Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,542,643	Δ1 bp	intergenic (+46/‑22)	b4316 → / → fimD	Pil/FimD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,542,640	0	G	.	98.9%	400.3 / ‑2.2	89	intergenic (+43/‑25)	b4316/fimD	Pil/FimD
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base . (41/47);  minor base A (1/0);  total (42/47)
Fisher's exact test for biased strand distribution p-value = 4.72e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01

CTTACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCCGGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACACACAATGCTT  >  NC_000913/4542565‑4542711                                                                            |                                                                        cTTACCCCCAAAATGACGGGCGTAATGTAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCCg                                                                         <  1:109762/76‑1 (MQ=255)  ttACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCCgg                                                                        >  2:5453060/1‑76 (MQ=255)  ttACCCCCAAAATGACAGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCCgg                                                                        <  1:761565/76‑1 (MQ=255)   tACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCCggg                                                                       >  1:4219938/1‑76 (MQ=255)   tACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCCggg                                                                       >  2:3511274/1‑76 (MQ=255)    aCCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCCgggt                                                                      >  1:1735660/1‑75 (MQ=255)      ccccAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCCgggtga                                                                    >  1:2185088/1‑73 (MQ=255)      ccccAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCCgggtga                                                                    >  2:1831666/1‑73 (MQ=255)      ccccAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCCgggtga                                                                    <  1:573288/76‑4 (MQ=255)        ccAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGAtt                                                                 <  2:5582244/76‑1 (MQ=255)        ccAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGAtt                                                                 <  1:5418395/76‑1 (MQ=255)        ccAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGAtt                                                                 <  2:5122357/76‑1 (MQ=255)        ccAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGAtt                                                                 <  2:1731037/76‑1 (MQ=255)          aaaaTGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGAtttt                                                               <  2:3534602/76‑1 (MQ=255)           aaaTGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTa                                                              <  2:4754245/76‑1 (MQ=255)           aaaTGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTa                                                              >  1:2578170/1‑76 (MQ=255)           aaaTGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTa                                                              <  2:4425972/76‑1 (MQ=255)           aaaTGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTa                                                              <  2:1256766/76‑1 (MQ=255)            agtGACGGTCGTAATGGACTAGCGCATGGGGAATTTTTCGCCTGACTCAAAAGCATTGGCTGCC‑GGGTGCTTTTaa                                                             <  1:5371120/74‑1 (MQ=255)            aaTGACGGGCGTAATGGAATAACGCAGGGGGGATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTaa                                                             <  2:4178891/76‑1 (MQ=255)            aaTGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGGATAAAAAGAATTGACTGCC‑GGGTGATTTTaa                                                             <  1:150470/76‑1 (MQ=255)            aaTGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTaa                                                             <  2:4307595/76‑1 (MQ=255)             aggACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAg                                                            <  2:231475/74‑1 (MQ=255)             aTGACGGGCGTAATGGAATCCCGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGTTGATTTTAAg                                                            <  2:1385423/76‑1 (MQ=255)               gACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGcc                                                          >  1:5173458/1‑76 (MQ=255)                aCGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCg                                                         >  1:5231046/1‑76 (MQ=255)                aCGCGCGTACTGGAATACCGCGGGTGAAGTGTTTCGCCTGAATAAAACGGATTGAGTGCC‑GGGTGATTTTAAGctt                                                         <  1:2193247/76‑3 (MQ=255)                  gggCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCgga                                                       >  2:1915014/1‑76 (MQ=255)                   ggCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCggag                                                      <  1:3874329/76‑1 (MQ=255)                   ggCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCggag                                                      <  1:3413516/76‑1 (MQ=255)                    gCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCggagg                                                     >  2:5278070/1‑76 (MQ=255)                      gTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGaa                                                   <  2:3099264/76‑1 (MQ=255)                      gTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGaa                                                   <  1:2233013/76‑1 (MQ=255)                      gTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGaa                                                   <  1:556653/76‑1 (MQ=255)                      gTAATGGAAGAACGCAGGGGGAATGTTGCGCCGGAATAAAAAGAATTGACTGCC‑GGGTGAGGTTAAGCCGGAGGaa                                                   <  1:590478/76‑1 (MQ=255)                        aaTGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGaata                                                 <  2:5263572/76‑1 (MQ=255)                        aaTGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGaata                                                 <  1:3511274/76‑1 (MQ=255)                        aaTGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATCGACTGCC‑GGGTGATTTTAAGCCGGAGGaata                                                 >  2:4688270/1‑76 (MQ=255)                         aTGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGaataa                                                >  1:3973640/1‑76 (MQ=255)                         aTGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGaataa                                                >  1:1692935/1‑76 (MQ=255)                          tGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGaataat                                               <  2:1799753/76‑1 (MQ=255)                             aaTAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTc                                            >  1:1749045/1‑76 (MQ=255)                              aTAACGCAGGGGGAATTTTTCGCCTGAATAAAAGGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCa                                           <  2:2753941/76‑1 (MQ=255)                              aTAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCa                                           <  2:1749045/76‑1 (MQ=255)                               tAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCat                                          >  2:3184312/1‑76 (MQ=255)                                aaCGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCata                                         >  1:595232/1‑76 (MQ=255)                                 aCGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCatat                                        >  2:848070/1‑76 (MQ=255)                                  cGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATc                                       >  2:4598910/1‑76 (MQ=255)                                   gCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCt                                      >  1:4831503/1‑76 (MQ=255)                                    cAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTg                                     >  2:4200617/1‑76 (MQ=255)                                    cAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTg                                     >  1:3940862/1‑76 (MQ=255)                                     aGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGa                                    >  1:1209620/1‑76 (MQ=255)                                      ggggtAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGaa                                   <  1:3458979/76‑1 (MQ=255)                                      gggggAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGaa                                   <  2:4001617/76‑1 (MQ=255)                                      gggggAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGaa                                   >  1:2021762/1‑76 (MQ=255)                                        gggAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAAtt                                 >  1:5050315/1‑76 (MQ=255)                                         ggAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAAttt                                <  2:4017663/76‑1 (MQ=255)                                          gAATTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTa                               >  2:4845911/1‑76 (MQ=255)                                          gAATTTTTCGCCTGAATAAAAAGAATTGACGGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTa                               <  2:137788/76‑1 (MQ=255)                                           aaTTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTaa                              <  1:4383524/76‑1 (MQ=255)                                           aaTTTTTCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTaa                              <  2:835737/76‑1 (MQ=255)                                             tttttCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGa                            <  2:3071769/76‑1 (MQ=255)                                             tttttCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGa                            <  1:266307/76‑1 (MQ=255)                                              ttttCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGAc                           >  2:1775190/1‑76 (MQ=255)                                                ttCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACtt                         >  2:5179282/1‑76 (MQ=255)                                                 tCGCCTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACttt                        <  2:3278460/76‑1 (MQ=255)                                                 tCGCATGAAAAAAAAGAAGTAACTACC‑GGGTGAGGTCAAGACGGAAGAATAATGTCATATCAGAAGTTAAGACatt                        >  1:1411706/1‑76 (MQ=255)                                                   gCCTGAATCAACAGAATTGACTGCC‑GGGTGGCTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGGCTTTAc                      <  2:5275693/76‑1 (MQ=255)                                                    ccTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTAcc                     >  1:5497500/1‑76 (MQ=255)                                                    ccTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTAcc                     <  1:3847028/76‑1 (MQ=255)                                                    ccTGAATAAAAAGAATCGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTAcc                     >  2:1566131/1‑76 (MQ=255)                                                     cTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCa                    >  2:5168194/1‑76 (MQ=255)                                                     cTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCa                    <  2:142413/76‑1 (MQ=255)                                                     cTGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCa                    >  2:1693931/1‑76 (MQ=255)                                                      tGAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAg                   <  2:2566495/76‑1 (MQ=255)                                                       gAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGc                  <  2:5752278/76‑1 (MQ=255)                                                       gAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGc                  <  1:1494854/76‑1 (MQ=255)                                                       gAATAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGc                  >  2:4565915/1‑76 (MQ=255)                                                        aaTAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCg                 <  2:1397414/76‑1 (MQ=255)                                                         aTAAAAAGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTCAATTTAAGACTTTGCCAGCGa                <  1:1703804/76‑1 (MQ=255)                                                          tAAAAAGAATTGACTGCC‑GGGTGATGTTAAGACGGAGGAATAATGTCATATCTGTATTTAAGACGTTACCAGCGaa               >  1:4212129/1‑76 (MQ=255)                                                           aaaaaGAATTGACTG‑CAGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGaaa              >  1:4432339/1‑76 (MQ=255)                                                            aaaaGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAac             <  1:5278071/76‑1 (MQ=255)                                                             aaaGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAaca            >  2:659523/1‑76 (MQ=255)                                                             aaaGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAaca            <  1:2998620/76‑1 (MQ=255)                                                              aaGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCCGCGAAacac           >  1:648296/1‑76 (MQ=255)                                                              aaGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAacac           >  2:3844416/1‑76 (MQ=255)                                                              aaGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAacac           >  2:2350207/1‑76 (MQ=255)                                                               aGAATTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAacaca          >  1:3211203/1‑76 (MQ=255)                                                                 aaTTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAAcacaca        <  2:1533325/76‑1 (MQ=255)                                                                  aTTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACACACaa       >  1:441498/1‑76 (MQ=255)                                                                  aTTGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACACACaa       <  2:3973639/76‑1 (MQ=255)                                                                   ttGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACACACAAt      >  2:2318409/1‑76 (MQ=255)                                                                    tGACTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACACACAATg     >  1:1218348/1‑76 (MQ=255)                                                                       cTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTGATATCTGAATTTAAGACTTTACCAGCGAAACACACAATGCtt  >  2:3137517/1‑76 (MQ=255)                                                                       cTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACACACAATGCtt  >  2:5394009/1‑76 (MQ=255)                                                                       cTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACACACAATGCtt  >  2:3084557/1‑76 (MQ=255)                                                                       cTGCC‑GGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACACACAATGCtt  >  1:1109244/1‑76 (MQ=255)                                                                            |                                                                        CTTACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCCGGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACACACAATGCTT  >  NC_000913/4542565‑4542711

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑