Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,470,558	G→A	pseudogene (42/3497 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	1,470,558	0	G	A	97.2%	237.4 / ‑2.0	71	pseudogene (42/3497 nt)	ydbA	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
Reads supporting (aligned to +/- strand):  ref base G (1/1);  new base A (37/32);  total (38/33)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01

AAAACACCGAAAGAGATAATTGAAAGGGGTGTTGCATTGACAGATTGAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTGAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCGGCACCGTCTCCCATTGTTTTACTGGCTACTAACGGAG  >  NC_000913/1470462‑1470654                                                                                                 |                                                                                                 aaaaCACCGAAAGAGATAATTGAAAGGGGTGTTGCATTGACAGATTGAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTaaaa                                                                                               >  1:115492/1‑100 (MQ=255) aaaaCACCGAAAGAGATAATTGAAAGGGGTGTTGCATTGACAGATTGAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTaaaa                                                                                               >  1:1242306/1‑100 (MQ=255) aaaaCACCGAAAGAGATAATTGAAAGGGGTGTTGCATTGACAGATTGAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTaaaa                                                                                               >  1:1243784/1‑100 (MQ=255)   aaCACCGAAAGAGATAATTGAAAGGGGTGTTGCATTGACAGATTGAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAAt                                                                                             >  2:1282354/1‑100 (MQ=255)        cGAAAGAGATAATTGAAAGGGGTGTTGCATTGACAGATTGAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATacaac                                                                                        >  2:227954/1‑100 (MQ=255)             gagaTAATTGAAAGGGGTGTTGCATTGACAGATTGAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGta                                                                                   >  1:1461075/1‑100 (MQ=255)                 tAATTGAAAGGGGTGTTGCATTGACAGATTGAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATaaa                                                                               >  2:617017/1‑100 (MQ=255)                  aaTTGAACGGGGTGTTGCATTGACAGATTGAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAAt                                                                              >  1:829027/1‑100 (MQ=255)                  aaTTGAAAGGGGTGTTGCATTGACAGATTGAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAAt                                                                              >  2:578681/1‑100 (MQ=255)                  aaTTGAAAGGGGTGTTGCATTGACAGATTGAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAAt                                                                              >  2:1322867/1‑100 (MQ=255)                   aTTGAAAGGGGTGTTGCATTGACAGATTGAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATa                                                                             <  2:1036758/100‑1 (MQ=255)                    ttGAAAGGGGTGTTGCATTGACAGATTGAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAg                                                                            <  1:90027/100‑1 (MQ=255)                    ttGAAAGGGGTGTTGCATTGACAGATTGAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAg                                                                            >  1:666512/1‑100 (MQ=255)                       aaaGGGGTGTTGCATTGACAGATTGAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGt                                                                           >  2:687183/1‑98 (MQ=255)                        aaGGGGTGTTGCATTGACAGATTGAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGc                                                                        >  2:1541241/1‑100 (MQ=255)                          ggggTGTTGCATTGACAGATTGAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCAc                                                                      >  2:1487709/1‑100 (MQ=255)                          ggggTGTTGCATTGACAGATTGAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCAc                                                                      <  1:628103/100‑1 (MQ=255)                           gggTGTTGCATTGACAGATTGAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACg                                                                     >  1:534946/1‑100 (MQ=255)                               gtTGCATTGACAGATTGAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGAtct                                                                 >  1:282618/1‑100 (MQ=255)                               gtTGCATTGACAGATTGAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGAtct                                                                 >  2:1224902/1‑100 (MQ=255)                                 tGCATTGACAGATTGAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCg                                                               >  2:454684/1‑100 (MQ=255)                                 tGCATTGACAGATTGAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCg                                                               <  1:242575/100‑1 (MQ=255)                                 tGCATTGACAGATTGAATCTACACAGTTGAAATTCAGAATTTAGGTTTTGCTTAAAAAAAAAAAAAAAATACAACAGGTATAAATAGTGGCACGAtctc                                                                <  2:1417713/99‑1 (MQ=255)                                  gCATTGACAGATTGAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGt                                                              >  1:68766/1‑100 (MQ=255)                                      tGACAGATTGAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGtta                                                            <  2:813977/98‑1 (MQ=255)                                       gACAGATTGAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGttatta                                                         >  2:698606/1‑100 (MQ=255)                                         cAGATTGAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACa                                                       >  2:1259350/1‑100 (MQ=255)                                           gATTGAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACaaa                                                     <  2:536492/100‑1 (MQ=255)                                           gATTGAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCGTTTGTTAATGGTAAAAATACAACAGGTAGAAATAGTGGCACGATCTCGTTATTACaaa                                                     <  2:333124/100‑1 (MQ=255)                                            aTTGAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACaaaa                                                    >  1:542192/1‑100 (MQ=255)                                             ttGAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAAt                                                   >  2:408678/1‑100 (MQ=255)                                               gAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATgg                                                 >  1:1339801/1‑100 (MQ=255)                                                aaTCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGt                                                <  2:1023213/100‑1 (MQ=255)                                                   cTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTaaa                                             <  1:1322874/100‑1 (MQ=255)                                                     acacTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATACATAGTGGCACGATCTCGTTATTACAAAATGGTAAAg                                            >  2:779111/1‑99 (MQ=255)                                                        cTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATcc                                        >  1:779811/1‑100 (MQ=255)                                                        cTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATcc                                        <  1:621676/100‑1 (MQ=255)                                                         tGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCg                                       <  2:1540268/100‑1 (MQ=255)                                                          gTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTCTAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCgg                                      >  1:353756/1‑100 (MQ=255)                                                          gTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCgg                                      >  2:821042/1‑100 (MQ=255)                                                          gTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCgg                                      <  2:1461053/100‑1 (MQ=255)                                                           ttGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCg                                       <  2:1339794/98‑1 (MQ=255)                                                           ttGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCGGc                                     <  2:666510/100‑1 (MQ=255)                                                            tGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCGGCa                                    >  1:332826/1‑100 (MQ=255)                                                                  tCAGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCGGCACCGtct                              >  2:1208550/1‑100 (MQ=255)                                                                    aGAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCGGCACCGtctc                             <  2:580053/99‑1 (MQ=255)                                                                     gAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCGGCACCGTCTccc                           >  1:209816/1‑100 (MQ=255)                                                                     gAATTTAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCGGCACCGTCTccc                           <  2:1487930/100‑1 (MQ=255)                                                                         ttAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCGGCACCGTCTCCCATTg                       <  2:997388/100‑1 (MQ=255)                                                                          tAGGTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCGGCACCGTCTCCCATTGt                      <  1:821047/100‑1 (MQ=255)                                                                            ggTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCGGCACCGTCTCCCATTGttt                    >  2:98835/1‑100 (MQ=255)                                                                            ggTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCGGCACCGTCTCCCATTGttt                    <  2:1404494/100‑1 (MQ=255)                                                                             gTTTTGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAATGGCACGCTCTCGTTATTACAAAATAGTAATGATCAGGAACAGTCTCATATTGtttt                   >  2:354434/1‑100 (MQ=255)                                                                               tttGCCTTTGTTACTGGTACAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCGGCACCGTCTCCCATTGTTTTAc                 <  2:128314/100‑1 (MQ=255)                                                                                ttGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCGGCACCGTCTCCCATTGTTTTACt                <  1:972937/100‑1 (MQ=255)                                                                                ttGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCGGCACCGTCTCCCATTGTTTTACt                <  2:60859/100‑1 (MQ=255)                                                                                 tGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCGGCGCCGTCTCCCATTGTTTTACTg               <  2:68766/100‑1 (MQ=255)                                                                                 tGCTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCGGCACCGTCTCCCATTGTTTTACTg               <  1:1441797/100‑1 (MQ=255)                                                                                   cTTTTGTTACTGGTGAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCGGCACCGTCTCCCATTGTTTTACTGGc             <  1:1533710/100‑1 (MQ=255)                                                                                   cTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCGGCACCGTCTCCCATTGTTTTACTGGc             <  1:1054011/100‑1 (MQ=255)                                                                                   cTTTTGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCGGCACCGTCTCCCATTGTTTTACTGGc             >  2:1499743/1‑100 (MQ=255)                                                                                    ttttGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCGGCACCGTCTCCCATTGTTTTACTGGct            <  1:1208555/100‑1 (MQ=255)                                                                                     tttGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCGGCACCGTCTCCCATTGTTTTACTGGcta           <  2:1243779/100‑1 (MQ=255)                                                                                     tttGTTACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCGGCACCGTCTCCCATTGTTTTACTGGcta           <  2:1242301/100‑1 (MQ=255)                                                                                         ttACTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCGGCACCGTCTCCCATTGTTTTACTGGCTACTaa       >  1:118600/1‑100 (MQ=255)                                                                                            cTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCGGCACCGTCTCCCATTGTTTTACTGGCTACTAACgg    <  2:445944/100‑1 (MQ=255)                                                                                            cTGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCGGCACCGTCTCCCATTGTTTTACTGGCTACTAACgg    <  1:1541251/100‑1 (MQ=255)                                                                                             tGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCGGCACCGTCTCCCATTGTTTTACTGGCTACTAACgga   <  1:1327609/100‑1 (MQ=255)                                                                                             tGGTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCGGCACCGTCTCCCATTGTTTTACTGGCTACTAACgga   >  2:239244/1‑100 (MQ=255)                                                                                              ggTGAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCGGCACCGTCTCCCATTGTTTTACTGGCTACTAACgg    >  2:1130926/1‑98 (MQ=255)                                                                                              ggTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATTCGGCACCGTCTCCCATTGTTTTACTGGATACTAACggag  >  2:1461676/1‑100 (MQ=255)                                                                                              ggTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCGGCACCGTCTCCCATTGTTTTACTGGCTACTAACggag  >  2:445458/1‑100 (MQ=255)                                                                                              ggTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCGGCACCGTCTCCCATTGTTTTACTGGCTACTAACggag  >  1:635292/1‑100 (MQ=255)                                                                                              ggTAAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCGGCACCGTCTCCCATTGTTTTACTGGCTACTAACggag  >  2:275726/1‑100 (MQ=255)                                                                                                 |                                                                                                 AAAACACCGAAAGAGATAATTGAAAGGGGTGTTGCATTGACAGATTGAATCTACACTGTTGAAATTCAGAATTTAGGTTTTGCTTTTGTTACTGGTGAAAATACAACAGGTATAAATAGTGGCACGATCTCGTTATTACAAAATGGTAAAGATCCGGCACCGTCTCCCATTGTTTTACTGGCTACTAACGGAG  >  NC_000913/1470462‑1470654

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑