Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,960,934	G→T	T86T (ACG→ACT)	rep →	ATP‑dependent DNA helicase Rep

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,960,934	0	G	T	100.0%	153.9 / NA	43	T86T (ACG→ACT)	rep	ATP‑dependent DNA helicase Rep
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (23/20);  total (23/20)

CGAGATGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACGTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATGAAAGCGAACTTCTCGTTGTTTGACGATACCG  >  NC_000913/3960859‑3961010                                                                            |                                                                             cgAGATGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTggg                                                                         >  1:791002/1‑81 (MQ=255) cgAGATGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTggg                                                                         >  1:790992/1‑81 (MQ=255)  gagaTGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTgggg                                                                        <  1:790942/81‑1 (MQ=255)  gagaTGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTgggg                                                                        >  1:790990/1‑81 (MQ=255)        aaaGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGa                                                                   >  2:791025/1‑80 (MQ=255)            agCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATatca                                                              >  1:790999/1‑81 (MQ=255)              cGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATatcat                                                             >  1:790993/1‑80 (MQ=255)               gtgtAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATatcatc                                                            >  1:790980/1‑80 (MQ=255)                tgtAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTTGGGCTGGATAtcatca                                                           >  1:790987/1‑80 (MQ=255)                tgtAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCaa                                                          <  2:790943/81‑1 (MQ=255)                 gtAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCaaa                                                         >  1:791001/1‑81 (MQ=255)                  tAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCaaa                                                         <  1:790944/80‑1 (MQ=255)                   aGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAAcg                                                       >  1:790988/1‑81 (MQ=255)                     ggCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAAcgcg                                                     <  1:790945/81‑1 (MQ=255)                        aGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAg                                                   >  2:791005/1‑80 (MQ=255)                        aGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGt                                                  <  2:790946/81‑1 (MQ=255)                         gACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTa                                                 <  2:790947/81‑1 (MQ=255)                           cGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATg                                               >  1:791020/1‑81 (MQ=255)                               ggggCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATgcggc                                           >  1:791007/1‑81 (MQ=255)                                gggCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATgcggc                                           <  1:790948/80‑1 (MQ=255)                                 ggCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGgcgc                                         <  2:790949/81‑1 (MQ=255)                                  gcgcAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCt                                        <  1:790950/81‑1 (MQ=255)                                   cgcAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCtt                                       <  1:790951/81‑1 (MQ=255)                                   cgcAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCtt                                       <  2:790952/81‑1 (MQ=255)                                   cgcAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCtt                                       <  1:790953/81‑1 (MQ=255)                                    gcAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTg                                      >  1:791013/1‑81 (MQ=255)                                    gcAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTg                                      >  1:791019/1‑81 (MQ=255)                                    gcAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTg                                      <  1:790954/81‑1 (MQ=255)                                    gcAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTg                                      >  2:790989/1‑81 (MQ=255)                                      aaaGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTgg                                     >  1:790994/1‑80 (MQ=255)                                         gagGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGAt                                  >  1:791011/1‑80 (MQ=255)                                          agGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATg                                 >  1:791000/1‑80 (MQ=255)                                                 tGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATGAAAGCGaa                         >  1:790996/1‑81 (MQ=255)                                                    gCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATGAAAGCGAACtt                      >  2:791027/1‑81 (MQ=255)                                                        atgatCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATGAAAGCGAACTtct                    <  2:790955/79‑1 (MQ=255)                                                           atCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATGAAAGCGAACTTCTCgtt                <  2:790957/80‑1 (MQ=255)                                                           atCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATGAAAGCGAACTTCTCgtt                <  1:790956/80‑1 (MQ=255)                                                                cACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATGAAAGCGAACTTCTCGTTGttt            <  1:790958/79‑1 (MQ=255)                                                                 aCTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATTAAAGCGAACTTCTCGTTGTTTGAc         <  2:790959/81‑1 (MQ=255)                                                                    ttCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATGAAAGCGAACTTCTCGTTGTTTGACGa       >  2:791010/1‑80 (MQ=255)                                                                       cATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATGAAAGCGAACTTCTCGTTGTTTGACGATAcc   >  1:790983/1‑81 (MQ=255)                                                                       cATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATGAAAGCGAACTTCTCGTTGTTTGACGATAc    <  2:790960/80‑1 (MQ=255)                                                                        aTACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATGAAAGCGAACTTCTCGTTGTTTGACGATACCg  <  1:790961/81‑1 (MQ=255)                                                                            |                                                                             CGAGATGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACGTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATGAAAGCGAACTTCTCGTTGTTTGACGATACCG  >  NC_000913/3960859‑3961010

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑