Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,220,860	G→T	6.7%	pseudogene (1260/2574 nt)	ycgH →	pseudogene; putative ATP‑binding component of a transport system

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,220,860	0	G	T	6.7%	207.1 / 3.0	60	pseudogene (1260/2574 nt)	ycgH	pseudogene; putative ATP‑binding component of a transport system
Reads supporting (aligned to +/- strand):  ref base G (30/26);  new base T (2/2);  total (32/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.90e-01

AATGGAGCGACTAAACTCGTCAGCGGCACAACCACGCTGAAGCTTTCAGAAAATACAATCTGGAATATGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCGGCTACGGACAGACTTATTGTTGAGG  >  NC_000913/1220735‑1220996                                                                                                                              |                                                                                                                                         aaTGGAGCGACTAAACTCGTCAGCGGCACAACCACGCTGAATCTTTCAGAAAATACAAGCTGGAATATGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATTATGGTCa                                                                                                                            >  2:1151314/1‑140 (MQ=255) aaTGGAGCGACTAAACACGTCAGCGGCACAACCACGCTTAAGCTTTCAGAAAATACAATCTGGAATATGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCa                                                                                                                            >  2:1151598/1‑140 (MQ=255)      aGCGACTAAACTCGTCAGCGGCACAACCACGCTGAAGCTTTCAGAAAATACAATCTGGAATATGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACAt                                                                                                                       >  1:1112339/1‑140 (MQ=255)      aGCGACTAAACTCGTCAGCGGCACAACCACGCTGAAGCTTTCAGAAAATACAATCTGGAATATGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACAt                                                                                                                       >  1:1159639/1‑140 (MQ=255)      aGCGACTAAACTCGTCAGCGGCACAACCACGCTGAAGCTTTCAGAAAATACAATCTGGAATATGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACAt                                                                                                                       >  1:282008/1‑140 (MQ=255)      aGCGACTAAACTCGTCAGCGGCACAACCACGCTGAAGCTTTCAGAAAATACAATCTGGAATATGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACAt                                                                                                                       >  1:330403/1‑140 (MQ=255)                cTCGTCAGCGGCACAACCACGCTGAAGCTTTCAGAAAATACAATCTGGAATATGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAgg                                                                                                             >  2:746968/1‑140 (MQ=255)                cTCGTCAGCGGCACAACCACGCTGAAGCTTTCAGAAAATACAATCTGGAATATGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAgg                                                                                                             >  2:746752/1‑140 (MQ=255)                   gTCAGCGGCACAACCACGCTGAAGCTTTCAGAAAATACAATCTGGAATATGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGaaa                                                                                                          >  1:669423/1‑140 (MQ=255)                   gTCAGCGGCACAACCACGCTGAAGCTTTCAGAAAATACAATCTGGAATATGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGaaa                                                                                                          >  1:510272/1‑140 (MQ=255)                      aGCGGCACAACCACGCTGAAGCTTTCAGAAAATACAATCTGGAATATGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAAc                                                                                                       >  2:568032/1‑140 (MQ=255)                      aGCGGCACAACCACGCTGAAGCTTTCAGAAAATACAATCTGGAATATGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAAc                                                                                                       >  2:304373/1‑140 (MQ=255)                           cacaACCACGCTGAAGCTTTCAGAAAATACAATCTGGAATATGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTaa                                                                                                  >  2:627181/1‑140 (MQ=255)                                    gCTGAAGCTTTCAGAAAATACAATCTGGAATATGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAg                                                                                         >  1:794271/1‑140 (MQ=255)                                     cTGAAGCTTTCAGAAAATACAATCTGGAATATGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAgg                                                                                        >  2:14402/1‑140 (MQ=255)                                               cAGAAAATACAATCTGGAATATGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTc                                                                              <  2:604775/140‑1 (MQ=255)                                                 gAAAATACAATCTGGAATATGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCgg                                                                            <  2:556227/140‑1 (MQ=255)                                                 gAAAATACAATCTGGAATATGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCgg                                                                            <  2:875377/140‑1 (MQ=255)                                                 gAAAATACAATCTGGAATATGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCgg                                                                            <  1:697473/140‑1 (MQ=255)                                                  aaaaTACAATCTGGAATATGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCTTAAAAGGTAATTATGTCGGt                                                                           >  2:1003785/1‑140 (MQ=255)                                                  aaaaTACAATCTGGAATATGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGt                                                                           >  1:822334/1‑140 (MQ=255)                                                  aaaaTACAATCTGGAATATGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGt                                                                           >  1:286872/1‑140 (MQ=255)                                                  aaaaTACAATCTGGAATATGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGAAGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGt                                                                           >  1:822362/1‑140 (MQ=255)                                                        cAATCTGGAATATGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTaataat                                                                     <  1:66567/140‑1 (MQ=255)                                                        cAATCTGGAATATGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTaataat                                                                     <  1:66334/140‑1 (MQ=255)                                                            cTGGAATATGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTc                                                                 <  2:424625/140‑1 (MQ=255)                                                                 atatGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCtt                                                            <  1:191051/140‑1 (MQ=255)                                                                     gAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCTTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAata                                                        >  1:639561/1‑140 (MQ=255)                                                                     gAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCTTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAata                                                        >  1:639703/1‑140 (MQ=255)                                                                          aTGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCgg                                                   <  2:236545/140‑2 (MQ=255)                                                                          aTGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGc                                                   <  1:790020/140‑1 (MQ=255)                                                                          aTGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGc                                                   <  2:238066/140‑1 (MQ=255)                                                                          aTGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGc                                                   <  2:146313/140‑1 (MQ=255)                                                                          aTGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATAATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGc                                                   <  1:988605/140‑1 (MQ=255)                                                                           tGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCTTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGCa                                                  <  2:415523/140‑1 (MQ=255)                                                                           tGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGCa                                                  <  1:923196/140‑1 (MQ=255)                                                                           tGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGCa                                                  <  2:323787/140‑1 (MQ=255)                                                                           tGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGCa                                                  <  1:95995/140‑1 (MQ=255)                                                                           tGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGCa                                                  <  2:425528/140‑1 (MQ=255)                                                                           tGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGCa                                                  <  1:705331/140‑1 (MQ=255)                                                                           tGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGCa                                                  <  1:705368/140‑1 (MQ=255)                                                                           tGACTCCGTTGTTACCCATCTGACTAATTCAGACACTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAAAAATGGTCAGCTTAATATCCGCa                                                  <  2:728653/140‑1 (MQ=255)                                                                                  gttgttACCCATCTGAAAAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACAATTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTAtt                                           <  2:506656/140‑1 (MQ=255)                                                                                        aCCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGtga                                     >  1:582804/1‑140 (MQ=255)                                                                                        aCCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGtga                                     >  1:903709/1‑140 (MQ=255)                                                                                         cccATCTGACTAATTCAGACAGTATTATCAATCTTTCTTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGtgat                                    <  2:639703/140‑1 (MQ=255)                                                                                         cccATCTGACTAATTCAGACAGTATTATCAATCTTTCTTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGtgat                                    <  2:639561/140‑1 (MQ=255)                                                                                           cATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGtgatga                                  >  1:870202/1‑140 (MQ=255)                                                                                           cATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGtgatga                                  >  1:1017908/1‑140 (MQ=255)                                                                                             tCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATa                                >  1:427199/1‑140 (MQ=255)                                                                                             tCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATa                                >  1:765386/1‑140 (MQ=255)                                                                                                gACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAAt                             <  1:1055771/140‑1 (MQ=255)                                                                                                gACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAAt                             <  1:838144/140‑1 (MQ=255)                                                                                                      ttCAGACAGTATTATCAAACTTTCGTATGATGATGGTCAAACATAAACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGAAGATAAATCGGCTa                       >  2:916040/1‑140 (MQ=255)                                                                                                           aCAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCGGCTACGGAc                  <  2:427199/140‑1 (MQ=255)                                                                                                                       aTCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCGGCTACGGACAGACTTAttgtt      <  1:353711/140‑1 (MQ=255)                                                                                                                         cTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCGGCTACGGACAGACTTATTGTTGa    >  1:706300/1‑140 (MQ=255)                                                                                                                         cTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCGGCTACGGACAGACTTATTGTTGa    >  1:462701/1‑140 (MQ=255)                                                                                                                         cTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCGGCTACGGACAGACTTATTGTTGa    >  1:462539/1‑140 (MQ=255)                                                                                                                           ttCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCGGCTACGGACAGACTTATTGTTGAgg  >  2:669576/1‑140 (MQ=255)                                                                                                                              |                                                                                                                                         AATGGAGCGACTAAACTCGTCAGCGGCACAACCACGCTGAAGCTTTCAGAAAATACAATCTGGAATATGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGCACCGTATTAGGTGATGATAAATCGGCTACGGACAGACTTATTGTTGAGG  >  NC_000913/1220735‑1220996

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑