Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,594,132	(C)8→7	pseudogene (3856/3861 nt)	yneO ←	pseudogene, AidA homolog

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,594,125	0	C	.	100.0%	229.4 / NA	49	pseudogene (1/1461 nt)	yneO	pseudogene, AidA homolog
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (23/26);  total (23/26)

CGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTT‑CCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCACGATATCCGTCGT  >  NC_000913/1593976‑1594270                                                                                                                                                       |                                                                                                                                                  cGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGc                                                                                                                                                   >  1:15396/1‑151 (MQ=255)   tCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGccc                                                                                                                                                 >  1:447309/1‑151 (MQ=255)      cgTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGccccc                                                                                                                                               <  2:443484/150‑1 (MQ=255)       gTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGccccccc                                                                                                                                             >  2:59117/1‑151 (MQ=255)                catcaGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATaa                                                                                                                                    <  1:196754/150‑1 (MQ=255)                      gCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCat                                                                                                                             <  1:1223987/151‑1 (MQ=255)                        cATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCatat                                                                                                                           <  1:105302/151‑1 (MQ=255)                               tCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGc                                                                                                                    >  2:849782/1‑151 (MQ=255)                                ccGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGc                                                                                                                    >  2:1172486/1‑150 (MQ=255)                                ccGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCa                                                                                                                   <  1:593348/151‑1 (MQ=255)                                 cGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGc                                                                                                                    >  1:131673/1‑149 (MQ=255)                                    tataGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAgtg                                                                                                                >  2:471784/1‑150 (MQ=255)                                             cGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTc                                                                                                      <  1:1024953/151‑1 (MQ=255)                                             cGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTc                                                                                                      >  1:438013/1‑151 (MQ=255)                                                 aaCGGTCAGTACATTCCCCGGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCg                                                                                                   <  1:789075/150‑1 (MQ=255)                                                 aaCGGTCAGTACATTCCCCGGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGa                                                                                                  <  1:783973/151‑1 (MQ=255)                                                    ggTCAGTACATTCCCCGGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACAt                                                                                               >  1:955588/1‑151 (MQ=255)                                                               tCCCCGGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGt                                                                                    >  1:219460/1‑151 (MQ=255)                                                                ccccGGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGt                                                                                    <  2:953250/150‑1 (MQ=255)                                                                  ccGGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTAt                                                                                 >  1:1075505/1‑151 (MQ=255)                                                                        tcccccccTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGata                                                                            <  1:913996/148‑1 (MQ=255)                                                                         cccccccTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATAtt                                                                          <  1:286630/150‑1 (MQ=255)                                                                         cccccccTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCACTGTTATGGACAtt                                                                          >  2:345064/2‑151 (MQ=255)                                                                            ccccTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAAt                                                                       >  2:254874/1‑151 (MQ=255)                                                                               cTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAAtgtg                                                                    >  1:19044/1‑151 (MQ=255)                                                                               cTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAAtgtg                                                                    >  1:1174247/1‑151 (MQ=255)                                                                                 tCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGtt                                                                  >  2:888108/1‑151 (MQ=255)                                                                                  cGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGtt                                                                  <  1:1229202/150‑1 (MQ=255)                                                                                  cGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTg                                                                 >  2:74068/1‑151 (MQ=255)                                                                                   gCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTTGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGtt                                                                  <  2:1061449/149‑1 (MQ=255)                                                                                     tATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTCATGTGTTGACt                                                              >  2:658646/1‑151 (MQ=255)                                                                                     tATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACt                                                              >  1:255190/1‑151 (MQ=255)                                                                                          aTTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATATCGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCa                                                         <  2:433674/151‑1 (MQ=255)                                                                                          aTTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCa                                                         <  1:1012185/151‑1 (MQ=255)                                                                                              gAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATAtt                                                     <  1:554967/151‑1 (MQ=255)                                                                                               aaCCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCGCCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTa                                                    <  1:455332/151‑1 (MQ=255)                                                                                                      ccgccATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGc                                               >  1:597179/1‑149 (MQ=255)                                                                                                       cgccATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCa                                              <  2:1219624/149‑1 (MQ=255)                                                                                                          cATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTc                                         <  1:1156817/151‑1 (MQ=255)                                                                                                          cATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTc                                         >  2:683247/1‑151 (MQ=255)                                                                                                              cgccAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGaa                                     <  2:324505/149‑1 (MQ=255)                                                                                                                ccAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAAc                                    <  1:1026760/150‑1 (MQ=255)                                                                                                                 cAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCg                                  >  1:537270/1‑151 (MQ=255)                                                                                                                   ggTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGa                                 >  1:9610/1‑150 (MQ=255)                                                                                                                              aTAGTGGTTTTAGCGTCACGCAGTG‑CCACACCATGCATAACGTTCATATGAGCTGCAGTCGTGGCATTTCCCGACATCACACCGCTGTTATGTATATTAATGTGTTGACTTGCGATATTAATGGCAGAGTCGGAACCGATAGCAATTTc                       <  2:508062/149‑1 (MQ=255)                                                                                                                              aTAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTccc                     >  2:555150/1‑151 (MQ=255)                                                                                                                                    gTTTTAGTGACCCGCTGAG‑CCCCCCCAGGCATATCGTTCATATCTCCTTCAGTGGTGACATTTCCCGACATCACACCACTGTTATGGATATTAATGTGTTGACTTGCCATTTTAATGGCAGAGTCGGAACCGAATGCAATGTccccccc                 <  2:642002/149‑1 (MQ=255)                                                                                                                                    gTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCa               <  1:1062456/151‑1 (MQ=255)                                                                                                                                      tttAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCAc              <  1:356281/150‑1 (MQ=255)                                                                                                                                          gCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCACCatat         >  2:367971/1‑151 (MQ=255)                                                                                                                                             acacGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCACGATATCcg      >  2:1201545/1‑151 (MQ=255)                                                                                                                                                cGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCACGATATCcgtcg   <  1:778589/151‑1 (MQ=255)                                                                                                                                                  cAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCACGATATCcgtcgt  <  1:330551/150‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                  CGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTT‑CCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCACGATATCCGTCGT  >  NC_000913/1593976‑1594270

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑