Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,348,749	0	A	G	50.0%	0.5 / 68.4	51	intergenic (‑70/+404)	PP_3820/galU	group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase
Reads supporting (aligned to +/- strand):  ref base A (12/13);  new base G (8/17);  total (20/31)
Fisher's exact test for biased strand distribution p-value = 3.87e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.52e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TTTCTGCATTACGGTTACCAACGAGACGGCGACGCCTACTGGCGGCATA‑‑ACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTACG‑TCACAGCGTTCCGTGCAAGTATTGGGCTTTGGCGATTTGTGCCACCTC  >  NC_002947/4348632‑4348894                                                                                                                        |                                                                                                                                                   tttCTGCATTACGGTTACCAACGAGACGGCGACGCCTACTGGCGGAATAGGGACAGTT‑GG‑CCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGTCGCCTTTCGACGCGCGGTAGCACAGt                                                                                                                    >  2:681156/1‑150 (MQ=11)  ttCTGCATTACGGTTACCAACGAGACGGCGACGCCTACTGGCGGCATA‑‑ACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGTCGCCTTTCGACGCGCGGTAGCACAGTg                                                                                                                   <  1:530108/150‑1 (MQ=17)           aCGGTTACCAACGAGACGGCGACGCCTACTGGCGGCATA‑‑ACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTa                                                                                                          <  2:704273/150‑1 (MQ=35)            cGGTTACCAACGAGACGGCGACGCCTACTGGCGGCATA‑‑ACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTAc                                                                                                         <  1:381772/150‑1 (MQ=25)                tACCAACGAGACGGCGACGCCTACTGGCGGAATA‑‑ACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTAc                                                                                                         >  1:416422/1‑146 (MQ=21)                tACCAACGAGACGGCGACGCCTACTGGCGGAATA‑‑ACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTAc                                                                                                         <  2:416422/146‑1 (MQ=25)                     aCGAGACGGCGACGCCTACTGGCGGCATA‑‑ACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGc                                                                                                             >  2:671660/1‑137 (MQ=18)                     aCGAGACGGCGACGCCTACTGGCGGCATA‑‑ACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGc                                                                                                             <  1:671660/137‑1 (MQ=21)                        agaCGGCGACGCCTACTGGCGGCATA‑‑ACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAgg                                                                                             <  1:94692/150‑1 (MQ=35)                            gtcGACGCCTACTGGCGGCATA‑‑ACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTaa                                                                                         >  2:457661/3‑150 (MQ=25)                                  gCCTACTGGCGGCATA‑‑ACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTcgcg                                                                                   <  2:435759/150‑1 (MQ=25)                                   ccTACTGGCGGCATA‑‑ACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTcgcgc                                                                                  <  1:213400/150‑1 (MQ=35)                                    cTACTGGCGGCATA‑‑ACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAAt                                                                                        >  1:186456/1‑143 (MQ=25)                                    cTACTGGCGGCATA‑‑ACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAAt                                                                                        <  2:186456/143‑1 (MQ=25)                                       cTGGCGGCATA‑‑ACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGAcc                                                                              >  2:439057/1‑150 (MQ=25)                                            ggcATA‑‑ACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCt                                                                         >  1:423484/1‑150 (MQ=34)                                              cATA‑‑ACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAgg                                                                                             >  1:741390/1‑128 (MQ=37)                                              cATA‑‑ACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAgg                                                                                             <  2:741390/128‑1 (MQ=37)                                              cATA‑‑ACCTGTTCGGCCCGTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGc                                                                       <  2:460442/150‑1 (MQ=25)                                               aTA‑‑ACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCt                                                                      >  2:231439/1‑150 (MQ=25)                                               aTA‑‑ACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCt                                                                      >  2:501089/1‑150 (MQ=35)                                                tA‑‑ACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGcat                                                                     >  1:10570/1‑148 (MQ=25)                                                    aCCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTAt                                                                   <  1:183432/150‑1 (MQ=25)                                                      cTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGc                                                                 <  1:47842/150‑1 (MQ=25)                                                           cGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTc                                                            <  1:492031/150‑1 (MQ=25)                                                           cGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTc                                                            <  1:439057/150‑1 (MQ=25)                                                               ccTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGAt                                                        <  1:681156/150‑1 (MQ=25)                                                                   ggtggCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTAc                                                    <  1:568570/150‑1 (MQ=35)                                                                       gcgcGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTACG‑Tca                                               <  1:231439/150‑1 (MQ=25)                                                                         gcgGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCGTCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCCACG‑Tcact                                             <  2:743709/150‑2 (MQ=255)                                                                           ggTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTACG‑TCACAGc                                           <  1:501089/150‑1 (MQ=35)                                                                             ttAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCt                                                      >  1:825016/1‑138 (MQ=37)                                                                             ttAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCt                                                      <  2:825016/138‑1 (MQ=37)                                                                                  cGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCTGGTCGCCTTTCTACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCACGCGACCTTCCTGCTTATGCCTGTCGGAGCTACG‑TCACAGCGTTCCGt                                    >  1:801965/1‑150 (MQ=11)                                                                                      aCTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTACG‑TCACAGCGTTCCGTGCaa                                <  1:457661/150‑1 (MQ=35)                                                                                            tacGGCGTCGGCTGAGTTCTACACGATCATCAAGTCGCCTTTCGTCGCGCGGTATCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCATATGCCTGTCGGATCTACG‑CCCCAGCGTTCCGTGCAAGTATTg                          <  2:10570/150‑1 (MQ=11)                                                                                               ggCTTCGGCTGACTTCTGCACGCTCGTCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTACG‑TCACAGCGTTCCGTGCAAGTATTGGGc                       >  1:344549/1‑150 (MQ=25)                                                                                                    cGGCTGACTTCTGCACGCTCGTCCCGTCGCCTTTCGACGCGCGGTAGCTCTTTGGCAAGCGTACAGATCTCCCCGGCTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTACG‑TCACAGCGTTCCGTGCAAGTATTGGGCTTTgg                  <  1:61195/150‑1 (MQ=11)                                                                                                    cGGCTGACTTCTGCACGCTCGTCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGCCCTTCCTGCTTATGCCTGTCGGATCTACG‑TCACAGCGTTCCGTGCAAGTATTGGGCTTTgg                  <  1:283045/150‑1 (MQ=21)                                                                                                    cGGCTGACTTCTGCACGCTCATCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTACG‑TCACAGCGTTCCGTGCAAGTATTGGGCTTTgg                  <  1:123510/150‑1 (MQ=35)                                                                                                     ggCTGACTTCTGCACGCTCGTCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTACG‑TCACAGCGTTCCGTGCAAGTATTGGGCTTTGGc                 >  2:808472/1‑150 (MQ=25)                                                                                                     ggCTGACTTCTGCACGCTCATCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTc                                                            >  2:706977/1‑108 (MQ=38)                                                                                                     ggCTGACTTCTGCACGCTCATCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTc                                                            <  1:706977/108‑1 (MQ=38)                                                                                                      gCTGACTTCTGCACGCTCATCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGc                                                                 >  1:373715/1‑102 (MQ=38)                                                                                                      gCTGACTTCTGCACGCTCATCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGc                                                                 <  2:373715/102‑1 (MQ=38)                                                                                                          aCTTCTGCACGCTCGTCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTACG‑TCACAGCGTTCCGTGCAAGTATTGGGCTTTGGCGAttt            <  1:808472/150‑1 (MQ=25)                                                                                                            ttCTGCACGCTCCTCCCGTCGTCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTACG‑TCACAGCGTTCCGTGCAAGTATTGGGCTTTGGCGATTtgt          <  2:511809/150‑1 (MQ=25)                                                                                                            ttCTGCACGCTCATCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCt                                                                             <  1:84948/84‑1 (MQ=40)                                                                                                            ttCTGCACGCTCATCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCt                                                                             >  2:84948/1‑84 (MQ=40)                                                                                                            ttCTGCACGCTCATCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTACG‑TCACAGCGTTCCGTGCAAGTATTGGGCTTTGGCGATTtgt          >  2:753418/1‑150 (MQ=34)                                                                                                                    gCTCATCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCAT‑ACAAACAGCCGCCCGCAGGGTTCCGTGCAAGTATTGGGCTTTGGCGTTTTGTGCCACCTc  >  2:483121/1‑150 (MQ=11)                                                                                                                        |                                                                                                                                                   TTTCTGCATTACGGTTACCAACGAGACGGCGACGCCTACTGGCGGCATA‑‑ACCTGTTCGGCCCTTGGTGGCGCGGTTAACCGCCACTTACTACGGCTTCGGCTGACTTCTGCACGCTCATCCCGTCGCCTTTCGACGCGCGGTAGCACAGTGGCAAGCGTACAGATCTCCCAGGGTAATTCGCGCGACCTTCCTGCTTATGCCTGTCGGATCTACG‑TCACAGCGTTCCGTGCAAGTATTGGGCTTTGGCGATTTGTGCCACCTC  >  NC_002947/4348632‑4348894

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑