Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_pgi	1,529,203	C→A	pseudogene (1302/2037 nt)	rhsE →	pseudogene, Rhs family

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_pgi	1,529,203	0	C	A	98.3%	160.9 / NA	59	pseudogene (1302/2037 nt)	rhsE	pseudogene, Rhs family
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base A (37/21);  total (38/21)
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

ACACCGGCGCGAAAAGTTCATTTTTACCACTGCGACCACCGGGGCCTGCCGCTGGCGCTCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGC  >  NC_000913_3_pae_pgi/1529159‑1529351                                             |                                                                                                                                                      acacCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCAcccg                                             >  1:790192/1‑148 (MQ=11) acacCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAg                                             >  3:223649/1‑150 (MQ=11) acacCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAg                                             >  4:647030/1‑150 (MQ=11) acacCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAg                                             >  1:545427/1‑150 (MQ=11) acacCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAg                                             >  1:349031/1‑150 (MQ=11)   acCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGcc                                           <  2:655290/150‑1 (MQ=11)   acCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGcc                                           >  2:1761104/1‑150 (MQ=11)   acCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGcc                                           >  3:919245/1‑150 (MQ=11)    ccGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCg                                          >  1:892355/1‑150 (MQ=11)     cGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGt                                         <  4:331493/150‑1 (MQ=11)       gcgcGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTAc                                       >  1:788955/1‑150 (MQ=11)       gcgcGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTAc                                       >  1:132918/1‑150 (MQ=11)       gcgcGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATAACCTGCACCAGCCGGAc                                       >  3:438716/1‑150 (MQ=11)        cgcgAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTAcc                                      <  1:1141416/150‑1 (MQ=11)        cgcgAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGCAAATAAAAA‑TCATTGAGGAGAACCCGCATCACCTGCACCAGCCGTAcc                                      <  4:55540/150‑1 (MQ=11)           gAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTc                                   >  3:205067/1‑150 (MQ=11)           gAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTc                                   <  4:42212/150‑1 (MQ=11)            aaaaGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCt                                  >  2:1874097/1‑150 (MQ=11)            aaaaGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCt                                  <  2:966406/150‑1 (MQ=11)                  tCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAgg                            <  2:132918/150‑1 (MQ=255)                  tCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAgg                            >  3:1003435/1‑150 (MQ=14)                  tCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAgg                            <  4:386494/150‑1 (MQ=11)                   catctttATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAggg                           <  2:1811574/146‑1 (MQ=14)                   cATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAggg                           <  2:883140/150‑1 (MQ=255)                      ctttATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGgcag                        <  2:892355/149‑1 (MQ=255)                       tttATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGgcagc                       >  3:561938/1‑150 (MQ=255)                       tttATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGgcagc                       >  1:1696447/1‑150 (MQ=255)                       tttATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGgcagc                       >  4:64271/1‑150 (MQ=255)                       tttATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGgcagc                       >  1:1929213/1‑150 (MQ=255)                       tttATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGACAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCGTCACCTGCACCAGCCGTACCGTCTGCCAGGgcagc                       >  2:571584/1‑150 (MQ=11)                        ttATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGgcagca                      <  1:1016292/150‑1 (MQ=255)                          atcACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGgcagcagc                    >  3:1086775/3‑150 (MQ=255)                           tcACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGgcagcagca                   >  2:150548/2‑150 (MQ=255)                           tcACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGAGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCGCCTGCACCAGCCGTACCGTCTCCCAGGgcagcagcc                   >  4:66795/2‑149 (MQ=14)                            cACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCat                  >  2:949089/1‑150 (MQ=255)                              cTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCatga                >  4:1214657/1‑150 (MQ=255)                              cTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCatga                <  2:1492489/150‑1 (MQ=255)                               tGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAggg                           >  2:1936839/1‑138 (MQ=255)                               tGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAggg                           <  1:1936839/138‑1 (MQ=255)                               tGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAgg                            >  4:736566/1‑137 (MQ=255)                               tGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAgg                            <  3:736566/137‑1 (MQ=255)                                 cGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCAtgatga             >  4:395816/1‑150 (MQ=255)                                  gACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATgag            <  1:757583/150‑1 (MQ=255)                                  gACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATgag            <  1:1761104/150‑1 (MQ=255)                                  gACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATgag            <  4:205067/150‑1 (MQ=255)                                  gACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATgag            >  1:712647/1‑150 (MQ=255)                                    ccaccGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGt                                         <  2:1935302/119‑1 (MQ=255)                                    ccaccGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGt                                         >  1:1935302/1‑119 (MQ=255)                                    ccaccGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATgagga          <  2:1298457/150‑1 (MQ=255)                                     caccGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATgaggag         >  2:1723548/1‑150 (MQ=255)                                       ccGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTc       >  1:1399555/1‑150 (MQ=255)                                       ccGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTc       >  4:405239/1‑150 (MQ=255)                                        cGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAAt                                                                        <  2:64770/84‑1 (MQ=255)                                        cGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAAt                                                                        >  1:64770/1‑84 (MQ=255)                                          gggACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGGGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCggg    >  3:570819/1‑150 (MQ=255)                                          gggACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCggg    >  4:442395/1‑150 (MQ=255)                                          gggACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCggg    >  3:931947/1‑150 (MQ=255)                                          gggACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCggg    >  1:849678/1‑150 (MQ=255)                                            gCCTGCCGATGGAGATTATCACGGAAGACGGCAATCCGGCGGGGCGCGAGGAGCGCGGTGGACGGGGC‑AGCAGCGTTGATGGGGAGGACCCGCATCGCCTGGACCAGCCGTGCCGTCTGCCAGGGCAGCAGCCTGATGAGGTGTCGGGGc  >  2:1663091/1‑150 (MQ=9)                                             |                                                                                                                                                      ACACCGGCGCGAAAAGTTCATTTTTACCACTGCGACCACCGGGGCCTGCCGCTGGCGCTCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGC‑TTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGC  >  NC_000913_3_pae_pgi/1529159‑1529351

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: ‑