Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,997,689	C→T	intergenic (‑89/+3)	insC1 ← / ← ygeQ	IS2 repressor TnpA/pseudogene, glycosyl hydrolase family 15, part of T3SS PAI ETT2 remnant

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,997,689	0	C	T	100.0%	224.1 / NA	68	intergenic (‑89/+3)	insC1/ygeQ	IS2 repressor TnpA/pseudogene, glycosyl hydrolase family 15, part of T3SS PAI ETT2 remnant
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (38/30);  total (38/30)

ATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAG  >  NC_000913/2997592‑2997823                                                                                                  |                                                                                                                                       atcaatcaTCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGa                                                                                                 >  2:187814/1‑137 (MQ=255) atcaatcaTCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGa                                                                                                 <  1:187814/137‑1 (MQ=255)      tcatcTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAg                                                                                          >  1:751527/1‑139 (MQ=255)         tcTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTGGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGat                                                                                       >  2:773656/1‑139 (MQ=255)             ttCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGGGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGataaat                                                                                   >  2:879237/1‑139 (MQ=255)                 ccAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGGGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACa                                                                               <  1:879237/139‑1 (MQ=255)                 ccAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACa                                                                               <  2:751527/139‑1 (MQ=255)                     tGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGataaat                                                                                   <  1:8392/131‑1 (MQ=255)                     tGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGataaat                                                                                   >  2:8392/1‑131 (MQ=255)                       aCTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTtcttct                                                                                                                    <  1:1091883/96‑1 (MQ=255)                       aCTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTtcttct                                                                                                                    >  2:1091883/1‑96 (MQ=255)                            tCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGa                                                                                                     <  1:472205/106‑1 (MQ=255)                            tCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGa                                                                                                     >  2:472205/1‑106 (MQ=255)                            tCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGc                                                                    >  2:547383/1‑139 (MQ=255)                            tCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGc                                                                    >  1:1133577/1‑139 (MQ=255)                                 aaaCTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAgg                                                                                         <  1:328182/113‑1 (MQ=255)                                 aaaCTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAgg                                                                                         >  2:328182/1‑113 (MQ=255)                                      aGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTttctt                                                                                                                      <  2:179871/79‑1 (MQ=255)                                      aGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTttctt                                                                                                                      >  1:179871/1‑79 (MQ=255)                                      aGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGataaa                                                                                    >  2:129766/1‑113 (MQ=255)                                      aGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGataaa                                                                                    <  1:129766/113‑1 (MQ=255)                                              gACTATCACTTATTTAAGTGATATTGGTTGTCTCGAGATTCAGGGGGCCAGTTTAATCTTGCTCTTTTCTTCTAGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTa                                                  <  1:352977/139‑1 (MQ=255)                                                  aTCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTAt                                                                                                           >  2:147564/1‑78 (MQ=255)                                                  aTCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTAt                                                                                                           <  1:147564/78‑1 (MQ=255)                                                  aTCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTa                                                                                           >  2:930276/1‑94 (MQ=255)                                                  aTCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTa                                                                                           <  1:930276/94‑1 (MQ=255)                                                  aTCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGt                                              >  1:605020/1‑139 (MQ=255)                                                   tCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCgg                                                            <  2:506090/124‑1 (MQ=255)                                                   tCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCgg                                                            >  1:506090/1‑124 (MQ=255)                                                           ttAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTttcttc                                                                                                                     >  2:472522/1‑59 (MQ=255)                                                           ttAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTttcttc                                                                                                                     <  1:472522/59‑1 (MQ=255)                                                             aaGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTttcttc                                                                                                                     >  2:181864/1‑57 (MQ=255)                                                             aaGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTttcttc                                                                                                                     <  1:181864/57‑1 (MQ=255)                                                             aaGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTc                                   >  1:362297/1‑139 (MQ=255)                                                             aaGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTc                                   >  1:265560/1‑139 (MQ=255)                                                              aGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTcc                                  >  1:413062/1‑139 (MQ=255)                                                                   tatTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTg                                                                                                      <  2:402252/66‑1 (MQ=255)                                                                   tatTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTg                                                                                                      >  1:402252/1‑66 (MQ=255)                                                                   tatTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATa                             >  2:559419/1‑139 (MQ=255)                                                                    atTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGgtgt                                                                                                               >  1:747752/1‑56 (MQ=255)                                                                    atTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGgtgt                                                                                                               <  2:747752/56‑1 (MQ=255)                                                                    atTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTtct                                                       >  2:816596/1‑112 (MQ=255)                                                                    atTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTtct                                                       <  1:816596/112‑1 (MQ=255)                                                                        gTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAg                                                                          <  2:931415/89‑1 (MQ=255)                                                                        gTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAg                                                                          >  1:931415/1‑89 (MQ=255)                                                                        gTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTtct                                                       <  1:141020/108‑1 (MQ=255)                                                                        gTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTtct                                                       >  2:141020/1‑108 (MQ=255)                                                                            tCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTg                                                    >  2:716865/1‑107 (MQ=255)                                                                            tCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTg                                                    <  1:716865/107‑1 (MQ=255)                                                                            tCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGa                    >  1:765209/1‑139 (MQ=255)                                                                             cTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGAt                                                                                                <  2:263069/62‑1 (MQ=255)                                                                             cTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGAt                                                                                                >  1:263069/1‑62 (MQ=255)                                                                             cTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTa                                                                                           >  1:1003138/1‑67 (MQ=255)                                                                             cTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTa                                                                                           <  2:1003138/67‑1 (MQ=255)                                                                             cTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGAt                   >  1:27002/1‑139 (MQ=255)                                                                             cTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGAt                   >  2:314605/1‑139 (MQ=255)                                                                                gagaTTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATtct                <  2:413062/139‑1 (MQ=255)                                                                                   aTTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGaa                                                                                                    >  1:810760/1‑52 (MQ=255)                                                                                   aTTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGaa                                                                                                    <  2:810760/52‑1 (MQ=255)                                                                                    ttCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTcccc            <  2:605020/139‑1 (MQ=255)                                                                                      cAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGAt                              >  2:456021/1‑119 (MQ=255)                                                                                      cAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGAt                              <  1:456021/119‑1 (MQ=255)                                                                                           ggCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATc     <  1:1026158/139‑1 (MQ=255)                                                                                              cAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTg                                                                                             <  1:624513/48‑1 (MQ=255)                                                                                              cAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTg                                                                                             >  2:624513/1‑48 (MQ=255)                                                                                              cAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAgg                                                                                         <  1:246265/52‑1 (MQ=255)                                                                                              cAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAgg                                                                                         >  2:246265/1‑52 (MQ=255)                                                                                              cAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAg  >  1:482591/1‑139 (MQ=255)                                                                                                  |                                                                                                                                       ATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAG  >  NC_000913/2997592‑2997823

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑