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%	141.7 / NA	40	T86T (ACG→ACT)	rep	ATP‑dependent DNA helicase Rep
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (18/22);  total (18/22)

GCGCGAGATGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACGTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATGAAAGCGAACTTCTCGTTGTTTGACGATACCG  >  NC_000913/3960856‑3961010                                                                               |                                                                             gcgcgAGATGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACttt                                                                            >  2:723712/1‑81 (MQ=255)   gcgAGATGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTgg                                                                          >  1:723716/1‑81 (MQ=255)    cgAGATGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTggg                                                                         >  1:723694/1‑81 (MQ=255)      agaTGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGc                                                                       <  2:723647/81‑1 (MQ=255)       gaTGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCt                                                                      <  1:723650/81‑1 (MQ=255)       gaTGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCt                                                                      >  1:723707/1‑81 (MQ=255)       gaTGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCt                                                                      <  1:723649/81‑1 (MQ=255)        aTGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTg                                                                     >  2:723692/1‑81 (MQ=255)          gAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGa                                                                   >  2:723714/1‑81 (MQ=255)              gagCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATatc                                                               <  2:723650/81‑1 (MQ=255)               agCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATatca                                                              <  2:723651/81‑1 (MQ=255)                       gggCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAAcgc                                                      <  1:723653/81‑1 (MQ=255)                       gggCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAAcgc                                                      <  1:723654/81‑1 (MQ=255)                        ggCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAAcgcg                                                     <  1:723655/81‑1 (MQ=255)                           aGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAg                                                   >  1:723705/1‑80 (MQ=255)                             aCGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTAt                                                >  1:723699/1‑81 (MQ=255)                             aCGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTAt                                                <  1:723656/81‑1 (MQ=255)                              cGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATg                                               >  2:723728/1‑81 (MQ=255)                               gCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATgc                                              >  1:723698/1‑81 (MQ=255)                                cTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATgcg                                             <  1:723657/81‑1 (MQ=255)                                     gcgcAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCt                                        >  2:723702/1‑81 (MQ=255)                                      cgcAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCtt                                       <  1:723660/81‑1 (MQ=255)                                      cgcAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCtt                                       <  1:723659/81‑1 (MQ=255)                                      cgcAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGCGGCTCGATATCATCAAACGCGAGTATGCGGCGCtt                                       <  1:723658/81‑1 (MQ=255)                                       gcAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTg                                      >  2:723699/1‑81 (MQ=255)                                         aaaGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTggg                                    <  1:723661/81‑1 (MQ=255)                                           agagGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGAt                                  <  2:723661/81‑1 (MQ=255)                                            gagGCGCGTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGAt                                  >  2:723694/1‑80 (MQ=255)                                                  cgTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATGAAAGc                            >  1:723722/1‑80 (MQ=255)                                                   gTGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATGAAAGCGa                          <  1:723663/81‑1 (MQ=255)                                                    tGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATGAAAGCGaa                         <  1:723664/81‑1 (MQ=255)                                                    tGGGCTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATGAAAGCGaa                         >  1:723714/1‑81 (MQ=255)                                                        cTGATGATCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATGAAAGCGAACTtc                     >  2:723722/1‑81 (MQ=255)                                                           atgatCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAATGCGAGTATGCGGCGCTTGGGATGAAAGCGAACTTCTCg                  <  1:723666/81‑1 (MQ=255)                                                           atgatCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATGAAAGCGAACTTCTCg                  <  1:723665/81‑1 (MQ=255)                                                            tgatCTCCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATGAAAGCGAACTTCTCgt                 <  1:723667/81‑1 (MQ=255)                                                                 tcCACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATGAAAGCGAACTTCTCGTTGttt            >  1:723742/1‑81 (MQ=255)                                                                  ccACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATGAAAGCGAACTTCTCGTTGttt            >  2:723701/1‑80 (MQ=255)                                                                   cACTTTCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATGAAAGCGAACTTCTCgttg               <  1:723668/76‑1 (MQ=255)                                                                       ttCCATACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATGAAAGCGAACTTCTCGTTGTTTGACGa       >  2:723709/1‑80 (MQ=255)                                                                           aTACTTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATGAAAGCGAACTTCTCGTTGTTTGACGATACCg  <  1:723669/81‑1 (MQ=255)                                                                               |                                                                             GCGCGAGATGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACGTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATGAAAGCGAACTTCTCGTTGTTTGACGATACCG  >  NC_000913/3960856‑3961010

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑