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%	153.3 / NA	47	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 (22/25);  total (22/25)

GGATATTATTTGATCAACCAGCATACGCTTGGCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATCTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTCACCACGCCGCTGGCGTTCTGGCGGATTTTCACCATCTGCCCGTTT  >  NC_000913/4427946‑4428208                                                                                                                                      |                                                                                                                                  ggATATTATTTGATCAACCAGCATACGCTTGGCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACcg                                                                                                                              <  1:457804/139‑1 (MQ=255)    tattatTTGATCAACCAGCATACGCTTGGCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCgcgc                                                                                                                           <  1:445994/139‑1 (MQ=255)              tCAACCAGCATACGCTTGGCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATaaaa                                                                                                                 >  2:53130/1‑139 (MQ=255)                    aGCATACGCTTGGCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCa                                                                                                           <  1:887815/139‑1 (MQ=255)                      cATACGCTTGGCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATc                                                                                                         <  2:828057/139‑1 (MQ=255)                       aTACGCTTGGCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATcc                                                                                                        >  1:1050201/1‑139 (MQ=255)                        tACGCTTGGCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCg                                                                                                       >  1:1004978/1‑139 (MQ=255)                               ggCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCg                                                                                                >  1:280943/1‑139 (MQ=255)                                gCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCgg                                                                                               <  2:105212/139‑1 (MQ=255)                                gCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCgg                                                                                               <  2:40870/139‑1 (MQ=255)                                gCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCgg                                                                                               >  2:385363/1‑139 (MQ=255)                                gCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCgg                                                                                               <  1:53130/139‑1 (MQ=255)                                         aTCACATCAGTATGGTTTCACCCCAGGGACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGAGGGTGAACAgg                                                                                      >  1:683790/1‑139 (MQ=255)                                         aTCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAgg                                                                                      <  1:798702/139‑1 (MQ=255)                                           cacaTCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGAc                                                                                    <  1:135885/139‑1 (MQ=255)                                           cacaTCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGAc                                                                                    <  1:244084/139‑1 (MQ=255)                                           cacaTCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGAc                                                                                    <  2:305379/139‑1 (MQ=255)                                               tCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGt                                                                                <  1:385363/139‑1 (MQ=255)                                               tCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGt                                                                                >  2:258575/1‑139 (MQ=255)                                               tCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGt                                                                                <  2:1050201/139‑1 (MQ=255)                                                   tATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGat                                                                            >  2:948083/1‑139 (MQ=255)                                                      ggattCACCCCAGGCACGAGAAGCCAGACGTAAGGTCATCAAAGAGACAAAACTTAGCTGGCTTTTGGTCGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGCCGGGTGAACAGGACCTGTTGaatat                                                                         >  1:539001/4‑139 (MQ=255)                                                        tttCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTc                                                                       >  1:439969/1‑139 (MQ=255)                                                         ttCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTcc                                                                      <  2:280943/139‑1 (MQ=255)                                                          tCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTccc                                                                     >  1:907232/1‑139 (MQ=255)                                                           cACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTcccc                                                                    <  2:439969/139‑1 (MQ=255)                                                                cAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATc                                                               <  2:662191/139‑1 (MQ=255)                                                                 aGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCa                                                              <  2:907232/139‑1 (MQ=255)                                                                  ggCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCaa                                                             >  2:722863/1‑139 (MQ=255)                                                                               aGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGt                                                >  1:365278/1‑139 (MQ=255)                                                                                   gTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGt                                                                                >  2:627528/1‑103 (MQ=255)                                                                                   gTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTGGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGt                                                                                <  1:627528/103‑1 (MQ=255)                                                                                    tAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCAATAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGTTTATTGCCCGTATCAATGGTTAAGCCCGTcacca                                           <  2:683790/139‑1 (MQ=255)                                                                                          catcaAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTCACCAcgccgc                                     <  2:1055118/139‑1 (MQ=255)                                                                                           atcaAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTCACCACGCCGCt                                    >  2:344345/1‑139 (MQ=255)                                                                                           atcaAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTCACCACGCCGCt                                    >  2:336118/1‑139 (MQ=255)                                                                                             caAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGAc                                                                                    >  1:312289/1‑89 (MQ=255)                                                                                             caAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGAc                                                                                    <  2:312289/89‑1 (MQ=255)                                                                                                  agaCAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCggg                                                                                              >  1:700462/1‑74 (MQ=255)                                                                                                  agaCAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCggg                                                                                              <  2:700462/74‑1 (MQ=255)                                                                                                     cAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTCACCACGCCGCTGGCGTTCTgg                          >  2:922015/1‑139 (MQ=255)                                                                                                       aTCCTTAGCTGGCTTTTGGTTGACGCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCa                                                              <  2:754586/101‑1 (MQ=255)                                                                                                       aTCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCa                                                              >  1:754586/1‑101 (MQ=255)                                                                                                                   cTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCgg                                                                                               <  1:443257/56‑1 (MQ=255)                                                                                                                   cTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCgg                                                                                               >  2:443257/1‑56 (MQ=255)                                                                                                                            gACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTCACCACGCCGCTGGCGTTCTGGCGGATTTTCACCATCTGCCCGtt   <  1:380057/139‑1 (MQ=255)                                                                                                                             aCCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTCACCACGCCGCTGGCGTTCTGGCGGATTTTCACCATCTGCCCGttt  >  2:507565/1‑139 (MQ=255)                                                                                                                                      |                                                                                                                                  GGATATTATTTGATCAACCAGCATACGCTTGGCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATCTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTCACCACGCCGCTGGCGTTCTGGCGGATTTTCACCATCTGCCCGTTT  >  NC_000913/4427946‑4428208

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑