Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,428,079	C→T	pseudogene (386/402 nt) *213* (TAG→TAA)	ytfA → ytfB ←	pseudogene, related to transcriptional regulators OapA family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,428,079	0	C	T	100.0%	135.4 / NA	43	pseudogene (386/402 nt) *213* (TAG→TAA)	ytfA ytfB	pseudogene, related to transcriptional regulators OapA family protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (27/16);  total (27/16)

ATATTATTTGATCAACCAGCATACGCTTGGCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATCTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTCACCACGCCGCTGGCGTTCTGGCGGATTTTCACCATC  >  NC_000913/4427948‑4428199                                                                                                                                    |                                                                                                                         atatTATTTGATCAACCAGCATACGCTTGGCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACcgcg                                                                                                                   >  1:612584/1‑139 (MQ=255)                         gCTTGGCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCt                                                                                           >  2:610043/1‑139 (MQ=255)                          cTTGGCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTg                                                                                          >  2:1043810/1‑139 (MQ=255)                              gCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACcg                                                                                                                     <  1:888202/108‑1 (MQ=255)                              gCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACcg                                                                                                                     >  2:888202/1‑108 (MQ=255)                              gCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCgg                                                                                      >  2:1079899/1‑139 (MQ=255)                                   gTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCA‑ACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCg                                                                                              <  1:465795/125‑1 (MQ=255)                                   gTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCA‑ACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCg                                                                                              >  2:465795/1‑125 (MQ=255)                                    tttATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAAc                                                                                <  2:612584/139‑1 (MQ=255)                                      tATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAg                                                                              <  1:1079899/139‑1 (MQ=255)                                            aTCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTg                                                                        <  1:1043810/139‑1 (MQ=255)                                             tCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCgcgc                                                                                                                  >  2:2585/1‑96 (MQ=255)                                             tCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCgcgc                                                                                                                  <  1:2585/96‑1 (MQ=255)                                             tCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGt                                                                       >  1:450096/1‑139 (MQ=255)                                             tCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGt                                                                       >  2:111146/1‑139 (MQ=255)                                                      tttCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTc                                                              >  2:344355/1‑139 (MQ=255)                                                        tCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCgcgc                                                                                                                  <  2:1046182/85‑1 (MQ=255)                                                        tCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCgcgc                                                                                                                  >  1:1046182/1‑85 (MQ=255)                                                        tCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGt                                                                       >  1:169023/1‑128 (MQ=255)                                                        tCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGt                                                                       <  2:169023/128‑1 (MQ=255)                                                         cACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTcccc                                                           >  1:590362/1‑139 (MQ=255)                                                                ggCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAAc                                                                                <  1:828045/111‑1 (MQ=255)                                                                ggCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAAc                                                                                >  2:828045/1‑111 (MQ=255)                                                                ggCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTg                                                                     <  2:444915/122‑1 (MQ=255)                                                                ggCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTg                                                                     >  1:444915/1‑122 (MQ=255)                                                                   aCTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATgg                                                 >  1:467861/1‑139 (MQ=255)                                                                     tggacacccgACATAAGGCCATCAAACAGACAAGCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATACAGCTGCCATCCGGCTGGCGGTTGAACAGGACCCGTTGATTCTTCCCCGTATCAATGGtt                                               <  1:732779/130‑1 (MQ=255)                                                                           ccAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACCGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGccc                                         >  1:657379/1‑139 (MQ=255)                                                                                           caAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGAc                                                                           <  2:570848/89‑1 (MQ=255)                                                                                           caAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGAc                                                                           >  1:570848/1‑89 (MQ=255)                                                                                           caAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTcacccgccagaacg                         >  2:353464/1‑129 (MQ=255)                                                                                                agaCAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGAc                                                                           >  1:104382/1‑84 (MQ=255)                                                                                                agaCAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGAc                                                                           <  2:104382/84‑1 (MQ=255)                                                                                                     aTCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGaa                                                                                                             <  2:178433/45‑1 (MQ=255)                                                                                                     aTCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGaa                                                                                                             >  1:178433/1‑45 (MQ=255)                                                                                                        cTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAGTGGTTAAGCCCGTCACCACGCCGCTGGCGTTCTGGCGGAt            >  1:398297/1‑139 (MQ=255)                                                                                                               ggCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTCACCACGCCGCTGGCGTTCTGGCGGATTTTCAcc     >  1:760835/1‑139 (MQ=255)                                                                                                                 cTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCgg                                                                                      >  2:385078/1‑56 (MQ=255)                                                                                                                 cTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCgg                                                                                      <  1:385078/56‑1 (MQ=255)                                                                                                                 cTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTCACCACGCCGCTGGCGTTCTGGCGGATTTTCACCAt   >  2:192338/1‑139 (MQ=255)                                                                                                                  ttttGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTCACCACGCCGCTGGCGTTCTGGCGGATTTTCACCATc  >  2:149966/1‑139 (MQ=255)                                                                                                                          gACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTa                                              <  2:150198/87‑1 (MQ=255)                                                                                                                          gACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTa                                              >  1:150198/1‑87 (MQ=255)                                                                                                                                    |                                                                                                                         ATATTATTTGATCAACCAGCATACGCTTGGCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATCTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTCACCACGCCGCTGGCGTTCTGGCGGATTTTCACCATC  >  NC_000913/4427948‑4428199

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑