Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,001,717	+C	coding (86/903 nt)	rarD ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,001,717	1	.	C	100.0%	162.2 / NA	65	T29R (ACG→AGG)	rarD	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (40/25);  total (40/25)

TAAAGAAAAACGACCAGATCACGCGATGCGTCAGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACG‑TGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACGCCCTGCCGCGTTTGTTTTGCAT  >  NC_000913/4001643‑4001785                                                                            |                                                                     tAAAGAAAAACGATCAGATCACGCGATGCGTCAGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACgc                                                                      <  2:3989192/76‑2 (MQ=255) tAAAGAAAAACGACCAGATCACGCGATGCGTCAGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACgc                                                                      >  2:1830425/1‑75 (MQ=255)   aaGAAAAACGACCAGATCACGCGATGCGTCAGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACgctg                                                                    >  1:4349603/1‑73 (MQ=255)      aaaaaCGACCAGATCACGCGATGCGTCAGGATTTCATCGGCGGGCCCGTAGTAAATCCACTTGCAGTACGCTGgcg                                                                 >  1:3785818/1‑76 (MQ=255)      aaaaaCGACCAGATCACGCGATGCGTCAGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGgcg                                                                 <  1:2028765/76‑1 (MQ=255)      aaaaaCGACCAGATCACGCGATGCGTCAGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGgcg                                                                 >  1:3756771/1‑76 (MQ=255)          aCGACCAGATCACGCGATGCGTCAGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCtat                                                             <  1:61518/76‑1 (MQ=255)           cGACCAGATCACGCGATGCGTCAGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCtata                                                            >  1:4019754/1‑76 (MQ=255)             aCCAGATCACGCTGTGCGTCAGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATAcc                                                          <  1:54285/76‑1 (MQ=255)             aCCAGATCACGCGATGCGTCAGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGGGGCTATAcc                                                          >  2:313129/1‑76 (MQ=255)             aCCAGAGCACGCGATGCGTCAGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATAcc                                                          <  2:4304220/76‑1 (MQ=255)                 gATCGCGCGGTGGGGCGGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCaa                                                      <  2:3383096/76‑1 (MQ=255)                 gATCACGCGATGCGTCAGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCaa                                                      <  2:473219/76‑1 (MQ=255)                 gATCACGCGATGCGTCAGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATAACCCaa                                                      >  1:4057106/1‑76 (MQ=255)                    cACGCGATGCGTCAGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCaaata                                                   <  1:408920/76‑1 (MQ=255)                     aCGCGATGCGTCAGGATTTCATCGGCGGGCACGTAGGAAATCAACTTGAAGTACGCTGGCGCTATACCCCaaataa                                                  >  1:1333114/1‑76 (MQ=255)                       gcgATGCGTCAGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCaaataaaa                                                <  2:1127909/76‑1 (MQ=255)                       gcgATGCGTCAGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCaaataaaa                                                >  1:2820803/1‑76 (MQ=255)                       gcgATGCGTCAGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCaaataaaa                                                >  1:64493/1‑76 (MQ=255)                           tGCGTCAGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAg                                            >  1:3274692/1‑76 (MQ=255)                             cGTCAGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCg                                          <  2:3140520/76‑1 (MQ=255)                              gtaaGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCgg                                         >  2:1415038/4‑76 (MQ=255)                              gTCAGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCCAATAAAATAAGCgg                                         >  1:3989334/1‑76 (MQ=255)                               tCAGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGc                                        >  1:3528348/1‑76 (MQ=255)                                   gATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAaga                                    <  2:4550035/76‑1 (MQ=255)                                    aTTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAagag                                   >  1:402103/1‑76 (MQ=255)                                     tttCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGc                                  >  2:3404287/1‑76 (MQ=255)                                       tCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGa                                >  2:4734976/1‑76 (MQ=255)                                       tCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGa                                <  2:4216898/76‑1 (MQ=255)                                         aTCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGt                              <  2:2812238/76‑1 (MQ=255)                                         aTCGGCGGGCACGGAGTAAATCAACTTGAAGTACGCCGGCGCTATACCCCAAATAAAAAAAACAGGAAGAGCggga                              >  1:4595964/1‑73 (MQ=255)                                           cggcggGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGtga                            >  1:485550/1‑74 (MQ=255)                                           cggcggGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTaa                            <  2:1011625/76‑1 (MQ=255)                                            ggcggGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAAt                           >  2:1708143/1‑76 (MQ=255)                                             gcggGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGAAAGAGCGAGTAATa                          >  2:21519/1‑76 (MQ=255)                                              cggGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATAc                         >  2:3086356/1‑76 (MQ=255)                                               gggCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACg                        >  2:430155/1‑76 (MQ=255)                                                 gCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACGcc                      >  1:2132122/1‑76 (MQ=255)                                                 gCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACGcc                      >  1:2176399/1‑76 (MQ=255)                                                 gCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACGcc                      >  2:3077500/1‑76 (MQ=255)                                                  cACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACGccc                     >  1:574583/1‑76 (MQ=255)                                                  cACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACGccc                     <  2:2815369/76‑1 (MQ=255)                                                  cACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACGccc                     >  2:1433160/1‑76 (MQ=255)                                                    cGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACGCCCTg                   <  1:1302330/76‑1 (MQ=255)                                                     gtagtaAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACGCCCTGc                  >  1:3109268/1‑76 (MQ=255)                                                      tagtaAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACGCCCTGcc                 <  2:3274692/76‑1 (MQ=255)                                                       agtaAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACGCCCTGCcg                >  2:1108368/1‑76 (MQ=255)                                                        gtaAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACGCCCTGCcgc               <  2:1482876/76‑1 (MQ=255)                                                        gtaAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACGCCCTGCcgc               <  1:3114720/76‑1 (MQ=255)                                                        gtaAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACGCCCTGCcgc               <  1:547735/76‑1 (MQ=255)                                                        gtaAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACGCCCTGCcgc               >  1:3444217/1‑76 (MQ=255)                                                         taAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACGCCCTGGcgcg              >  2:2678546/1‑76 (MQ=255)                                                          aaaTCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACGCCCTGCCGCgt             <  2:2383427/76‑1 (MQ=255)                                                           aaTCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACGCCCTGCCGCgtt            >  2:4776568/1‑76 (MQ=255)                                                            aTCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACGCCCTGCCGCgttt           <  1:4550076/76‑1 (MQ=255)                                                              cAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACGCCCTGCCGCgtttgt         <  2:621747/76‑1 (MQ=255)                                                              cAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACGCCCTGCCGCgtttgt         <  1:1708144/76‑1 (MQ=255)                                                              cAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACGCCCTGCCGCgtttgt         >  1:4072788/1‑76 (MQ=255)                                                               aaCTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACGCCCTGCCGCgtttgtt        >  1:4435480/1‑76 (MQ=255)                                                               aaCTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACGCCCTGCCGCgtttgtt        >  1:1046506/1‑76 (MQ=255)                                                               aaCTGGAGGTACGCTGGCGCGATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACGCCCTGCCGCgtttgtt        <  2:3444217/76‑1 (MQ=255)                                                                 cTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACGCCCTGCCGCGTTTGtttt      >  2:3095385/1‑76 (MQ=255)                                                                 cTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACGCCCTGCCGCGTTTGtttt      >  2:1714650/1‑76 (MQ=255)                                                                   tGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACGCCCTGCCGCGTTTGTTTTGc    >  1:3279537/1‑76 (MQ=255)                                                                     aaGTACGCTGGCGCTATACCCCAAATAAAATACGCGGCCAGAGAGAGTAATACGCCATGCAGCGTGTGTTTTGcat  >  2:1215664/1‑76 (MQ=255)                                                                     aaGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACGCCCTGCCGCGTTTGTTTTGcat  <  1:609063/76‑1 (MQ=255)                                                                     aaGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACGCCCTGCCGCGTTTGTTTTGcat  >  1:1812882/1‑76 (MQ=255)                                                                     aaGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACGCCCTGCCGCGTTTGTTTTGcat  >  2:1184087/1‑76 (MQ=255)                                                                            |                                                                     TAAAGAAAAACGACCAGATCACGCGATGCGTCAGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACG‑TGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGTAATACGCCCTGCCGCGTTTGTTTTGCAT  >  NC_000913/4001643‑4001785

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑