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%	196.5 / NA	62	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 (34/28);  total (34/28)

GGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTC  >  NC_000913/2997559‑2997808                                                                                                                                   |                                                                                                                        ggTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTg                                                                                                                 <  2:501674/139‑1 (MQ=17) ggTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTg                                                                                                                 <  2:628840/139‑1 (MQ=17)   tACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGct                                                                                                               >  1:307780/1‑139 (MQ=18)          tCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTttct                                                                                                        >  1:215334/1‑139 (MQ=255)           cTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTttctt                                                                                                       >  2:603267/1‑139 (MQ=255)            tGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTttcttc                                                                                                      <  2:222661/139‑1 (MQ=255)              cGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTg                                                                                                    <  2:215334/139‑1 (MQ=255)                     ccGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTa                                                                                             <  2:625311/139‑1 (MQ=255)                             aaGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTttcttc                                                                                                      <  1:775213/122‑1 (MQ=255)                             aaGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTttcttc                                                                                                      >  2:775213/1‑122 (MQ=255)                             aaGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGaa                                                                                     >  1:124504/1‑139 (MQ=255)                              aGACATTAATCATCTGTTCTCCACTTACTATTCTAATAGCTAGTATTAAGACTATAACTTATTTAAGTGATATTGGTTGTCTGGAGATGCAGGGGGCCAGTTTAAACTTGCTCTTTGCTTCTGGTGTTTATCTTTGaaa                                                                                    <  1:271062/139‑1 (MQ=17)                              aGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGaaa                                                                                    <  2:124504/139‑1 (MQ=255)                                  atcaatcaTCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTttcttc                                                                                                      >  1:2413/1‑117 (MQ=255)                                  atcaatcaTCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTttcttc                                                                                                      <  2:2413/117‑1 (MQ=255)                                   tcaatcaTCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGAttt                                                                               >  2:483673/1‑139 (MQ=255)                                     aatcaTCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGt                                                                             <  1:194331/139‑1 (MQ=255)                                                        aCTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGt                                                          >  1:632543/1‑139 (MQ=255)                                                        aCTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTAGTAGGATAAATAACATTAAGt                                                          >  2:469404/1‑139 (MQ=255)                                                             tCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTg                                                                                                    >  1:300064/1‑92 (MQ=255)                                                             tCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTg                                                                                                    <  2:300064/92‑1 (MQ=255)                                                             tCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGgtgt                                                                                                <  1:323450/96‑1 (MQ=255)                                                             tCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGgtgt                                                                                                >  2:323450/1‑96 (MQ=255)                                                                        gtttataagggaTCGCTTATTTTAGTGATATTTGTTGTTTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCCTCTTGTTTTTTTCTTTGAAAGATTTTTTGGATTAATAACATTAAGGAAAGCCGCATCGGCtt                                          <  2:149203/128‑1 (MQ=21)                                                                        gTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCtt                                          <  2:85298/139‑1 (MQ=255)                                                                        gTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCtt                                          >  1:589223/1‑139 (MQ=255)                                                                               gACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTa                                   <  2:137318/139‑1 (MQ=255)                                                                                aCTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTATCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTaa                                  >  1:546707/1‑139 (MQ=255)                                                                                  tATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATg                                >  2:754779/1‑139 (MQ=255)                                                                                   aTCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTg                                                                                                                 <  1:666312/57‑1 (MQ=255)                                                                                   aTCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTg                                                                                                                 >  2:666312/1‑57 (MQ=255)                                                                                   aTCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGAt                                                                                 >  2:385023/1‑89 (MQ=255)                                                                                   aTCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGAt                                                                                 <  1:385023/89‑1 (MQ=255)                                                                                   aTCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGt                               >  1:5266/1‑139 (MQ=255)                                                                                   aTCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGt                               >  1:488081/1‑139 (MQ=255)                                                                                   aTCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGt                               >  2:208401/1‑139 (MQ=255)                                                                                     cACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGataaa                                                                     <  1:239390/99‑1 (MQ=255)                                                                                     cACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGataaa                                                                     >  2:239390/1‑99 (MQ=255)                                                                                          aTTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTttcttc                                                                                                      >  2:696813/1‑61 (MQ=255)                                                                                          aTTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTttcttc                                                                                                      <  1:696813/61‑1 (MQ=255)                                                                                          aTTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCtt                        >  2:704776/1‑139 (MQ=255)                                                                                            ttAAGTGATATTGGTTTTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATc                          <  2:709984/135‑1 (MQ=255)                                                                                            ttAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATc                          >  1:709984/1‑135 (MQ=255)                                                                                            ttAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCtttt                      >  1:448432/1‑139 (MQ=255)                                                                                              aaGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTc                    >  2:154785/1‑139 (MQ=255)                                                                                                gTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGataaa                                                                     >  2:621259/1‑88 (MQ=255)                                                                                                gTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGataaa                                                                     <  1:621259/88‑1 (MQ=255)                                                                                                gTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCa                  >  2:581480/1‑139 (MQ=255)                                                                                                 tGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAg                 <  1:728458/139‑1 (MQ=255)                                                                                                  gATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCGGCATCGGCTTCTCTGTATTGTCTGTCtcttatacac                >  1:149203/1‑133 (MQ=38)                                                                                                  gATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCtttt                      >  2:792206/1‑133 (MQ=255)                                                                                                  gATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCtttt                      <  1:792206/133‑1 (MQ=255)                                                                                                             tCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGa     >  2:320861/1‑139 (MQ=255)                                                                                                               tGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGAtt   >  1:59222/1‑139 (MQ=255)                                                                                                               tGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGAtt   <  2:363791/139‑1 (MQ=255)                                                                                                                ggAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATtc  <  1:483673/139‑1 (MQ=255)                                                                                                                       cAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACAtt                                                              <  2:63267/72‑1 (MQ=255)                                                                                                                       cAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACAtt                                                              >  1:63267/1‑72 (MQ=255)                                                                                                                       cAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGcc                                                    >  2:525184/1‑82 (MQ=255)                                                                                                                       cAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGcc                                                    <  1:525184/82‑1 (MQ=255)                                                                                                                               cAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCACATCgg                                             >  1:797059/1‑81 (MQ=255)                                                                                                                               cAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCACATCgg                                             <  2:797059/81‑1 (MQ=255)                                                                                                                                   |                                                                                                                        GGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTC  >  NC_000913/2997559‑2997808

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑