Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP025268	2,997,620	T→C	*144* (TAA→TAG)	CXP41_RS24400 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP025268	2,997,620	0	T	C	100.0%	112.3 / NA	35	*144* (TAA→TAG)	CXP41_RS24400	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (19/16);  total (19/16)

TGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGGAGAAACAATGATTATTA  >  NZ_CP025268/2997488‑2997755                                                                                                                                     |                                                                                                                                        tgaAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTc                                                                                                                                 >  1:5565903/1‑140 (MQ=255)          aatGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGTCt                                                                                                                        >  1:4286493/1‑140 (MQ=255)          aatGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGTCt                                                                                                                        >  1:4285867/1‑140 (MQ=255)                atatAATTAAAAATAAAATTTTTGCGT‑AAAAAAACACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCaa                                                                                                                  >  1:1569148/1‑140 (MQ=255)                              aaaatTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGTCTTGCCAAAACAGAATTATTCa                                                                                                    <  2:4285867/140‑1 (MQ=255)                              aaaatTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGTCTTGCCAAAACAGAATTATTCa                                                                                                    <  2:4286493/140‑1 (MQ=255)                                   ttttGCTT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCATAACAGAATTATTCATATcc                                                                                               <  2:2453627/140‑1 (MQ=255)                                                             aTTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACAtttttt                                                                      <  1:10040331/140‑1 (MQ=255)                                                             aTTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACAtttttt                                                                      <  1:9113430/140‑1 (MQ=255)                                                                                atTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGc                                                   >  2:5738991/1‑140 (MQ=255)                                                                                       tatTACAATTAGATTATATTCAAATCATTAACCTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCAGATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCg                                            <  1:7181153/140‑1 (MQ=255)                                                                                          taaaaTTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATTATTCCTCAGGGCTTGCCAAAACAGAATTATTCATTTACAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAg                                         <  2:6380764/137‑1 (MQ=255)                                                                                                     tataTTCAAATCATTAAACTTGAGCCAGGGAGCTNTAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCNTGTTCGCAGATTTCGTTAAc                              <  1:5738991/140‑1 (MQ=255)                                                                                                       tatTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCt                            >  2:1312621/1‑140 (MQ=255)                                                                                                         ttCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGtt                                 >  1:4572949/1‑133 (MQ=255)                                                                                                         ttCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGtt                                 <  2:4572949/133‑1 (MQ=255)                                                                                                         ttCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTg                          >  1:4210648/1‑140 (MQ=255)                                                                                                         ttCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGAAGATTTCGTTAACCTTg                          >  2:4858430/1‑140 (MQ=255)                                                                                                           cAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTc                        <  2:4210648/140‑1 (MQ=255)                                                                                                            aaaTCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCa                       >  1:4210204/1‑140 (MQ=255)                                                                                                              aTCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAgg                     >  1:5430301/1‑140 (MQ=255)                                                                                                                 aTTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAAtgtg                                                                                     <  2:2143598/73‑1 (MQ=255)                                                                                                                 aTTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAAtgtg                                                                                     >  1:2143598/1‑73 (MQ=255)                                                                                                                 aTTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGga                  >  1:4742610/1‑140 (MQ=255)                                                                                                                   tAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGtt                                 >  2:7283218/1‑123 (MQ=255)                                                                                                                   tAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGtt                                 <  1:7283219/123‑1 (MQ=255)                                                                                                                               aGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGGAGAAACAATGattat    <  2:5565903/140‑1 (MQ=255)                                                                                                                                gggAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATcc                                                                                               <  2:2961148/48‑1 (MQ=255)                                                                                                                                gggAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATcc                                                                                               <  2:2960906/48‑1 (MQ=255)                                                                                                                                gggAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATcc                                                                                               >  1:2961148/1‑48 (MQ=255)                                                                                                                                gggAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATcc                                                                                               >  1:2960906/1‑48 (MQ=255)                                                                                                                                 ggAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGgaga                >  2:2196356/1‑126 (MQ=255)                                                                                                                                 ggAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGgaga                <  1:2196356/126‑1 (MQ=255)                                                                                                                                 ggAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGGAGAAACAATGAttatta  >  1:7566130/1‑140 (MQ=255)                                                                                                                                 ggAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGGAGAAACAATGAttatta  >  1:7566115/1‑140 (MQ=255)                                                                                                                                     |                                                                                                                                        TGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGGAGAAACAATGATTATTA  >  NZ_CP025268/2997488‑2997755

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑