Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,348,749	0	A	G	43.6%	25.7 / 58.7	55	intergenic (‑70/+404)	PP_3820/galU	group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase
Reads supporting (aligned to +/- strand):  ref base A (16/15);  new base G (13/11);  total (29/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01
Rejected as consensus: Frequency below/above cutoff threshold.

TTCTGCATTACGGTTACCAACGAGACGGCGACGCCTACTGGCGGCATAACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTACGTCACAGCGTTCCGTGCAAGTATTGGGCTTTGGCGATTTGTGCCACCTCACCC  >  NC_002947/4348633‑4348898                                                                                                                     |                                                                                                                                                        ttCTGCATTACGGTTACCAACGAGACGGCGACGCCTACTGGCGGCATAACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTg                                                                                                                      <  1:426195/150‑1 (MQ=32)       aTTACGGTTACCAACGAGACGGCGACGCCTACTGGCGGCATAACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGc                                                                                                                <  2:570628/150‑1 (MQ=21)                  cAACGAGACGGCGACGCCTACTGGCGGCATAACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGAtctc                                                                                                     >  2:622463/1‑150 (MQ=25)                  cAACGAGACGGCGACGCCTACTGGCGGCATAACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGAtctc                                                                                                     >  1:144791/1‑150 (MQ=35)                   aaCGAGACGGCGACGCCTACTGGCGGCATAACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTcc                                                                                                    >  1:332140/1‑150 (MQ=35)                       agaCGGCGACGCCTACTGGCGGCATAACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAgg                                                                                                <  2:151028/150‑1 (MQ=35)                           ggCGACGCCTACTGGCGGCATAACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTAGAGATCTCCCAGGGTaa                                                                                            >  1:286581/1‑150 (MQ=25)                            gCGACGCCTACTGGCGGCATAACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAAt                                                                                           <  2:224501/150‑1 (MQ=25)                               aCGCCTACTGGCGGCATAACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTcg                                                                                        >  2:480052/1‑150 (MQ=35)                                   cTACTGGCGGCATAACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAACGGTACAGATCTCCAAGGGCAATTcgcgcg                                                                                    >  2:703363/1‑150 (MQ=255)                                    tACTGGCGGCATAACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGa                                                                                   >  1:389477/1‑150 (MQ=25)                                         gcggcATAACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTc                                                                              <  1:532342/150‑1 (MQ=35)                                             cATAACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGc                                                                          <  1:328559/150‑1 (MQ=25)                                              aTAACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCt                                                                         >  1:248506/1‑150 (MQ=25)                                               tAACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCATGTGCAGGCTCAGGTCGGGCGG‑‑GGACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCAGGAGCTTGCTGCtt                                                                        >  1:184051/1‑150 (MQ=2)                                                   cTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGc                                                                    <  1:295788/150‑1 (MQ=35)                                                   cTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGc                                                                    <  2:144791/150‑1 (MQ=35)                                                     gTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCt                                                                  <  1:672906/150‑1 (MQ=25)                                                     gTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCt                                                                  <  1:622463/150‑1 (MQ=25)                                                      ttCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTg                                                                 >  1:216844/1‑150 (MQ=25)                                                      ttCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCt                                                                         <  2:483935/142‑1 (MQ=35)                                                      ttCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCt                                                                         >  1:483935/1‑142 (MQ=35)                                                        cGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTc                                                               >  1:450515/1‑150 (MQ=25)                                                        cGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTc                                                               <  1:142350/150‑1 (MQ=35)                                                         ggCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCg                                                              <  1:122790/150‑1 (MQ=25)                                                            ccTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGAt                                                           >  1:281425/1‑150 (MQ=25)                                                            ccTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGt                                                                                                                       >  1:162923/1‑90 (MQ=32)                                                            ccTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGt                                                                                                                       <  2:162923/90‑1 (MQ=32)                                                            ccTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGAt                                                           >  2:482033/1‑150 (MQ=35)                                                                ggtggCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTAc                                                       <  1:449195/150‑1 (MQ=35)                                                                    gcgcGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCaa                                                                                                                  <  2:180474/87‑1 (MQ=25)                                                                    gcgcGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCaa                                                                                                                  >  1:180474/1‑87 (MQ=25)                                                                    gcgcGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTgg                                                                                                                     <  1:300957/84‑1 (MQ=33)                                                                    gcgcGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTgg                                                                                                                     >  2:300957/1‑84 (MQ=35)                                                                    gcgcGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTACGTca                                                   >  2:202049/1‑150 (MQ=34)                                                                      gcgGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTACGTcaca                                                 >  1:84837/1‑150 (MQ=35)                                                                            aaCCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTACGTCACAGCGTTc                                           >  1:922/1‑150 (MQ=35)                                                                             aCCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGAGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTCCGTCACAGCGTTcc                                          <  1:703363/150‑1 (MQ=21)                                                                              ccGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTACGTCACAGCGTTCCg                                         >  1:420164/1‑150 (MQ=35)                                                                               cGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTAc                                                       >  2:598868/1‑135 (MQ=37)                                                                               cGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTAc                                                       <  1:598868/135‑1 (MQ=37)                                                                                         tacGGCTTCGGCTGACTTCTGCACGCTCGTCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTACGTCACAGCGTTCCGTGCAAGTATTg                              <  1:476028/150‑1 (MQ=25)                                                                                          acGGCTTCGGCTGACTTCTGCACGCTCATCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTACGTCACAGCGTTCCGTGCAAGTATTgg                             <  1:482033/150‑1 (MQ=35)                                                                                              cTTCGGCTGACTTCTGCACGCTCGTCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTACGTCACAGCGTTCCGTGCAAGTATTGGGCtt                         >  1:315683/1‑150 (MQ=25)                                                                                              cTTCGGCTGACTTCTGCACGCTCATCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTACGTCACAGCGTTCCGTGCAAGTATTGGGCtt                         >  1:598882/1‑150 (MQ=35)                                                                                               ttCGGCTGACTTCTGCACGCTCGTCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCGACGTCACAGCGTTCCGTGCAAGTATTGGGCttt                        <  2:184051/150‑1 (MQ=21)                                                                                                   gCTGACTTCTGCACGCTCATCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTACGTCACAGCGTTCCGTGCAAGTATTGGGCtttagat                    >  1:35815/1‑146 (MQ=21)                                                                                                    cggACTTCTGCACGCGCATCGCGT‑G‑GCCTTACGACGCGCGGTAGCAGAGTGGCATGCGTACCGTTCTCCCAGGGTAATTCGCGCGATCTTCCTGCTTATGCCTGTCGGATCTACGTCACAGCGTTCCGTGCAAGTATTAGGCCTTGGCGa                   <  2:286581/148‑1 (MQ=11)                                                                                                    cTGACTTCTGCACGCTCGTCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTACGTCACAGCGTTCCGTGCAAGTATTGGGCTTTGGCGa                   >  1:417636/1‑150 (MQ=25)                                                                                                         ttCTGCACGCTCGTCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTACGTCACAGCGTTCCGTGCAAGTATTGTGCttt                        >  1:302125/1‑140 (MQ=19)                                                                                                         ttCTGCACGCTCGTCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTACGTCACAGCGTTCCGTGCAAGTATTGGGCttt                        <  2:302125/140‑1 (MQ=21)                                                                                                         ttCTGCACGCTCATCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTACGTCACAGCGTTCCGTGCAAGTATTGGGCTTTGGCGATTtgt              >  1:175641/1‑150 (MQ=35)                                                                                                              cACGCTCATCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTACGTCACAGCGTTCCGTGCAAGTATTGGGCTTTGGCGATTTGTGCCAc         <  2:420164/150‑1 (MQ=35)                                                                                                               aCGCTCGTCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTACGTCACAGCGTTCCGTGCAAGTATTGGGCTTTGGCGATTTGTGCCAcc        >  1:545955/1‑150 (MQ=25)                                                                                                                cGCTCATCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTACGTCACAGCGTTCCGTGCAAGTATTGGGCTTTGGCGATTTGTGCCACCt       <  2:598882/150‑1 (MQ=35)                                                                                                                     aTCCCGT‑C‑GCCTTTCGACGCGCTGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTACGTCACAGCGTTCCGTGCAAGTATTGGGCTTTGGCGATTTGTGCCACCTCAccc  >  1:561506/1‑150 (MQ=25)                                                                                                                     |                                                                                                                                                        TTCTGCATTACGGTTACCAACGAGACGGCGACGCCTACTGGCGGCATAACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGT‑C‑GCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTACGTCACAGCGTTCCGTGCAAGTATTGGGCTTTGGCGATTTGTGCCACCTCACCC  >  NC_002947/4348633‑4348898

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑