Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,466,639	C→T	21.7%	pseudogene (1248/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,466,639	0	C	T	21.7%	98.7 / 22.5	56	pseudogene (1248/2513 nt)	ydbA	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
Reads supporting (aligned to +/- strand):  ref base C (21/22);  new base T (6/6);  total (28/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGGCGACAGCGCAACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACC  >  NC_000913/1466492‑1466786                                                                                                                                                    |                                                                                                                                                    cGGCGACAGCGCAACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACgg                                                                                                                                                   <  1:811540/150‑1 (MQ=255)     gACAGCGCAACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGACCATCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGtgat                                                                                                                                               >  2:222139/1‑150 (MQ=255)        aGCGCTACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGAc                                                                                                                                            <  2:772931/150‑1 (MQ=255)         gggctaCGGTGGATAACAAGGGCACGATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGTTAGACGGCGACCAGGCTGTTGTTAAAAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACg                                                                                                                                           <  2:1175700/145‑1 (MQ=14)         gcgcAACGGTGGATAACAAGGGCACCATGACCGTCACCGCTCCGGAGTCCATCGGGATCCAGGTTGACGGCGCCCAGGCCGTTGTGAAATACGAAGGCGAGAGCGCGATCACCAACGGGGGCACCGGCACGCAGCTGAACGGTGAGGACg                                                                                                                                           >  2:1095462/1‑150 (MQ=14)         gcgcAACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACg                                                                                                                                           <  2:937288/150‑1 (MQ=255)              aCGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCCCg                                                                                                                                      >  2:628409/1‑150 (MQ=255)                 gTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTCACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCa                                                                                                                                   >  2:731404/1‑150 (MQ=255)                    gATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAaac                                                                                                                                >  2:1063621/1‑150 (MQ=255)                     aTAACAAGGGCACCCTGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAaaca                                                                                                                               <  2:170637/150‑1 (MQ=255)                     aTAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCTGTATCCAGTTTGACGGAGACCAGGCGGTTGTTAAAAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAaaca                                                                                                                               <  2:622997/150‑1 (MQ=255)                           aGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACg                                                                                                                         <  1:517250/150‑1 (MQ=255)                           aGGGCACCATGACCGTCACCGATCCGGAGTCCATAGGTATCCACGTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCCCCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACg                                                                                                                         >  2:1106925/1‑150 (MQ=255)                             ggCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTAAAAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGc                                                                                                                       >  2:697368/1‑150 (MQ=255)                              gCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGTTGACGGCGACCAGGCGGTAGTGAACAACGAAGGCGAGAGCGCGATCACCAACGGCGGCACCGGCACGCAGATAAACGGTGAAGACGCCACCGCGAAAAACAAGGGCa                                                                                                                      >  1:647066/1‑150 (MQ=14)                                            aCCGATCCGGAGTCCATCGGTATCCAGTTGGACGGCGACAAGGCGTTAGTCAACAACGAAGGCGAGAGCTCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGAc                                                                                                        <  2:367835/150‑1 (MQ=14)                                                       gTCCATCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTc                                                                                             >  2:1309381/1‑150 (MQ=255)                                                           aTCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCTCGGCAAACAACAACGGGAAAACCACCGTTGACGGCAAGGATTCCAcc                                                                                         <  1:1072529/150‑1 (MQ=255)                                                            tCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAATGGTGGCACCGGCACGCAGAATAACGGTGATGCCGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGCCAAGGATACCTCCg                                                                                        >  2:217068/1‑150 (MQ=18)                                                             cGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCgg                                                                                       <  2:568759/150‑1 (MQ=255)                                                                      ggTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACACCGGCAAAACCACCGTTGACGGCAAGGATGCCACCGGTCCGGAAAt                                                                              >  1:872158/1‑150 (MQ=255)                                                                       ggtGATGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCTCCATCACCCCCGGTGGAACCGGCACGCAGATTAACGGTTATGACGCGAAGGAAAACAACAACGGAAAAACCACCGTTGACGGCACGGATTCGACGGGTGCGGaaagg                                                                             >  2:1216157/3‑148 (MQ=17)                                                                             ggCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGc                                                                       <  2:593273/150‑1 (MQ=255)                                                                               cGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCaa                                                                     >  2:19674/1‑150 (MQ=255)                                                                                  ccAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATaa                                                                  >  2:18421/1‑150 (MQ=255)                                                                                   cAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTTGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAAc                                                                 <  1:222139/150‑1 (MQ=255)                                                                                   cAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATAAACGGTGAAGACGCCACGGCAAAAAACAAAGGCAAAACCACAGTTGACGGAAAGGATTCCACCGGTACGAAAATAGCGGGCAAAAAc                                                                 >  1:10356/1‑150 (MQ=17)                                                                                      gCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAAtcaacggt                                                                       >  2:125934/1‑134 (MQ=255)                                                                                      gCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAAtcaacggt                                                                       <  1:125934/141‑8 (MQ=255)                                                                                          ttgttAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAgg                                                          >  2:741681/1‑150 (MQ=255)                                                                                           tgttAACAACGAAGGCGAGAGCGCCATCACCAAAGGTGTCACCGGCACTCAGATCAAAGGTAAATACGCCACCGCGAATAACATAGGAAAAACCACTCTTGATGGAAATGATTCCTCGGGTACCAAAATCTCTGGCATTATCggcattgt                                                         >  2:697564/1‑144 (MQ=255)                                                                                                 caacGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGTGATTCa                                                   >  2:488406/1‑150 (MQ=255)                                                                                                    cGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGTGATTCAGGa                                                >  1:634341/1‑150 (MQ=255)                                                                                                       aGGCGAGAGCGCCATCACCAACTGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGTGATTCAGGACgg                                             <  2:638085/150‑1 (MQ=255)                                                                                                       aGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGTGATTCAGGACgg                                             <  2:394678/150‑1 (MQ=255)                                                                                                        ggCGAGAGCACCATCACCAACGGTGGCACCGGCACCCAGATTAATGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGAAATAACGGTAAGGTGATTCAGGACGGc                                            >  2:218558/1‑150 (MQ=11)                                                                                                            agagCACCATCACCAACGGTGGCACCGGCACCCAGATTAATGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGTGATTCAGGACGGCGATc                                        <  1:218558/150‑1 (MQ=255)                                                                                                             gagCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGTGATTCAGGACGGCGATCt                                       <  1:19674/150‑1 (MQ=255)                                                                                                               gcgcCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGTGATTCAGGACGGCGATCTgg                                     <  1:1063621/150‑1 (MQ=255)                                                                                                                  ccATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGTGATTCAGGACGGCGATCTGGATg                                  <  1:1309381/150‑1 (MQ=255)                                                                                                                               tGGCACCGGCACCCAGATTAATGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTTCGGAAATTGCTGGCAATAACGGGAAGGt                                                         <  1:152538/114‑1 (MQ=255)                                                                                                                               tGGCACCGGCACCCAGATTAATGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGt                                                         >  2:152538/1‑114 (MQ=255)                                                                                                                               tGGCACCGGCACCCAGATTAATGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGt                                                         >  2:148135/1‑114 (MQ=255)                                                                                                                               tGGCACCGGCACCCAGATTAATGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGt                                                         <  1:148135/114‑1 (MQ=255)                                                                                                                                  cACCGGCACCCAGATTAATGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGTGATTCa                                                   <  2:1113909/117‑1 (MQ=255)                                                                                                                                  cACCGGCACCCAGATTAATGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGTGATTCa                                                   >  1:1113909/1‑117 (MQ=255)                                                                                                                                      ggCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGt              <  1:1106925/150‑1 (MQ=255)                                                                                                                                      ggCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGt              <  1:628409/150‑1 (MQ=255)                                                                                                                                          cccAGATTAATGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGTGATTCAGGACGGCGATCTGGATg                                  <  2:331098/124‑1 (MQ=255)                                                                                                                                          cccAGATTAATGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATAGCTGGGAATAACGGGAAGGTGATTCAGGACGGCGATCTGGATg                                  >  1:331098/3‑126 (MQ=255)                                                                                                                                           gCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGa         <  1:731404/150‑1 (MQ=255)                                                                                                                                              gATTAATGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAg                                                           <  1:593690/97‑1 (MQ=255)                                                                                                                                              gATTAATGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAg                                                           >  2:593690/1‑97 (MQ=255)                                                                                                                                              gATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAATTTGCTGGCAATAACGGGAAGGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGatat      >  2:1198820/1‑150 (MQ=255)                                                                                                                                                  aaCTGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGAAAGTATTCCACCGGTACTGAAATTGCTGTCAATAACGGGAAGGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCAcc  <  1:1177327/150‑1 (MQ=17)                                                                                                                                                  aaCGGTGAAGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGCAAGGTGAATCAGGAAGGCGTACTGGATGTAAGCGGCGGCGGTCACGGTATTGATATCaac  >  2:956773/1‑148 (MQ=17)                                                                                                                                                    |                                                                                                                                                    CGGCGACAGCGCAACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACC  >  NC_000913/1466492‑1466786

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑