Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,574,259	A→G	pseudogene (341/2937 nt)	yjiV →	pseudogene, conserved hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,574,259	0	A	G	100.0%	181.1 / NA	48	pseudogene (341/2937 nt)	yjiV	pseudogene, conserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (23/25);  total (23/25)

TGTGAACCAGCGACAAAATTGTGACTGTGGAAGCCCTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGAAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTCAGCCTCCGTTGATTATTGCCGCAGGAGAGACCAGCGAGGCAG  >  NC_000913/4574140‑4574393                                                                                                                        |                                                                                                                                       tgtgAACCAGCGACAAAATTGTGACTGTGGAAGCCCTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGaa                                                                                                                     >  1:711005/1‑139 (MQ=255) tgtgAACCAGCGACAAAATTGTGACTGTGGAAGCCCTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGaa                                                                                                                     <  2:39905/139‑1 (MQ=255)   tgAACCAGCGACAAAATTGTGACTGTGGAAGCCCTGTATACGAAGTTGCATTCTGTCATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAAtt                                                                                                                   >  1:505509/1‑139 (MQ=255)      aCCAGCGACAAAATTGTGACTGTGGAAGCCCTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATtctc                                                                                                                >  1:508090/1‑139 (MQ=255)          gCGACAAAATTGTGACTGTGGAAGCCCTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATaa                                                                                                                                  >  2:636695/1‑117 (MQ=255)          gCGACAAAATTGTGACTGTGGAAGCCCTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATaa                                                                                                                                  <  1:636695/117‑1 (MQ=255)          gCGACAAAATTGTGACTGTGGAAGCCCTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTg                                                                                                            >  2:249898/1‑139 (MQ=255)            gACAAAATTGTGACTGTGGAAGCCCTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCa                                                                                                          <  2:572503/139‑1 (MQ=255)            gACAAAATTGTGACTGTGGAAGCCCTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCa                                                                                                          <  1:601512/139‑1 (MQ=255)                       gACTGTGGAAGCCCTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTAc                                                                                               <  2:83316/139‑1 (MQ=255)                            tgGAAGCCCTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCCAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGtt                                                                                          >  2:512390/1‑139 (MQ=255)                             ggAAGCCCTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTg                                                                                         <  2:508090/139‑1 (MQ=255)                                    cTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGa                                                                                  >  2:371678/1‑139 (MQ=255)                                            gAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACag                                                                          >  2:210095/1‑139 (MQ=255)                                               gTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTg                                                                                            >  1:248726/1‑118 (MQ=255)                                               gTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTg                                                                                            <  2:248726/118‑1 (MQ=255)                                                 tGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATtct                                                                                                                 <  2:493035/95‑1 (MQ=255)                                                 tGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATtct                                                                                                                 >  1:493035/1‑95 (MQ=255)                                                 tGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCa                                                                                                          >  1:256770/1‑102 (MQ=255)                                                 tGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCa                                                                                                          <  2:256770/102‑1 (MQ=255)                                                 tGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAgaagaa                                                                     >  2:628599/1‑139 (MQ=255)                                                     ttCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAg                                                                 <  1:522242/139‑1 (MQ=255)                                                        tGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCg                                                              >  1:432374/1‑139 (MQ=255)                                                                 tGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAgaga                                                     <  1:491260/139‑1 (MQ=255)                                                                  gTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGa                                                                                                                      >  1:579525/1‑73 (MQ=255)                                                                  gTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGa                                                                                                                      <  2:579525/73‑1 (MQ=255)                                                                        aGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGttt                                              >  1:142861/1‑139 (MQ=255)                                                                         gCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGtttt                                             >  1:716391/1‑139 (MQ=255)                                                                             cATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTCAGc                                         <  1:210095/139‑1 (MQ=255)                                                                              aTCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTCAGcc                                        <  2:142861/139‑1 (MQ=255)                                                                              aTCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTCAGcc                                        <  1:371678/139‑1 (MQ=255)                                                                                       cACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTCAGc                                         <  1:533387/129‑1 (MQ=255)                                                                                       cACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTCAGc                                         >  2:533387/1‑129 (MQ=255)                                                                                         cGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGt                                                                                                 <  2:108000/71‑1 (MQ=255)                                                                                         cGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGt                                                                                                 >  1:108000/1‑71 (MQ=255)                                                                                          gggACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAGGAAAAAGTCGAAAAAGAGAACAGTTTTCAGCCTCCGTTGattat                            <  2:505509/139‑1 (MQ=255)                                                                                          gggACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAAATCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTCAGCCTCCGTTGattat                            <  2:567318/139‑1 (MQ=255)                                                                                           ggACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACa                                                                                     <  2:19186/81‑1 (MQ=255)                                                                                           ggACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACa                                                                                     >  1:19186/1‑81 (MQ=255)                                                                                            gACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTCAGCCTCCGTTGATTATTg                          >  1:296055/1‑139 (MQ=255)                                                                                                      gCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTCAGCCTCCGTTGATTATTGc                         <  2:230583/130‑1 (MQ=255)                                                                                                      gCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTCAGCCTCCGTTGATTATTGc                         >  1:230583/1‑130 (MQ=255)                                                                                                                ccAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTCAGCCTCCGTTGATTATTGCCGCAGGAGAGACCAGCGAg      <  1:249898/139‑1 (MQ=255)                                                                                                                 cAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTc                                            <  2:494913/100‑1 (MQ=255)                                                                                                                 cAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTc                                            >  1:494913/1‑100 (MQ=255)                                                                                                                 cAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTCAGCCTCCGTTGATTATTGCCGCAGGAGAGACCAGCGAgg     <  2:296055/139‑1 (MQ=255)                                                                                                                   gTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTCAGCCTCCGTTGATTATTGCCGCAGGAGAGACCAGCGAGGCa   <  1:628599/139‑1 (MQ=255)                                                                                                                    tGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTCAGCCTCCGTTGATTATTGCCGCAGGAGAGACCAGCGAGGCAg  >  2:500986/1‑139 (MQ=255)                                                                                                                        |                                                                                                                                       TGTGAACCAGCGACAAAATTGTGACTGTGGAAGCCCTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGAAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTCAGCCTCCGTTGATTATTGCCGCAGGAGAGACCAGCGAGGCAG  >  NC_000913/4574140‑4574393

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑