Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,820,144	Δ1 bp	intergenic (+24/+18)	b4542 → / ← oraA	hypothetical protein/OraA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,820,143	0	G	.	100.0%	408.5 / NA	90	intergenic (+23/+19)	b4542/oraA	hypothetical protein/OraA
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base . (52/38);  total (52/38)

CAGCTCCAGCGTGTCTTAACCGCCGGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAAGGTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCTGGATATCTTCCATCAGATAGCCA  >  NC_000913/2820070‑2820213                                                                          |                                                                       caGCTCCAGCGTGTCTTAACCGCCGGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAAgta                                                                      >  1:4719475/1‑74 (MQ=255) caGCTCCAGCGTGTCTTAACCGCCGGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAAgta                                                                      >  1:2119026/1‑74 (MQ=255)    cTCCAGCGTGTCTTAACCGCCGGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTaaaa                                                                  <  2:1252272/76‑1 (MQ=255)    cTCCAGCGTGTCTTAACCGCCGGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTaaaa                                                                  >  1:4071791/1‑76 (MQ=255)     tCCAGGGTGTTTTAACCGCCGGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAAt                                                                 <  2:1086945/76‑1 (MQ=255)     tCCAGCGTGTCTTAACCGCCGGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTaaaaa                                                                 >  1:3622595/1‑75 (MQ=255)     tCCAGCGTGTCTTAACCGCCGGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAAt                                                                 >  2:2763026/1‑76 (MQ=255)     tCCAGCGTGTCTTAACCGCCGGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAAt                                                                 >  2:2806192/1‑76 (MQ=255)     tCCAGCGTGTCTTAACCGCCGGGCAGGTAACTGAAAAGCGGGAATAAGATAAGATTTCTTGACTCGGCA‑GTaaaac                                                                 >  1:4857069/1‑75 (MQ=255)      ccAGCGTGTCTTAACCGCCGGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATa                                                                <  2:1181297/76‑1 (MQ=255)      ccAGCGTGTCTTAACCGCCGGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATa                                                                >  1:4176954/1‑76 (MQ=255)      ccAGCGTGTCTTAACCGCCGGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATa                                                                <  1:2063336/76‑1 (MQ=255)       cAGCGTGTCTTAACCGCCGGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATAc                                                               >  1:4469384/1‑76 (MQ=255)       cAGCGTGTCTTAACCGCCGGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATAc                                                               >  2:3348505/1‑76 (MQ=255)       cAGCGTGTCTTAACCGCCGGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATAc                                                               <  2:4023041/76‑1 (MQ=255)       cAGCGTGTCTTAACCGCCGGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATAc                                                               >  2:476947/1‑76 (MQ=255)        aGCGTGTCTTAACCGCCGGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATAcc                                                              >  1:2145270/1‑76 (MQ=255)        aGCGTGTCTTAACCGCCGGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATAcc                                                              >  1:704177/1‑76 (MQ=255)        aGCGTGTCTTAACCGCCGGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATAcc                                                              <  2:2212489/76‑1 (MQ=255)        aGCGTGTCTTAACCGCCGGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATAcc                                                              >  1:3318500/1‑76 (MQ=255)         gCGTGTCTTAACCGCCGGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCg                                                             <  1:230926/76‑1 (MQ=255)          cttgtCTTAACCGCCGGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTTACTGGGAA‑GTAAAATACCGt                                                            <  1:835385/74‑1 (MQ=255)          cGTGTCTTAACCGCCGGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGt                                                            <  2:4045777/76‑1 (MQ=255)            tgtCTTAACCGCCGGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGGA‑GTAAAATACCGTAt                                                          <  1:2962576/76‑1 (MQ=255)            tgtCTTAACCGCCGGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATCCCGTAt                                                          <  1:4398212/76‑1 (MQ=255)              tCTTAACCGCCGGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGc                                                        >  2:4382332/1‑76 (MQ=255)                ttAACCGCCGGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGt                                                      <  1:246821/76‑1 (MQ=255)                ttAACCGCCGGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGt                                                      >  1:1003843/1‑76 (MQ=255)                   aCCGCCGGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCa                                                   <  2:975315/76‑1 (MQ=255)                   aCCGCCGGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCa                                                   <  2:3808336/76‑1 (MQ=255)                    ccgccgGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAg                                                  <  2:363102/76‑1 (MQ=255)                    ccgccgGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAg                                                  <  1:3090471/76‑1 (MQ=255)                      gccgGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTc                                                >  1:3494735/1‑76 (MQ=255)                       ccgGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCg                                               <  2:2118156/76‑1 (MQ=255)                         gggCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGc                                             >  1:1602030/1‑76 (MQ=255)                          ggCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCa                                            >  2:4699413/1‑76 (MQ=255)                          ggCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTGCAGTCGCCa                                            >  2:4723764/1‑76 (MQ=255)                          ggCTGGTAACTGAAAAGCGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCa                                            >  2:4855756/1‑76 (MQ=255)                           gCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCaa                                           <  1:3086230/76‑1 (MQ=255)                           gCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCaa                                           <  2:743070/76‑1 (MQ=255)                            cTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCaaa                                          <  1:1249322/76‑1 (MQ=255)                             tGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCaaaa                                         <  2:4014099/76‑1 (MQ=255)                                tAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAAttt                                      <  2:3652799/76‑1 (MQ=255)                                 aaCTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTc                                     <  2:2914948/76‑1 (MQ=255)                                  aCTGAAAAGTGGGAATAAGATCAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCg                                    >  2:4537304/1‑76 (MQ=255)                                    tGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGcc                                  >  2:4790268/1‑76 (MQ=255)                                    tGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGcc                                  >  1:1338406/1‑76 (MQ=255)                                    tGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGcc                                  <  1:493637/76‑1 (MQ=255)                                      aaaaGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCaa                                >  1:750937/1‑76 (MQ=255)                                      aaaaGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCaa                                >  2:1511542/1‑76 (MQ=255)                                       aaaGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCaaa                               >  2:3753276/1‑76 (MQ=255)                                        aaGTGGGAATAAGATAAGTTTTCTTGACTGGTAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAAt                              <  1:447746/76‑1 (MQ=255)                                         aGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACTGTATGCGTTCAGTCGGCAAAATTTCGCCAAAtc                             <  2:3213323/76‑1 (MQ=255)                                         aGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAAtc                             >  2:2722173/1‑76 (MQ=255)                                         aGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAAtc                             >  2:1412505/1‑76 (MQ=255)                                         aGTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAAtc                             >  1:4686029/1‑76 (MQ=255)                                          gTGGGAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAAtct                            <  1:1185077/76‑1 (MQ=255)                                             ggAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCt                         <  2:4686029/76‑1 (MQ=255)                                              gAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCTg                        >  2:154176/1‑76 (MQ=255)                                              gAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCTg                        >  2:4209578/1‑76 (MQ=255)                                              gAATAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCTg                        >  1:506969/1‑76 (MQ=255)                                               aaTAAGATAAGTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCTgg                       >  1:2049555/1‑76 (MQ=255)                                                 taagataagTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCTGGat                     <  1:209614/76‑1 (MQ=255)                                                 taagataagTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTAGGCAAAATTTCGCCAAATCTCATGGat                     >  1:62053/1‑76 (MQ=255)                                                   agataagTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCTGGatat                   >  2:2118404/1‑76 (MQ=255)                                                    gataagTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCTGGATATc                  >  2:2861250/1‑76 (MQ=255)                                                    gataagTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCTGGATATc                  >  1:4478799/1‑76 (MQ=255)                                                     ataagTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCTGGATATCt                 <  1:4537304/76‑1 (MQ=255)                                                       aagTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCTGGATATCTTc               >  1:106003/1‑76 (MQ=255)                                                        agTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCACATCTCCTGGATATCTTcc              >  2:1785810/1‑76 (MQ=255)                                                        agTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCTGGATATCTTcc              >  1:1283824/1‑76 (MQ=255)                                                        agTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCTGGATATCTTcc              >  1:3609577/1‑76 (MQ=255)                                                         gTTTTCTTGACTGTGAA‑GTAAAATACCGTATGCGTTCAGTCGTCAAAATTTCGCCAAATCTCCTGGATATCTTCCa             >  1:340290/1‑76 (MQ=255)                                                         gTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCTGGATATCTTCCa             <  2:2960328/76‑1 (MQ=255)                                                         gTTTTCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCTGGATATCTTCCa             >  1:292513/1‑76 (MQ=255)                                                          ttttCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCTGGATATCTTCCAt            >  1:946746/1‑76 (MQ=255)                                                          ttttCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCTGGATATCTTCCAt            >  2:4391072/1‑76 (MQ=255)                                                            ttCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCTGGATATCTTCCATCa          >  2:4565142/1‑76 (MQ=255)                                                             tCTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCTGGATATCTTCCATCAg         <  2:3494735/76‑1 (MQ=255)                                                              cTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCTGGATATCTTCCATCAgt        >  2:4510314/1‑75 (MQ=255)                                                              cTTGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCTGGATATCTTCCATCAGa        <  2:4364023/76‑1 (MQ=255)                                                               ttGACTGGGAA‑GTAAAATACCGGATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCATGGATATATTCCATCAGAt       >  1:779443/1‑76 (MQ=255)                                                                tGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCTGGATATCTTCCATCAGATa      >  1:4802538/1‑76 (MQ=255)                                                                tGACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCTGGATATCTTCCATCAGATa      >  1:4749049/1‑76 (MQ=255)                                                                 gACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCTGGATATCTTCCATCAGATAg     >  1:2272184/1‑76 (MQ=255)                                                                 gACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCTGGATATCTTCCATCAGATAg     <  2:1747922/76‑1 (MQ=255)                                                                 gACTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCTGGATATCTTCCATCAGATAg     <  2:2613227/76‑1 (MQ=255)                                                                  aCTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCTGGATATCTTCCATCAGATAGc    >  1:547857/1‑76 (MQ=255)                                                                   cTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCTGGATATCTTCCATCAGATAGcc   <  2:2530805/76‑1 (MQ=255)                                                                   cTGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCTGGATATCTTCCATCAGATAGcc   <  2:4284897/76‑1 (MQ=255)                                                                    tGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCTGGATATCTTCCATCAGATAGCCa  >  2:878273/1‑76 (MQ=255)                                                                    tGGGAA‑GTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCTGGATATCTTCCATCAGATAACCa  <  2:110856/76‑1 (MQ=255)                                                                          |                                                                       CAGCTCCAGCGTGTCTTAACCGCCGGGCTGGTAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGACTGGGAAGGTAAAATACCGTATGCGTTCAGTCGGCAAAATTTCGCCAAATCTCCTGGATATCTTCCATCAGATAGCCA  >  NC_000913/2820070‑2820213

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑