Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_002947	1,932,640	+C	intergenic (‑107/+43)	rluA ← / ← minE	bifunctional tRNA pseudouridine(32) synthase TrmQ/ribosomal large subunit pseudouridine synthase RluA/cell division topological specificity factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,932,638	1	.	C	100.0%	175.4 / NA	51	intergenic (‑105/+45)	rluA/minE	bifunctional tRNA pseudouridine(32) synthase TrmQ/ribosomal large subunit pseudouridine synthase RluA/cell division topological specificity factor
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (25/26);  total (25/26)

GGCGTCTTCGAAGAGGATCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGC‑‑‑‑‑CGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTG‑CCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATATTT  >  NC_002947/1932495‑1932781                                                                                                                                                      |                                                                                                                                                ggcgTCTTCGAAGAGGATCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGC‑‑‑‑‑CGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATTCGTCCCCTTGAGGAGCGGGCTTG‑ccagc                                                                                                                                            >  3:143777/1‑146 (MQ=255)    gTCTTCGAAGAGGATCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGC‑‑‑‑‑CGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTG‑cccgcg                                                                                                                                           >  4:307668/1‑143 (MQ=255)       ttCGAAGAGGATCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGC‑‑‑‑‑CGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGCAggg                                                                                                                                       >  3:71951/1‑149 (MQ=255)         cGAAGAGGATCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGC‑‑‑‑‑CGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTATGAGCGGGCTTGCCCGCGAAggg                                                                                                                                       <  6:103708/147‑1 (MQ=255)          gAAGAGGATCTGCACATTCGACAGCGGCATTGCAGGCCTCACCAAAATCGCAGTAAACGCTGGGGC‑‑‑‑‑CGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATAGGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCt                                                                                                                                     <  1:44669/148‑1 (MQ=38)                   cTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGC‑‑‑‑‑CGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCGACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGc                                                                                                                           >  2:307575/1‑149 (MQ=255)                     ggACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGC‑‑‑‑‑CGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGccc                                                                                                                         >  5:197279/1‑149 (MQ=255)                         aTTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGC‑‑‑‑‑CGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCaaa                                                                                                                     >  4:257169/1‑149 (MQ=255)                             gACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGC‑‑‑‑‑CGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGt                                                                                                                 >  4:302436/1‑149 (MQ=255)                             gACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGCCCCACCAGCGCTTTGCGGCCCTTCGCGGGCAACCCCGCCCCAACAAAGCATATGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCaa                                                                                                                      <  1:131227/149‑1 (MQ=25)                              aCAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGC‑‑‑‑‑CGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTc                                                                                                                <  3:307668/149‑1 (MQ=255)                                  cGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGC‑‑‑‑‑CGCTTTGCGGCCCTTCGCGGGCAAGCCCACTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAggg                                                                                                                                       >  4:158965/1‑122 (MQ=255)                                  cGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGC‑‑‑‑‑CGCTTTGCGGCCCTTCGCGGGCAAGCCCACTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAggg                                                                                                                                       <  3:158965/122‑1 (MQ=255)                                             gTCTCACTAAAATCGCAGAAACCGGTGGGGC‑‑‑‑‑CGTTTTGCGGCCCTTCGCGTGCACGCCCGCTCCAACAATGTATATGCGTCCCCTTTCGGTGGGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAg                                                                                                 <  4:143777/149‑1 (MQ=255)                                                 cACGAAAATAGCAGTAAACGCTGGGGC‑‑‑‑‑CGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGAt                                                                                             >  1:212554/1‑149 (MQ=255)                                                  aCGAAAATAGCTGTAAACGCTGGGGC‑‑‑‑‑CGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAATGCATTTGCGTCCCCTGTTGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGa                                                                                              <  1:23009/147‑1 (MQ=37)                                                  aCGAAAATAGCAGTAAACGCTGGGGC‑‑‑‑‑CGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATc                                                                                            >  6:101029/1‑149 (MQ=255)                                                  aCGAAAATAGCAGTAAACGCTGGGGC‑‑‑‑‑CGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATAAGCGTCCCCTGGAGGAGCGGGCATGCCCGCGAAGGGCTGCAAGGCAGGCCCAAATTGTCGAATACGCCGCTCAGCGCTc                                                                                            >  1:365534/1‑149 (MQ=37)                                                           gCAGTAAACGCTGGGGC‑‑‑‑‑CGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAggg                                                                                    <  6:197279/148‑1 (MQ=255)                                                              gTAAACGCTGGGGC‑‑‑‑‑CGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAggg                                                                                    >  5:175303/1‑145 (MQ=255)                                                              gTAAACGCTGGGGC‑‑‑‑‑CGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAggg                                                                                    <  6:175303/145‑1 (MQ=255)                                                               tAAACGCTGGGGC‑‑‑‑‑CGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATg                                                                               <  3:257169/149‑1 (MQ=255)                                                                  ccggtGGGGC‑‑‑‑‑CGCTTGGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGTATATGCGTCCCCTGTAGGAGGGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTc                                                                            <  4:71951/145‑1 (MQ=38)                                                                        gggC‑‑‑‑‑CGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGAt                                                                                <  3:324665/139‑1 (MQ=255)                                                                        gggC‑‑‑‑‑CGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGAt                                                                                >  4:324665/1‑139 (MQ=255)                                                                                 cGCTTTGGGGCCGTGCGGGGGCACGCCCGAGCGTACAAAGTATCTGCGTCCCCTTTCGGCGCGGGATTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGaa                                                                  <  5:241341/149‑1 (MQ=255)                                                                                   cTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATc                                                                <  2:212554/149‑1 (MQ=255)                                                                                   cTTTGCGGCCCTTCGCGGGCAAGCCCGCGCCTACAAAGGATATGCGTCCCGTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATc                                                                <  7:160514/149‑1 (MQ=255)                                                                                      tGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCg                                                               <  1:307575/147‑1 (MQ=255)                                                                                           cccTTCGCGGGCAAGCCCGCTCCTACAAAGTATATGCGTCCCCTGTAGTAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCa                                                                                                  <  5:144164/107‑1 (MQ=37)                                                                                              ttCGCGGGCAAGCCCGCTACTACAAAGGATATGCGTCCCCTGTTTGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTTTGGACTAAGCGGATAAGCGATACGGCAGGGTGATGTTAAGCTCCAGAATCGAGCAGCTGcc                                                     >  2:211279/1‑149 (MQ=38)                                                                                                          cccGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTg                                                  >  6:313110/1‑140 (MQ=255)                                                                                                          cccGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTg                                                  <  5:313110/140‑1 (MQ=255)                                                                                                                  tACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGagca                                                           >  6:131045/1‑123 (MQ=255)                                                                                                                  tACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGagca                                                           <  5:131045/123‑1 (MQ=255)                                                                                                                  tACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGatat                                 >  4:231286/1‑149 (MQ=255)                                                                                                                              gCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGt                     >  5:228799/1‑149 (MQ=255)                                                                                                                               cGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGGCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTg                                                                                  >  1:275188/1‑87 (MQ=37)                                                                                                                               cGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTg                                                                                  <  2:275188/87‑1 (MQ=255)                                                                                                                                 tCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGc                  >  1:27700/1‑149 (MQ=255)                                                                                                                                  ccccTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAgg                                                                                     >  4:161668/1‑81 (MQ=255)                                                                                                                                  ccccTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAgg                                                                                     <  3:161668/81‑1 (MQ=255)                                                                                                                                   cccTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGat                                   <  7:77768/130‑1 (MQ=255)                                                                                                                                   cccTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGat                                   >  8:77768/1‑130 (MQ=255)                                                                                                                                    ccTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCa                                                                           <  7:187268/89‑1 (MQ=255)                                                                                                                                    ccTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCa                                                                           >  8:187268/1‑89 (MQ=255)                                                                                                                                     cTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGAt              >  3:49311/1‑149 (MQ=255)                                                                                                                                       gTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATg             <  5:232012/148‑1 (MQ=255)                                                                                                                                           gAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGcac                             <  5:248503/128‑1 (MQ=255)                                                                                                                                           gAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGcac                             >  6:248503/1‑128 (MQ=255)                                                                                                                                                ggCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATAtt   <  3:182146/149‑1 (MQ=255)                                                                                                                                                 gCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATAttt  >  6:366090/1‑149 (MQ=255)                                                                                                                                                 gCTTGCCCGCGAAGGGCCGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATAttt  >  7:113413/1‑149 (MQ=255)                                                                                                                                                      |                                                                                                                                                GGCGTCTTCGAAGAGGATCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGC‑‑‑‑‑CGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTG‑CCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATATTT  >  NC_002947/1932495‑1932781

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑