Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_014034	1,303,926	T→G	100%	intergenic (+113/+44)	urtE → / ← RCAP_rcc01231	urea ABC transporter ATP‑binding protein UrtE/UbiH/UbiF/VisC/COQ6 family ubiquinone biosynthesis hydroxylase

Read alignment evidence...
	seq id	position		change	freq	score	reads	annotation	genes	product
*	NC_014034	1,303,926	0	T→G	100.0%	158.8	77	intergenic (+113/+44)	urtE/RCAP_rcc01231	urea ABC transporter ATP‑binding protein UrtE/UbiH/UbiF/VisC/COQ6 family ubiquinone biosynthesis hydroxylase
Reads supporting (aligned to +/- strand):  new base (53/24):  ref base (0/0):  total (53/24)

TTGGGGCAAGATAAACCCCATCCTTTCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCC....GCCAAGA..TGGGGG..GC.CCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATCCCCAAGCCCGCCCGC  >  NC_014034/1303857‑1303994                                                                            |                                                                        ttGGGGCAAGATAAACCCCATCCTTTCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGgggcgg                                              >  2:3852948/1‑101 (MQ=14)  tGGGGCAAGATAAACCCCATCCTTTCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGgggcggg                                             >  1:3730453/1‑101 (MQ=14)  tGGGGCAAGATAAACCCCATCCTTTCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGgggcggg                                             >  2:289724/1‑101 (MQ=14)     ggCAAGATAAACCCCATCCTTTCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCgggccg                                          >  2:1897536/1‑101 (MQ=14)     ggCAAGATAAACCCCATCCTTTCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCgggccg                                          <  2:181274/101‑1 (MQ=14)      gCAAGATAAACCCCATCCTTTCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCgggccgc                                         >  1:1758879/1‑101 (MQ=14)       cAAGATAACCCCCACCCTTTCCCCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCgggccgca                                        <  2:3598580/101‑1 (MQ=2)       cAAGATAAACCCCATCCTTTCACCTTGCCGCAAATATCCCGGGGGGCGAATTGGCCGAAGGCCAAGAGGGGGGGG..GCGCCCCCTTTTCGGGGCgggccgcc                                        >  1:1236477/1‑100 (MQ=12)       cAAAATAAACCCCATCTTTTCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCgggccgca                                        <  2:1618899/101‑1 (MQ=9)        aaGATAAACCCCATCCTTTCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCgggccgcag                                       >  2:902827/1‑101 (MQ=14)         aGATAACCCCCATCCTTTCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCgggccgcagg                                      <  2:1022336/101‑1 (MQ=9)         aGATAAACCCCATCCTTTCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCgggccgcagg                                      >  2:720527/1‑101 (MQ=14)          gATAAACCCCATCCTTTCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCgggccgcaggg                                     >  1:1561472/1‑101 (MQ=14)           aTAAACCCCATCCTTTCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCgggccgcagggc                                    >  2:4096517/1‑101 (MQ=14)           aTAAACCCCATCCTTTCACCTTGCCGCAAATATCCCGGGGGGCGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCgggccccagggc                                    >  1:729885/1‑101 (MQ=9)            tAAACCCCATCCTTTCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCgggccgcagggcc                                   >  2:337291/1‑101 (MQ=14)            tAAACCCCATCCTTTCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCgggccgcagggcc                                   >  1:3121861/1‑101 (MQ=14)             aaaCCCCATCCTTTCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCgggccgcagggccg                                  >  1:277369/1‑101 (MQ=14)             aaaCCCCATCCTTTCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCgggccgcagggccg                                  >  2:1183999/1‑101 (MQ=14)             aaaCCCCATCCTTTCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCgggccgcagggccg                                  >  2:2755943/1‑101 (MQ=14)             aaaCCCCATCCTTTCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCgcgccgcgggtata                                  >  1:4148002/1‑97 (MQ=2)             aaaCCCCATCCTTTCACCTTGCCGCAAATATCCCGGGGGGGGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCgggccgcagggccg                                  >  1:2515029/1‑101 (MQ=9)                ccccATCCTTTCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCAc                               >  1:495094/1‑101 (MQ=14)                ccccATCCTTTCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCAc                               >  1:343098/1‑101 (MQ=14)                  ccATCCTTTCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCAccc                             >  1:1041489/1‑101 (MQ=14)                   cATCCTTTCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCCCCCt                            >  2:1950147/1‑101 (MQ=9)                   cATCCTTTCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCt                            >  1:1875246/1‑101 (MQ=14)                    aTCCTTTCCCCTTGCCGCAAATGTCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTg                           <  1:3391972/101‑1 (MQ=9)                    aTCCTTTCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTg                           <  2:873801/101‑1 (MQ=14)                      ccTTTCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTgcc                         >  2:955140/1‑99 (MQ=9)                      ccTTTCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTc                         <  2:1782451/101‑1 (MQ=14)                       cTTTCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCa                        >  2:2574388/1‑101 (MQ=14)                        tttCACCTTGCCGCAAATATCCCGGGGGGGGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAg                       >  2:569413/1‑101 (MQ=9)                         ttCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAgc                      >  2:2953048/1‑101 (MQ=14)                         ttCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAgc                      >  1:2336722/1‑101 (MQ=14)                          tccccTGGCCGCAATTACCCGGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAgcg                     <  2:2937855/98‑1 (MQ=9)                          tCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAgcg                     <  2:1052266/101‑1 (MQ=14)                          tCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAgcg                     >  2:3761273/1‑101 (MQ=14)                           cACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAgcgc                    >  2:1374795/1‑101 (MQ=17)                            cccTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCa                   <  1:2571444/100‑1 (MQ=9)                            aCCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCa                   >  1:2482617/1‑101 (MQ=17)                            aCCTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCa                   >  1:57595/1‑101 (MQ=17)                              cTTGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATc                 <  1:3414684/101‑1 (MQ=17)                               ttGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATcc                >  2:2489452/1‑101 (MQ=17)                               ttGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGACGCAGGGCCGGCCCCCGTCAGAGCATcc                >  2:2440748/1‑101 (MQ=2)                                tGCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATccc               <  2:230960/101‑1 (MQ=17)                                 gcagCAAATCTCCGGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATcccc              <  1:1475190/98‑1 (MQ=12)                                 gCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATcccc              <  2:3332587/101‑1 (MQ=17)                                 gCCGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATcccc              >  2:2414289/1‑101 (MQ=17)                                   cGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATCCCCaa            <  2:1622509/101‑1 (MQ=17)                                   cGCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATCCCCaa            <  1:703689/101‑1 (MQ=17)                                   cGCAAATACCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATCCCCaa            <  2:971688/101‑1 (MQ=12)                                    gCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATCCCCAAg           >  2:2601793/1‑101 (MQ=17)                                    gCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATCCCCAAg           <  1:1930832/101‑1 (MQ=17)                                    gCAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATCCCCAAg           >  1:2614464/1‑101 (MQ=17)                                    gCAAATATCCCGGGGGGGGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGAAGGGCCGCACCCTGTCAGCGCACccccgcg           >  1:4057937/1‑98 (MQ=9)                                     cAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATCCCCAAgc          >  1:2849983/1‑101 (MQ=17)                                     cAAATATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATCCCCAAgc          >  2:629049/1‑101 (MQ=17)                                      aaaTATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATCCCCAAgcc         >  2:1635754/1‑101 (MQ=17)                                      aaaTATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATCCCCAAgcc         >  2:1561851/1‑101 (MQ=17)                                      aaaTATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATCCCCAAgcc         >  1:2051878/1‑101 (MQ=17)                                       aaTATCCGGGGGGGTGAAGTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATCCCCAAgccc        <  2:4119840/101‑1 (MQ=12)                                       aaTATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATCCCCAAgccc        <  1:26126/101‑1 (MQ=17)                                       aaTATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATCCCCAAgccc        >  2:1065187/1‑101 (MQ=17)                                       aaTATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATCCCCAAgccc        >  2:1159689/1‑101 (MQ=17)                                       aaTATCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATCCCCAAgccc        <  2:1695344/101‑1 (MQ=17)                                        atatCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATCCCCAAgcccg       >  2:3302172/1‑101 (MQ=17)                                         tatCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATCCCCAAgcccgc      >  2:282599/1‑101 (MQ=18)                                         tatCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATCCCCAAgcccgc      <  2:438978/101‑1 (MQ=18)                                          ccccgggggggTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATCCCCAAgcccgcc     <  1:2944731/96‑1 (MQ=12)                                          atCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATCCCCAAgcccgcc     >  2:614280/1‑101 (MQ=18)                                          atCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATCCCCAAgcccgcc     >  2:3571587/1‑101 (MQ=18)                                          atCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATCCCCAAgcccgcc     >  1:508911/1‑101 (MQ=18)                                          atCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATCCCCAAgcccgcc     >  2:1217831/1‑101 (MQ=18)                                           tCCCGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATCCCCAAgcccgccc    >  2:777840/1‑101 (MQ=18)                                            cccGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATCCCCAAgcccgcccc   >  1:2686425/1‑100 (MQ=12)                                            cccGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATCCCCAAGcccgcccg   >  1:1811778/1‑101 (MQ=18)                                             ccGGGGGGTGAATTGGCCGAAGGCCAAGA..GGGGGGCAGCGCCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATCCCCAAGCccgcccgc  <  1:3236409/101‑1 (MQ=18)                                                                            |                                                                        TTGGGGCAAGATAAACCCCATCCTTTCACCTTGCCGCAAATATCCCGGGGGGTGAATTGGCC....GCCAAGA..TGGGGG..GC.CCCCCTTTTCGGGGCGGGCCGCAGGGCCGCACCCTGTCAGCGCATCCCCAAGCCCGCCCGC  >  NC_014034/1303857‑1303994 Base quality scores:  ATCG  < 3 ≤  ATCG  < 15 ≤  ATCG  < 24 ≤  ATCG  < 33 ≤  ATCG  < 40 ≤  ATCG