Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,031,991	Δ1 bp	coding (327/1419 nt)	dcm ←	DNA cytosine methyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,031,991	0	C	.	100.0%	278.9 / NA	66	coding (327/1419 nt)	dcm	DNA cytosine methyltransferase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (36/30);  total (36/30)

CACGCCTTCTTTATGGCTGAGGGTGATGTCGCGGATATCTTCATTAAAATGATGCGTCGCCGGATCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCACTGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCGGTGGTTTGGGTAATAACGTTTGCAGATGGGCGAACTCTTTCT  >  NC_000913/2031862‑2032124                                                                                                                                  |                                                                                                                                      cacGCCTTCTTTATGGCTGAGGGTGATGTCGCGGATATCTTCATTAAAATGATGCGTCGCCGGATCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCaa                                                                                                                             >  2:595159/1‑139 (MQ=255)    gCCTTCTTTATGGCTGAGGGTGATGTCGCGGATATCTTCATTAAAATGATGCGTCGCCGGATCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCg                                                                                                                          >  2:307559/1‑139 (MQ=255)    gCCTTCTTTATGGCTGAGGGTGATGTCGCGGATATCTTCATTAAAATGATGCGTCGCCGGATCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCg                                                                                                                          >  2:1354026/1‑139 (MQ=255)        tcttTATGGCTGAGGGTGATGTCGCGGATATCTTCATTAAAATGATGCGTCGCCGGATCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTc                                                                                                                      >  2:256039/1‑139 (MQ=255)                      ggTGATGTCGCGGATATCTTCATTAAAATGATGCGTCGCCGGATCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGa                                                                                                        >  2:751055/1‑139 (MQ=255)                               gcgGATATCTTCATTAAAATGATGCGTCGCCGGATCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCaa                                                                                               <  2:312919/139‑1 (MQ=255)                                cgGATATCTTCATTAAAATGATGCGTCGCCGGATCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAAt                                                                                              >  2:629846/1‑139 (MQ=255)                                      tCTTCATTAAAATGATGCGTCGCCGGATCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGc                                                                                        >  1:1402181/1‑139 (MQ=255)                                       cTTCATTAAAATGATGCGTCGCTGGATCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGACg                                                                                       <  1:629846/139‑1 (MQ=255)                                       cTTCATTAAAATGATGCGTCGCCGGATCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCg                                                                                       <  2:1402181/139‑1 (MQ=255)                                       cTTCATTAAAATGATGCGTCGCCGGATCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCg                                                                                       <  1:1354026/139‑1 (MQ=255)                                         tCATTAAAATGATGCGTCGCCGGATCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGaa                                                                                     >  1:44833/1‑139 (MQ=255)                                           aTTAAAATGATGCGTCGCCGGATCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATa                                                                                   >  2:87898/1‑139 (MQ=255)                                                  tgatgCGTCGCCGGATCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGAt                                                                            >  2:369096/1‑139 (MQ=255)                                                    atgCGTCGCCGGATCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATaa                                                                          >  2:399147/1‑139 (MQ=255)                                                            ccGGATCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCg                                                                                          <  1:1191899/115‑1 (MQ=255)                                                            ccGGATCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCg                                                                                          >  2:1191899/1‑115 (MQ=255)                                                             cGGATCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACg                                                                 <  1:307559/139‑1 (MQ=255)                                                                aTCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCAt                                                              >  1:768549/1‑139 (MQ=255)                                                                aTCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCAt                                                              <  1:751055/139‑1 (MQ=255)                                                                      ataatGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCg                                                        <  2:480446/139‑1 (MQ=255)                                                                        aatGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGga                                                      <  2:1263162/139‑1 (MQ=255)                                                                            gTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGgatgat                                                  >  1:1071527/1‑139 (MQ=255)                                                                               ggCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGAtgtg                                               >  1:989455/1‑139 (MQ=255)                                                                                          tGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAg                                                                                  >  1:609609/1‑93 (MQ=255)                                                                                          tGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAg                                                                                  <  2:609609/93‑1 (MQ=255)                                                                                           gCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCa                                                               >  2:1349363/1‑111 (MQ=255)                                                                                           gCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCa                                                               <  1:1349363/111‑1 (MQ=255)                                                                                           gCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCGGTGGTTTgg                                   >  2:68276/1‑139 (MQ=255)                                                                                           gCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCGGTGGTTTgg                                   >  1:47008/1‑139 (MQ=255)                                                                                              tACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGa                                                                                                            <  1:674942/63‑1 (MQ=255)                                                                                              tACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGa                                                                                                            >  2:674942/1‑63 (MQ=255)                                                                                              tACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCg                                                                                          <  1:771796/81‑1 (MQ=255)                                                                                              tACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCg                                                                                          >  2:771796/1‑81 (MQ=255)                                                                                              tACCGCATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCGGTGGTTTGGGta                                <  1:1137115/139‑1 (MQ=255)                                                                                                   cATGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCGGTGGTTTGGGTAATAAc                           >  1:678151/1‑139 (MQ=255)                                                                                                    aTGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCa                                                               <  1:540237/102‑1 (MQ=255)                                                                                                    aTGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCa                                                               >  2:540237/1‑102 (MQ=255)                                                                                                    aTGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCggtggt                                       <  2:157552/126‑1 (MQ=255)                                                                                                    aTGTTTGTTCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCggtggt                                       >  1:157552/1‑126 (MQ=255)                                                                                                      gtttgttCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCaa                                                                                               >  1:4695/1‑68 (MQ=255)                                                                                                      gtttgttCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCaa                                                                                               <  2:4695/68‑1 (MQ=255)                                                                                                         tgttCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCggtggt                                       <  2:537351/121‑1 (MQ=255)                                                                                                         tgttCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCggtggt                                       >  1:537351/1‑121 (MQ=255)                                                                                                         tgttCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCGGTGGTTTGGGTAATAACGTTTGc                     >  2:60533/1‑139 (MQ=255)                                                                                                           ttCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCaaaa                                                                                                                  <  1:916872/44‑1 (MQ=255)                                                                                                           ttCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCaaaa                                                                                                                  >  2:916872/1‑44 (MQ=255)                                                                                                           ttCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGAt                                                                                <  2:1457888/78‑1 (MQ=255)                                                                                                           ttCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGAt                                                                                >  1:1457888/1‑78 (MQ=255)                                                                                                           ttCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCGGTGGTTTGGGtaata                             <  1:834687/129‑1 (MQ=255)                                                                                                           ttCCATTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCGGTGGTTTGGGtaata                             >  2:834687/1‑129 (MQ=255)                                                                                                               aTTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCggtggt                                       <  2:110072/115‑1 (MQ=255)                                                                                                               aTTCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCggtggt                                       >  1:110072/1‑115 (MQ=255)                                                                                                                ttCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCGGTGGTTTGGGtaat                              <  2:1081085/123‑1 (MQ=255)                                                                                                                ttCGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCGGTGGTTTGGGtaat                              >  1:1081085/1‑123 (MQ=255)                                                                                                                  cGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCGGTGGTTTGGGTAATAACGTTTGCAGATGGGCg            <  2:768549/139‑1 (MQ=255)                                                                                                                  cGCTGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCGGTGGTTTGGGTAATAACGTTTGCAGATGGGCg            <  1:256039/139‑1 (MQ=255)                                                                                                                     tGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGTCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCg                                                        >  1:689154/1‑92 (MQ=255)                                                                                                                     tGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCg                                                        <  2:689154/92‑1 (MQ=255)                                                                                                                     tGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCGGTGGTTTGGGTAATAACGTTTGCAGATGGGCg            <  2:435929/136‑1 (MQ=255)                                                                                                                     tGGTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCGGTGGTTTGGGTAATAACGTTTGCAGATGGGCg            >  1:435929/1‑136 (MQ=255)                                                                                                                      ggTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAg                                                                                  >  2:16549/1‑65 (MQ=255)                                                                                                                      ggTAAACACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAg                                                                                  <  1:16549/65‑1 (MQ=255)                                                                                                                          aaCACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGa                                                                     <  2:428724/74‑1 (MQ=255)                                                                                                                          aaCACGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGa                                                                     >  1:428724/1‑74 (MQ=255)                                                                                                                            cacGCA‑TGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCGGTGGTTTGGGTAATAACGTTTGCAGATGGGCGAACTCTTtct  <  1:68276/139‑1 (MQ=255)                                                                                                                                  |                                                                                                                                      CACGCCTTCTTTATGGCTGAGGGTGATGTCGCGGATATCTTCATTAAAATGATGCGTCGCCGGATCGCAATAATGGTTGGCTTTATAAGTGCGTACCGCATGTTTGTTCCATTCGCTGGTAAACACGCACTGTCCGCCAATCGATTCAAAACCGCGACGGATGCCGCCAATTCCGGCGAATAGATCGATAAAGCGAAACGCATAATGCGGATGATGTGCCGGTGGTTTGGGTAATAACGTTTGCAGATGGGCGAACTCTTTCT  >  NC_000913/2031862‑2032124

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑