Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP002094	444,791	(T)8→9	intergenic (+275/‑718)	LLNZ_02320 → / → glmM	hypothetical protein/phosphoglucosamine mutase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP002094	444,783	1	.	T	100.0%	260.7 / NA	65	intergenic (+267/‑726)	LLNZ_02320/glmM	hypothetical protein/phosphoglucosamine mutase
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base T (38/27);  total (38/27)

TAAATACTTTGTCAGTGGTTATAACAGCAGTGCAACAGTTCATTTATCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAA‑TTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATCAGAATTGAACAACTTCCAGGTGGGGTGACGGCA  >  CP002094/444685‑444873                                                                                                    |                                                                                           taaataCTTTGTCAGTGGTTATAACAGCAGTGCAACAGTTCATTTATCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGaaa                                                                                             <  1:1039707/99‑1 (MQ=255)    ataCTTTGTCAGTGGTTATAACAGCAGTGCAACAGTTCATTTATCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAA‑ttt                                                                                         <  2:47854/99‑1 (MQ=255)    ataCTTTGTCAGTGGTTATAACAGCAGTGCAACAGTTCATTTATCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAA‑ttt                                                                                         >  2:894755/1‑99 (MQ=255)     taCTTTGTCAGTGGTTATAACAGCAGTGCAACAGTTCATTTATCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAA‑tttt                                                                                        >  2:1172918/1‑99 (MQ=255)      aCTTTGTCAGTGGTTATAACAGCAGTGCAACAGTTCATTTATCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAA‑ttttt                                                                                       <  2:1636966/99‑1 (MQ=255)       cTTTGTCAGTGGTTATAACAGCAGTGCAACAGTTCATTTATCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAA‑tttttt                                                                                      >  2:713172/1‑99 (MQ=255)        tttGTCAGTGGTTATAACAGCAGTGCAACAGTTCATTTATCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAA‑ttttttt                                                                                     <  1:1034291/99‑1 (MQ=255)          tGTCAGTGGTTATAACAGCAGTGCAACAGTTCATTTATCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAA‑ttttttttt                                                                                   <  1:1041623/99‑2 (MQ=255)             cAGTGGTTATAACAGCAGTGCAACAGTTCATTTATCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAA‑tttttttttaag                                                                                >  2:1348617/1‑95 (MQ=255)             cAGTGGTTATAACAGCAGTGCAACAGTTCATTTATCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAA‑tttttttttaag                                                                                <  1:401453/99‑5 (MQ=255)               gTGGTTATAACAGCAGTGCAACAGTTCATTTATCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAgtg                                                                               <  1:797475/99‑1 (MQ=255)               gTGGTTATAACAGCAGTGCAACAGTTCATTTATCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAgtg                                                                               <  2:1627444/99‑1 (MQ=255)                 ggTTATAACAGCAGTGCAACAGTTCATTTATCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGtt                                                                             <  2:1540582/99‑1 (MQ=255)                 ggTTATAACAGCAGTGCAACAGTTCATTTATCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGtt                                                                             <  2:6789/99‑1 (MQ=255)                  gTTATAACAGCAGTGCAACAGTTCATTTATCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTg                                                                            <  2:487667/99‑1 (MQ=255)                  gTTATAACAGCAGTGCAACAGTTCATTTATCAGCATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTg                                                                            >  2:1254273/1‑99 (MQ=255)                   ttATAACAGCAGTGCAACAGTTCATTTATCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGa                                                                           >  2:328172/1‑99 (MQ=255)                    tataACAGCAGTGCAACAGTTCATTTATCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGAt                                                                          >  1:1055463/1‑99 (MQ=255)                     ataACAGCAGTGCAACAGTTCATTTATCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGAtt                                                                         <  1:1397899/99‑1 (MQ=255)                         cagcagTGCAACAGTTCATTTATCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAAc                                                                     <  2:1123364/99‑1 (MQ=255)                          agcagTGCAACAGTTCATTTATCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACt                                                                    >  1:176205/1‑99 (MQ=255)                           gcagTGCAACAGTTCATTTATCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTa                                                                   >  1:683652/1‑99 (MQ=255)                            cagTGCAACAGTTCATTTATCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTaa                                                                  >  2:828957/1‑99 (MQ=255)                             agTGTAACAGTTCATTTATCAGGATATAATCGTCTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTaaa                                                                 <  1:199329/99‑1 (MQ=255)                               tGCAACAGTTCATTTATCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAAtt                                                               >  2:1007375/1‑99 (MQ=255)                                  aaCAGTTCATTTATCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGaa                                                            >  1:1447017/1‑99 (MQ=255)                                     aGTTCATTTATCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAAc                                                         <  2:1447017/99‑1 (MQ=255)                                      gTTCATTTATCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACt                                                        <  1:836814/99‑1 (MQ=255)                                      gTTCATTTATCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACt                                                        >  2:334506/1‑99 (MQ=255)                                         cATTTATCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGt                                                     <  2:1438617/99‑1 (MQ=255)                                           tttATCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTaa                                                   >  1:1273967/1‑99 (MQ=255)                                             tATCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAAt                                                 <  2:1340163/99‑1 (MQ=255)                                              aTCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAAtt                                                >  2:667117/1‑99 (MQ=255)                                               tCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAAttt                                               >  2:714805/1‑99 (MQ=255)                                                    atatAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGt                                          >  2:1396134/1‑99 (MQ=255)                                                     tataATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAAc                                                         >  2:1143989/1‑83 (MQ=255)                                                     tataATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAAc                                                         <  1:1143989/83‑1 (MQ=255)                                                      ataATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTc                                        <  2:421352/99‑1 (MQ=255)                                                         aTCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCaa                                     <  2:825031/99‑1 (MQ=255)                                                         aTCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCaa                                     >  2:384434/1‑99 (MQ=255)                                                         aTCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCaa                                     >  1:1088230/1‑99 (MQ=255)                                                         aTCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCaa                                     <  1:76370/99‑1 (MQ=255)                                                           cGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATc                                   <  1:557811/99‑1 (MQ=255)                                                           cGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATc                                   <  2:492103/99‑1 (MQ=255)                                                             aCTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATCAg                                 >  2:9501/1‑99 (MQ=255)                                                             aCTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATCAg                                 >  1:1190041/1‑99 (MQ=255)                                                              cTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATCAGa                                >  1:130518/1‑99 (MQ=255)                                                              cTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATCAGa                                >  1:1617420/1‑99 (MQ=255)                                                               tttCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATCAGaa                               <  2:803070/99‑1 (MQ=255)                                                               tttCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATCAGaa                               <  2:668049/99‑1 (MQ=255)                                                                ttCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATCAGAAt                              >  2:415959/1‑99 (MQ=255)                                                                ttCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATCAGAAt                              >  1:948062/1‑99 (MQ=255)                                                                 tCAATTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATCAGAAtt                             <  2:22940/99‑1 (MQ=255)                                                                   aaTTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATCAGAATTGa                           <  2:1079899/99‑1 (MQ=255)                                                                    aTTACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATCAGAATTGaa                          <  1:781066/99‑1 (MQ=255)                                                                      tACCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATCAGAATTGaaca                        >  2:1164939/1‑99 (MQ=255)                                                                       aCCAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATCAGAATTGaacaa                       >  2:1108575/1‑99 (MQ=255)                                                                        ccAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATCAGAATTGaacaac                      <  2:855208/99‑1 (MQ=255)                                                                         cAATGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATCAGAATTGAACAACt                     >  2:1467530/1‑99 (MQ=255)                                                                           aTGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATCAGAATTGAACAACTTc                   >  1:1564780/1‑99 (MQ=255)                                                                            tGAAGAAAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATCAGAATTGAACAACTTcc                  >  2:146917/1‑99 (MQ=255)                                                                              aagaaAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATCAGAATTGAACAACTTCCAg                >  2:100702/1‑99 (MQ=255)                                                                              aagaaAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATCAGAATTGAACAACTTCCAg                >  2:84981/1‑99 (MQ=255)                                                                                gaaAACTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATCAGAATTGAACAACTTCCAGGt              <  1:1348617/99‑1 (MQ=255)                                                                                  aaaCTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATCAGAATTGAACAACTTCCAGGTgg            <  2:1005215/99‑1 (MQ=255)                                                                                   aaCTCAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATCAGAATTGAACAACTTCCAGGTggg           >  1:1082682/1‑99 (MQ=255)                                                                                     cTCAGATGCTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATCAGAATTGAACAACTTCCAGGTGGGGt         >  1:515555/1‑99 (MQ=255)                                                                                       cAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATCAGAATTGAACAACTTCCAGGTGGGGTGa       <  2:1656395/99‑1 (MQ=255)                                                                                       cAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATCAGAATTGAACAACTTCCAGGTGGGGTGa       >  2:1159764/1‑99 (MQ=255)                                                                                       cAGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATCAGAATTGAACAACTTCCAGGTGGGGTGa       >  2:1502940/1‑99 (MQ=255)                                                                                        aGATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATCAGAATTGAACAACTTCCAGGTGGGGTGAc      >  1:9894/1‑99 (MQ=255)                                                                                         gATACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATCAGAATTGAACAACTTCCAGGTGGGGTGACg     >  2:1619625/1‑99 (MQ=255)                                                                                           tACTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGAAAATTTGATGTTCCAATCAGAATTGAAAAACTTCCAGGTGGGGTGACGGc   >  2:811240/1‑99 (MQ=255)                                                                                            aCTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATCAGAATTGAACAACTTCCAGGTGGGGTGACGGca  >  1:585878/1‑99 (MQ=255)                                                                                            aCTAGAAATTTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATCAGAATTGAACAACTTCCAGGTGGGGTGACGGca  >  1:305467/1‑99 (MQ=255)                                                                                                    |                                                                                           TAAATACTTTGTCAGTGGTTATAACAGCAGTGCAACAGTTCATTTATCAGGATATAATCGACTTTCAATTACCAATGAAGAAAACTCAGATACTAGAAA‑TTTTTTTTAAGTGTTGATTTAACTAAATTGAAAACTGGTAAATTTGATGTTCCAATCAGAATTGAACAACTTCCAGGTGGGGTGACGGCA  >  CP002094/444685‑444873

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑