Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,292,944	T→C	intergenic (‑22/‑583)	hns ← / → tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,292,944	0	T	C	100.0%	296.9 / NA	81	intergenic (‑22/‑583)	hns/tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (39/42);  total (39/42)

GCGTTTCAAGTGTACATTCTCTTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATATTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTATTTTGTGCCG  >  NC_000913/1292847‑1293039                                                                                                  |                                                                                                gCGTTTCAAGTGTACATTCTCTTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTg                                                                                               <  1:1599708/100‑1 (MQ=255)     ttCAAGTGTACATTCTCTTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGggt                                                                                           >  1:1269136/1‑100 (MQ=255)       cAAGTGTACATTCTCTTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGggt                                                                                           >  2:958539/1‑98 (MQ=255)         aGTGTACATTCTCTTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGtt                                                                                       <  2:1415249/100‑1 (MQ=255)            gtACATTCTCTTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTttgt                                                                                    >  1:95879/1‑100 (MQ=255)            gtACATTCTCTTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTttgt                                                                                    <  2:141574/100‑1 (MQ=255)             tACATTCTCTTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTttgtt                                                                                   >  2:753585/1‑100 (MQ=255)              aCATTCTCTTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTttgttg                                                                                  <  2:541218/100‑1 (MQ=255)               cATTCTCTTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGa                                                                                 <  2:1369851/100‑1 (MQ=255)               cATTCTCTTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGa                                                                                 >  2:821492/1‑100 (MQ=255)                 ttCTCTTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAgg                                                                               <  2:6187/100‑1 (MQ=255)                 ttCTCTTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAgg                                                                               <  2:1425137/100‑1 (MQ=255)                 ttCTCTTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAgg                                                                               <  1:1539806/100‑1 (MQ=255)                 ttCTCTTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAgg                                                                               >  1:1343688/1‑100 (MQ=255)                 atctcTTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAgg                                                                               <  1:1192769/99‑1 (MQ=255)                  tctcTTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGt                                                                              >  2:1482929/1‑100 (MQ=255)                  tctcTTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGt                                                                              <  1:1139719/100‑1 (MQ=255)                  gatcctGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGt                                                                              <  1:507690/95‑1 (MQ=255)                    tctTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAAGTTTAAGTGCTTCGCTCAGTGGAGTAATCTCAAACTTGTACTGGGGGGGTTGGTGGAGGgaa                                                                            >  1:379466/1‑100 (MQ=255)                     ctTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACGGGGGGGGTTTGTTGAGGtaat                                                                           >  1:92589/1‑100 (MQ=255)                     ctTGCCTGCGCACGAAGAGGACGGATGGTGTGCAGAATTTTAAGTGCTTCGCTCATGGTAGGAATCTCAAACTGATACTGGGGTGGTTTGTTGAggagat                                                                           >  2:1192763/1‑96 (MQ=255)                       tGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGtagatc                                                                         >  2:507689/1‑96 (MQ=255)                        gCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTaataat                                                                        >  1:1649822/1‑100 (MQ=255)                        gCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTaataat                                                                        <  1:964900/100‑1 (MQ=255)                          cTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATag                                                                      <  2:505804/100‑1 (MQ=255)                             cgcACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGc                                                                   <  1:1449244/100‑1 (MQ=255)                              gcACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGcc                                                                  >  1:281446/1‑100 (MQ=255)                              gcACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGcc                                                                  >  2:1089181/1‑100 (MQ=255)                               cACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCt                                                                 >  2:1188130/1‑100 (MQ=255)                                aCGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTAATTGTAGTAATCTCAAACTTATCCTGGGGTGGTTTGTTGAGGTAATAATAGAGCCtt                                                                <  2:602754/100‑1 (MQ=255)                                  gAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTaa                                                              <  2:1944376/100‑1 (MQ=255)                                      agTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTc                                                          >  1:1710092/1‑100 (MQ=255)                                       gTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCa                                                         >  2:592054/1‑100 (MQ=255)                                        tACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAg                                                        <  2:1362015/100‑1 (MQ=255)                                        tACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAg                                                        <  2:66649/100‑1 (MQ=255)                                        tACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAg                                                        >  1:1808536/1‑100 (MQ=255)                                        tACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAg                                                        >  2:662789/1‑100 (MQ=255)                                         aCGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGt                                                       <  2:412802/100‑1 (MQ=255)                                         aCGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGt                                                       <  1:37643/100‑1 (MQ=255)                                           ggATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTtg                                                     <  2:1783543/100‑1 (MQ=255)                                           ggATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTtg                                                     >  2:1255483/1‑100 (MQ=255)                                              tgttgtTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGc                                                  <  2:1649809/100‑1 (MQ=255)                                              tgttgtTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGc                                                  <  2:95878/100‑1 (MQ=255)                                                 tgttCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAAt                                               >  2:339763/1‑100 (MQ=255)                                                  gttCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAGTTCCGTTGTGCAATa                                              >  1:2012992/1‑100 (MQ=255)                                                  gttCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATa                                              >  1:217772/1‑100 (MQ=255)                                                  gttCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATa                                              >  2:1549764/1‑100 (MQ=255)                                                  gttCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATa                                              >  2:440875/1‑100 (MQ=255)                                                     cAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGcc                                           >  1:179316/1‑100 (MQ=255)                                                     cAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGcc                                           <  1:1844488/100‑1 (MQ=255)                                                       gAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAg                                         >  1:1747132/1‑100 (MQ=255)                                                        aaTTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAgg                                        <  1:958543/100‑1 (MQ=255)                                                          ttttAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGaa                                      <  2:444399/100‑1 (MQ=255)                                                            ttAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATg                                    >  2:1172142/1‑100 (MQ=255)                                                            ttAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATg                                    <  1:378978/100‑1 (MQ=255)                                                            ttAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATg                                    <  1:440876/100‑1 (MQ=255)                                                               aGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTaa                                 >  2:729397/1‑100 (MQ=255)                                                                gTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAg                                >  1:2018933/1‑100 (MQ=255)                                                                      cGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTc                          >  2:2011277/1‑100 (MQ=255)                                                                      cGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTc                          >  2:584657/1‑100 (MQ=255)                                                                      cGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTc                          <  2:476090/100‑1 (MQ=255)                                                                       gCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCa                         >  1:286380/1‑100 (MQ=255)                                                                        cTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCaa                        <  1:753588/100‑1 (MQ=255)                                                                         tCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCaaa                       <  2:893486/100‑1 (MQ=255)                                                                           aTTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAAt                     <  2:1343679/100‑1 (MQ=255)                                                                            ttGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAAtt                    <  2:217771/100‑1 (MQ=255)                                                                               tagtaATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGtt                 <  1:625598/100‑1 (MQ=255)                                                                                agtaATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTc                <  2:723930/100‑1 (MQ=255)                                                                                   aaTCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCttt             <  2:417818/100‑1 (MQ=255)                                                                                   aaTCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCttt             >  2:1402458/1‑100 (MQ=255)                                                                                    aTCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTa            >  1:856990/1‑100 (MQ=255)                                                                                     tctcAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTAt           <  1:95796/100‑1 (MQ=255)                                                                                     tctaAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCttt             <  2:508841/98‑1 (MQ=255)                                                                                       tcAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATCGCCAGTAATGTAAGTAATTCAAAATTGTTCTTTAttt         >  2:1372926/1‑100 (MQ=255)                                                                                       tcAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTAttt         <  1:188744/100‑1 (MQ=255)                                                                                        cAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTAtttt        >  2:1057511/1‑100 (MQ=255)                                                                                         aaaCTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTATTTtg       <  2:379465/100‑1 (MQ=255)                                                                                           aCTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTATTTtgtg     >  1:1470764/1‑100 (MQ=255)                                                                                            cTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTATTTTGTgc    >  2:1562423/1‑100 (MQ=255)                                                                                            cTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTATTTTGTgc    <  1:1281609/100‑1 (MQ=255)                                                                                              tataCTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTATTTTGTgccg  <  1:1188136/100‑1 (MQ=255)                                                                                                  |                                                                                                GCGTTTCAAGTGTACATTCTCTTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATATTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTATTTTGTGCCG  >  NC_000913/1292847‑1293039

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑