGTTGAGATCTCGGACACTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCACCCTGACCAACAAAGACGGTCTGCCGATCAATAACCACTCGGAGCTGTACTTCAAGCTGACCGATGGCACTACTGTCGTCGTGGCAGCCAACAGCACCACCGGTTCGGCCACTGTA  >  NC_002947/198218‑198514                                                                                                                                                      |                                                                                                                                                    cTTGATGCAGGCTCCATCACGCTCAGTGTTACCGACGCTACAGTTCCGGGTGCCACCTTCGAGAAGCTGGCCTTGGGTGGCCCGGCTACCGTTGAGATCTCGGACACTATCAGTGAAGTGGTGGCCAACCCGACTGCCACCCCTTCGGTg                                                                                                                                                     >  2:242112/1‑150 (MQ=255)          ggCTCCATCACGCTCAGTGTTACCGACGCTACAGTTCCGGGTGCCACCTTCGAGAAGCTGGCCTTGGGTGGCCCGGCTACCGTTGAGATCTCGGACACTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTCACCGAAggg                                                                                                                                            <  2:1070973/150‑2 (MQ=255)           gCTCCATCACGCTCAGTGTTACCGACGCTACAGTTCCCGGTGCCACCTTCGAGAAGCTGGCCTTGGGTGGCCCGGCTACCGTTGAGATCTCGGACACTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCg                                                                                                                                           >  1:114785/1‑150 (MQ=255)                aTCACGCTCAGTGTTACCGACGCTACAGTTCCGGGTGCCACCTTCGAGAAGCTGGCCTTGGGTGGCCCGGCTACCGTTGAGATCTCGGACACTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGTgag                                                                                                                                      >  2:204783/1‑150 (MQ=255)                  cACGCTCAGTGTTACCGACGCTACAGTTCCGGGTGCCACCTTCGAGAAGCTGGCCTTGGGTGGCCCGGCTACCGTTGAGATCTCGGACACTATCAGTGAAGGGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGAt                                                                                                                                    <  1:655453/150‑1 (MQ=255)                  cACGCTCAGTGTTACCGACGCTACAGTTCCGGGTGCCACCTTCGAGAAGCTGGCCTTGGGTGGCCCGGCTACAGTTGAGATCTCGGACACTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGAACGAAGCGGGTgagaa                                                                                                                                    >  2:1371101/1‑149 (MQ=255)                     gCTCAGTGTTACCGACGCTACAGTTCCGGGTGCCACCTTCGAGAAGCTGGCCTTGGGTGGCCCGGCTACCGTTGAGATCTCGGACACTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCAc                                                                                                                                 <  2:1252484/150‑1 (MQ=255)                           tgtTACCGACGCTACAGTTCCGGGTGCCACCTTGGATCTGCTGGCCTTGGGTGGCCCGGCTACCGTTGAGATCTCGGACACTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTacac                                                                                                                           <  2:114785/150‑1 (MQ=255)                                  gACGCTACAGTTCCGGGTGCCACCTTCGAGAAGCTGGCCTTGGGTGGCCCGGCTACCGTTGAGATCTCGGACACTATAAGTGCATAGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCAcc                                                                                                                    >  1:799520/1‑150 (MQ=255)                                   aCGCTACAGTTCCGGGTGCCACCTTCGAGAAGCTGGCCTTGGGTGGCCCGGCTACCGTTGAGATCTCGGACACTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCAccc                                                                                                                   <  1:11984/150‑1 (MQ=255)                                       tACAGTTCCGGGTGCCACCTTCGAGAAGCTGGCCTTGGGTGGCCCGGCTACCGTTGAGATCTCGGACACTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCACCCTGAc                                                                                                               >  2:672025/1‑150 (MQ=255)                                           gTTCCGGGTGCCACCTTCGAGAAGCTGGCCTTGGGTGGCCCGGCTACCGTTGAGATCTCGGACACTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCACCCTGACcaac                                                                                                           <  2:1298810/150‑1 (MQ=255)                                              ccGGGTGCCACCTTCGAGAAGCTGGCCTTGGGTGGCCCGGCTACCGTTGAGATCTCGGACACTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCACCCTGACCAACaaa                                                                                                        <  2:832287/150‑1 (MQ=255)                                                gggTGCCACCTTCGAGAAGCTGGCCTTGGGTGGCCCGGCTACCGTTGAGATCTCGGACACTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCACCCTGACCAACAAAGa                                                                                                      <  1:204783/150‑1 (MQ=255)                                                 ggTGCCACCTTCGAGAAGCTGGCCTTGGGTGGCCCGGCTACCGTTGAGATCTCGGACACTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCACCCTGACCAACAAAGAc                                                                                                     <  2:60701/150‑1 (MQ=255)                                                  gTGCCACCTTCGAGAAGCTGGCCTTGGGTGGCCCGGCTACAGTTGAGATCTCGGACACTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCACCCTGACCAACAAAGACg                                                                                                    <  1:1371101/150‑1 (MQ=255)                                                     ccACCTTCGAGAAGCTGGCCTTGGGTGGCCCGGCTACCGTTGAGATCTCGGACACTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGt                                                                                                                                         >  2:899200/1‑110 (MQ=255)                                                     ccACCTTCGAGAAGCTGGCCTTGGGTGGCCCGGCTACCGTTGAGATCTCGGACACTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGt                                                                                                                                         <  1:899200/110‑1 (MQ=255)                                                       aCCTTCGAGAAGCTGGCCTTGGGTGGCCCGGCTACCGTTGAGATCTCGGACACTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCACCCTGACCAACAAAGACGGTCTg                                                                                               >  2:1362668/1‑150 (MQ=255)                                                                        cTTGGGTGGCCCGGCTACCGTTGAGATCTCGGACACTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCACCCTGACCAACAAAGACGGTCTGCCGATCAATAACCACTc                                                                              >  1:789750/1‑150 (MQ=255)                                                                        cTTGGGTGGCCCGGCTACCGTTGAGATCTCGGACACTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCACCCTGACCAACAAAGACGGTCTGCCGATCAATAACCACTc                                                                              >  2:139179/1‑150 (MQ=255)                                                                            ggTGGCCCGGCTACCGTTGAGATCTCGGACACTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCACCCTGACCAACAAAGACGGTCTGCCGATCAATAACCACTCGGAg                                                                          <  2:789750/150‑1 (MQ=255)                                                                                  ccGGCTACCGTTGAGATCTCGGACACTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCACCCTGACCAACAAAGACGGTCTGCCGATCAATAACCACTCGGAGCTGTAc                                                                    >  2:1012641/1‑150 (MQ=255)                                                                                  ccGGCTACCGTTGAGATCTCGGACACTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTCACCGAAggg                                                                                                                                            <  2:997332/78‑2 (MQ=255)                                                                                  ccGGCTACCGTTGAGATCTCGGACACTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTCACCGAAggg                                                                                                                                            >  1:997332/1‑77 (MQ=255)                                                                                     gCTACCGTTGAGATCTCGGACACTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCACCCTGACAAACAAAGACGGTCTTCCCACCAAGAACCACTCGGAGCTGTACTTc                                                                 >  2:1225470/1‑150 (MQ=17)                                                                                         ccGTTGAGATCTCGGACACTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCACCCTGACCAACAAAGACGGTCTGCCGATCAATAACCACTCGGAGCTGTAc                                                                    <  2:925926/143‑1 (MQ=255)                                                                                         ccGTTGAGATCTCGGACACTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCACCCTGACCAACAAAGACGGTCTGCCGATCAATAACCACTCGGAGCTGTAc                                                                    >  1:925926/1‑143 (MQ=255)                                                                                           gTTGAGATCTCGGACACTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCACCCTGACCAACAAAGACGGTCTGCCGATCAATAACCACTCGGAGCTGTACTTCAAGCTg                                                           >  1:251378/1‑150 (MQ=255)                                                                                                  ttcctgACACTATCGGTGGAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCACCCTGACCAACAAAGACGGTCTGCCGATCAATAACCACTCGGAGCTGTACTTCAAGCTGACCGATg                                                    >  2:380362/6‑150 (MQ=255)                                                                                                  tctcGGACACTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCACCCTGACCAACAAAGACGGTCTGCCGATCAATAACCACTCGGAGCTGTACTTCAAGCTGACCGATg                                                    >  2:990172/1‑150 (MQ=255)                                                                                                  tctcGGACACTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCACCCTGACCAACAAAGACGGTCTGCCGATCAATAACCACTCGGAGCTGTACTTCAAGCTGACCGATg                                                    >  2:684673/1‑150 (MQ=255)                                                                                                    tcGGACACTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCACCCTGACCAACAAAGACGGTCTGCCGATCAATAACCACTCGGAGCTGTACTTCAAGCTGACCGATGGc                                                  >  1:418637/1‑150 (MQ=255)                                                                                                    tcGGACACTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCACCCTGACCAACAAAGACGGTCTGCCGATCAATAACCACTCGGAGCTGTACTTCAAGCTGACCGATGGc                                                  >  2:309582/1‑150 (MQ=255)                                                                                                        acacTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCACCCTGACCAACAAAGACGGTCTGCCGATCAATAACCACTCGGAGCTGTACTTCAAGCTGACCGATGGCacta                                              <  1:1012641/150‑1 (MQ=255)                                                                                                          acTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCACCCTGACCAACAAAGACGGTCTGCCGATCAATAACCACTCGGAGCTGTACTTCAAGCTGACCGATGGCactact                                            <  1:139179/150‑1 (MQ=255)                                                                                                          acTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCACCCTGACCAACAAAGACGGTCTGCCGATCAATAACCACTCGGAGCTGTACTTCAAGCTGACCGATGGCactact                                            >  2:1325768/1‑150 (MQ=255)                                                                                                                 gTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCACCCTGACCAACAAAGACGGTCTGCCGATCAATAACCACTCGGAGCTGTACTTCAAGCTGACCGATGGCACTACTGtcgtcg                                     >  2:182800/1‑150 (MQ=40)                                                                                                                  tGAAGTGGTGGCCAAACTGACTGCGACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTGGACCATCACCCTGACCAACAAAGGCGGTCTGCCGATCAATAACCACTCGGAGCTGTACTTCAAGCTGACCGATGGCACTACTGTcgtcgt                                    <  1:1225470/150‑1 (MQ=255)                                                                                                                  tGAAGTGGTGGCCAAACTGACTGCACACCCTTCCGTTACCGAAGGCGGTGAGATCACCTACACCATCACCCTGTCCAACAAAGAAGGTCTGCCGATCAATAACCACTCGGAGCTGTACTTCAAGCTGACCGATGGCACTACTGTcgtcgt                                    <  1:672025/150‑1 (MQ=14)                                                                                                                             caaaaCCGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCACCCTGACCAACAAAGACGGTCTGCCGATCAATAACCACTCGGAGCTGTACTTCAAGCTGACCGATGGCACTACTGTCGTCGTGGCAGCCAACa                         <  1:242112/148‑1 (MQ=255)                                                                                                                               aaaCTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCACCCTGACCAACAAAGACGGTCTGCCGATCAATAACCACTCGGAGCTGTACTTCAAGCTGACCGATGGCACTACTGTCGTCGTGGCAGCCAACAGc                       >  1:669998/1‑150 (MQ=38)                                                                                                                               aaaCTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCACCCTGACCAACAAAGACGGTCTGCCGATCAATAACCACTCGGAGCTGTACTTCAAGCTGACCGATGGCACTACTGTCGTCGTGGCAGCCAACAGc                       <  1:182800/150‑1 (MQ=38)                                                                                                                                aaCTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCa                                                                                                                      <  2:1340104/54‑1 (MQ=33)                                                                                                                                aaCTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCa                                                                                                                      >  1:1340104/1‑54 (MQ=33)                                                                                                                                          accgccTTCGGTCACCGAAGGGGGTGAGATCACCTACACCATCACCCTGACCAACAAAGACGGTCTGCCGATCAATAACCACTCGGAGCTGTACTTCAAGCTGACCGATGGCACTACTGTCGTCGTGGCAGCCAACAGCACCACCGGTTc            >  1:117058/5‑150 (MQ=255)                                                                                                                                            ccccTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCACCCTGACCAACAAAGACGGTCTGCCGATCAATAACCACTCGGAGCTGTACTTCAAGCTGACCGATGGCACTACTGTCGTCGTGGCAGCCAACAGCACCACCGGTTCgg          >  2:1166118/1‑150 (MQ=35)                                                                                                                                               cTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCACCCTGACCAACAAAGACGGTCTGCCGATCAATAACCACTCGGAGCTGTACTTCAAGCTGACCGATGGCACTACTGTCGTCGTGGCAGCCAACAGCACCACCGGTTCGGCCa       >  2:183335/1‑150 (MQ=35)                                                                                                                                                    gTGACCGAAGGCGGTGAGATCACCTACACCATCACCCTGACCAACAAAGACGGTCTGCCGATCAATAACCACTCGGAGCTGTACTTCAAGCTGACCGATGGCACTACTGTCGTCGTGGCAGCCAACAGCACCACCGGTTCGGCCACTGTa  <  1:1362668/150‑1 (MQ=35)                                                                                                                                                      |                                                                                                                                                    CTTGATGCAGGCTCCATCACGCTCAGTGTTACCGACGCTACAGTTCCGGGTGCCACCTTCGAGAAGCTGGCCTTGGGTGGCCCGGCTACCGTTGAGATCTCGGACACTATCAGTGAAGTGGTGGCCAAACTGACTGCCACCCCTTCGGTGACCGAAGGCGGTGAGATCACCTACACCATCACCCTGACCAACAAAGACGGTCTGCCGATCAATAACCACTCGGAGCTGTACTTCAAGCTGACCGATGGCACTACTGTCGTCGTGGCAGCCAACAGCACCACCGGTTCGGCCACTGTA  >  NC_002947/198218‑198514

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑