Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,922,961	G→A	intergenic (‑521/+96)	atpI ← / ← rsmG	ATP synthase accessory factor/16S rRNA m(7)G527 methyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,922,961	0	G	A	100.0%	218.0 / NA	61	intergenic (‑521/+96)	atpI/rsmG	ATP synthase accessory factor/16S rRNA m(7)G527 methyltransferase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (30/31);  total (30/31)

CCATTGACATTTTTAATAATGTTTTAACAGCCAATGATGGTTCTTAGCGCCGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTGAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGGTTGTTGTTAACAGTCTAACCGGTCAATTTTTTATGATTTTTTTGATAAAAATTAAATTTTATTTGCTTTAATCACCACCAGATGACGTTCG  >  NC_000913/3922825‑3923096                                                                                                                                         |                                                                                                                                        ccATTGACATTTTTAATAATGTTTTAACAGCCAATGATGGTTCTTAGCGCCGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAAc                                                                                                                                      >  2:327339/1‑140 (MQ=255)        cATTTTTAATAATGTTTTAACAGCCAATGATGGTTCTTAGCGCCGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGt                                                                                                                               >  1:479207/1‑140 (MQ=255)        cATTTTTAATAATGTTTTAACAGCCAATGATGGTTCTTAGCGCCGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGt                                                                                                                               <  1:327339/140‑1 (MQ=255)             ttAATAATGTTTTAACAGCCAATGATGGTTCTTAGCGCCGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAAt                                                                                                                          >  2:623540/1‑140 (MQ=255)               aataatGTTTTAACAGCCAATGATGGTTCTTAGCGCCGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGt                                                                                                                        >  2:117843/1‑140 (MQ=255)                 taatGTTTTAACAGCCAATGATGGTTCTTAGCGCCGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTaa                                                                                                                      <  2:694769/140‑1 (MQ=255)                     gTTTTAACAGCCAATGATGGTTCTTAGCGCCGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTg                                                                                                                                   >  1:645793/1‑123 (MQ=255)                     gTTTTAACAGCCAATGATGGTTCTTAGCGCCGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTg                                                                                                                                   <  2:645793/123‑1 (MQ=255)                      ttttAACAGCCAATGATGGTTCTTAGCGCCGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGt                                                                                                                 <  2:1187392/140‑1 (MQ=255)                         tAACAGCCAATGATGGTTCTTAGCGCCGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTtat                                                                                                              >  2:969551/1‑140 (MQ=255)                         tAACAGCCAATGATGGTTCTTAGCGCCGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTtat                                                                                                              >  2:90101/1‑140 (MQ=255)                           aCAGCCAATGATGGTTCTTAGCGCCGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTatat                                                                                                            <  2:479207/140‑1 (MQ=255)                            cAGCCAATGATGGTTCTTAGCGCCGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATc                                                                                                           <  2:375092/140‑1 (MQ=255)                               ccAATGATGGTTCTTAGCGCCGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGt                                                                                                                 >  1:904256/1‑131 (MQ=255)                               ccAATGATGGTTCTTAGCGCCGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGt                                                                                                                 <  2:904256/131‑1 (MQ=255)                               ccAATGATGGTTCTTAGCGCCGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGt                                                                                                        >  2:937030/1‑140 (MQ=255)                               ccAATGATGGTTCTTAGCGCCGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGCAAACGTGGCGTTAAATGTAACCAGTTATATCAGt                                                                                                        >  2:792539/1‑140 (MQ=255)                                cAATGATGGTTCTTAGCGCCGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTa                                                                                                       >  2:208947/1‑140 (MQ=255)                                cAATGATGGTTCTTAGCGCCGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTa                                                                                                       >  1:11791/1‑140 (MQ=255)                                cAATGATGGTTCTTAGCGCCGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTa                                                                                                       <  1:937030/140‑1 (MQ=255)                                        gTTCTTAGCGCCGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCt                                                                                               >  2:1130449/1‑140 (MQ=255)                                         ttCTTAGCGCCGATTTTTAGCAGACTTATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTg                                                                                              >  1:1140495/1‑140 (MQ=255)                                         ttCTTAGCGCCGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTg                                                                                              >  2:1188939/1‑140 (MQ=255)                                          tCTTAGCGCCGATTTTTAGCAGACTTATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTgg                                                                                             <  2:1140495/140‑1 (MQ=255)                                            ttAGCGCCGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGgtt                                                                                           <  1:969551/140‑1 (MQ=255)                                            ttAGCGCCGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGgtt                                                                                           <  1:90101/140‑1 (MQ=255)                                             tAGCGCCGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGgttg                                                                                          >  2:1114043/1‑140 (MQ=255)                                              aGCGCCGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTgg                                                                                             >  1:1029837/1‑136 (MQ=255)                                              aGCGCCGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTgg                                                                                             <  2:1029837/136‑1 (MQ=255)                                               gcgcCGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGgttgtt                                                                                        <  1:623540/140‑1 (MQ=255)                                               gcgcCGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGgttgt                                                                                         >  2:1138876/1‑139 (MQ=255)                                               gcgcCGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGgttgt                                                                                         <  1:1138876/139‑1 (MQ=255)                                                   cGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGGTTGTTGTTa                                                                                    <  1:208947/140‑1 (MQ=255)                                                   cGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGGTTGTTGTTa                                                                                    <  1:1188939/140‑1 (MQ=255)                                                            gCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGGTTGTTGTTAACAGTCTaa                                                                           <  1:1114043/140‑1 (MQ=255)                                                               gACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGgttgttgtt                                                                                     <  1:857980/127‑1 (MQ=255)                                                               gACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGgttgttgtt                                                                                     >  2:857980/1‑127 (MQ=255)                                                                aCTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGGTTGTTGTTAACAGTCTAAc                                                                          >  1:429418/1‑137 (MQ=255)                                                                aCTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGGTTGTTGTTAACAGTCTAAc                                                                          <  2:429418/137‑1 (MQ=255)                                                                 cTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGGTTGTTGTTAACAGTCTAACCGGt                                                                      <  2:11791/140‑1 (MQ=255)                                                                  tGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGGTTGTTGTTAACAGTCTAACCGGTc                                                                     >  1:208023/1‑140 (MQ=255)                                                                    atatTTTCACTAATGACTTATTTTCTGCTTACC‑AAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGGTTGTTGTTAACAGTCTAACCGGTCAAt                                                                  >  2:133569/1‑140 (MQ=255)                                                                              tAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGGTTGTTGTTAACAGTCTAACCGGTCAATTTTTTATGa                                                         >  2:665776/1‑140 (MQ=255)                                                                               aaTGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGGTTGTTGTTAACAGTCTAACCGGTCAATTTTTTATGAt                                                        >  2:1204822/1‑140 (MQ=255)                                                                                        ttttCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGGTTGTTGTTAACAGTCTAACCGGTCAATTTTTTATGATTTTTTTGAt                                               <  1:258144/140‑1 (MQ=255)                                                                                             tGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGGTTGTTGTTAACAGTCTAGCCGGTCAATTTTTTATGATTTTTTTGATaaaaa                                          >  2:384570/1‑140 (MQ=255)                                                                                               cTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGGTTGTTGTTAACAGTCTAACCGGTCAATTTTTTATGATTTTTTTGATAAaaatt                                        >  2:204110/1‑140 (MQ=255)                                                                                                  aCCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGGTTGTTGTTAACAGTCTAACCGGTCAATTTTTTATGATTTTTTTGATAAaaattaaa                                     >  1:801214/1‑140 (MQ=255)                                                                                                    cAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGGTTGTTGTTAACAGTCTAACCGGTCAATTTTTTATGATTTTTTTGATAAaaattaaatt                                   >  1:175219/1‑140 (MQ=255)                                                                                                    cAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGGTTGTTGTTAACAGTCTAACCGGTCAATTTTTTATGATTTTTTTGATAAaaattaaatt                                   >  1:1157736/1‑140 (MQ=255)                                                                                                        aaaaGCCACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGGTTGTTGTTAACAGTCTAACCGGTCAATTTTTTATGATTTTTTTGATAAAAATTAAATTTTAt                               <  1:204110/140‑1 (MQ=255)                                                                                                             ccACGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGGTTGTTGTTAACAGTCTAACCGGTCAATTTTTTATGATTTTTTTGATAAAAATTAAATTTTATTTGCt                          <  1:311804/140‑1 (MQ=255)                                                                                                                cGTTATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGGTTGTTGTTAACAGTCTAACCGGTCAATTTTTTATGATTTTTTTGATAAAAATTAAATTTTATTTGCTTTa                       <  2:801214/140‑1 (MQ=255)                                                                                                                  ttATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGGTTGTTGTTAACAGTCTAGCCGGTCAATTTTTTATGATTTTTTTGATAAAAATTAAATTTTATTTGCTTTAAt                     <  1:384570/140‑1 (MQ=255)                                                                                                                  ttATCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGGTTGTTGTTAACAGTCTAACCGGTCAATTTTTTATGATTTTTTTGATAAAAATTAAATTTTATTTGCTTTAAt                     <  1:133569/140‑1 (MQ=255)                                                                                                                    aTCTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGGTTGTTGTTAACAGTCTAACCGGTCAATTTTTTATGATTTTTTTGATAAAAATTAAATTTTATTTGCTTTAATca                   <  1:1204822/140‑1 (MQ=255)                                                                                                                      cTTGTTGATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGGTTGTTGTTAACAGTCTAACCGGTCAATTTTTTATGATTTTTTTGATAAAAATTAAATTTTATTTGCTTTAATcacc                 <  1:312377/140‑1 (MQ=255)                                                                                                                          ttgATGCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGGTTGTTGTTAACAGTCTAACCGGTCAATTTTTTATGATTTTTTTGATAAAAATTAAATTTTATTTGCTTTAATCAccacca             >  2:662097/1‑140 (MQ=255)                                                                                                                               gCAAAAGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGGTTGTTGTTAACAGTCTAACCGGTCAATTTTTTATGATTTTTTTGATAAAAATTAAATTTTATTTGCTTTAATCACCACCAGATGa        >  2:678858/1‑140 (MQ=255)                                                                                                                                   aaGAGTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGGTTGTTGTTAACAGTCTAACCGGTCAATTTTTTATGATTTTTTTGATAAAAATTAAATTTTATTTGCTTTAATCACCACCAGATGACGtt    <  1:1130449/140‑1 (MQ=255)                                                                                                                                     gagTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGGTTGTTGTTAACAGTCTAACCGGTCAATTTTTTATGATTTTTTTGATAAAAATTAAATTTTATTTGCTTTAATCACCACCAGATGACGTTCg  <  1:117843/140‑1 (MQ=255)                                                                                                                                     gagTAAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGGTTGTTGTTAACAGTCTAACCGGTCAATTTTTTATGATTTTTTTGATAAAAATTAAATTTTATTTGCTTTAATCACCACCAGATGACGTTCg  <  1:678858/140‑1 (MQ=255)                                                                                                                                         |                                                                                                                                        CCATTGACATTTTTAATAATGTTTTAACAGCCAATGATGGTTCTTAGCGCCGATTTTTAGCAGACTGATATTTTCACTAATGACTTATTTTCTGCTTACCAAAAAAAGCCACGTTATCTTGTTGATGCAAAAGAGTGAACGTGGCGTTAAATGTAACCAGTTATATCAGTAGAAAACCTGGTTGTTGTTAACAGTCTAACCGGTCAATTTTTTATGATTTTTTTGATAAAAATTAAATTTTATTTGCTTTAATCACCACCAGATGACGTTCG  >  NC_000913/3922825‑3923096

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑