Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	238,929	T→C	pseudogene (174/357 nt)	yafU ←	pseudogene

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	238,929	0	T	C	100.0%	160.0 / NA	43	pseudogene (174/357 nt)	yafU	pseudogene
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (22/21);  total (22/21)

TTCCCTTTTCCATTTATCAAGTTCCTGTTGCCGTTTTAGTCCATCTCTAATTGCATATTTTAATTTTTCTGATAAATGGCATTGAGCATCGATTTCATTTAAAACAACTGTACACACTATCCCTGTCAGTAAAATTGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAACACAGGCAAAAGAAGCCAGACTTCCAATAGCGGTTGCAACACCACCGGCTATAACTGCTTTGGCCACATCCATTGAAAAATCGCCAAGAAAATTA  >  NC_000913/238794‑239061                                                                                                                                        |                                                                                                                                     ttCCCTTTTCCATTTATCAAGTTCCTGTTGCCGTTTTAGTCCATCTCTAATTGCATATTTTAATTTTTCTGATAAATGGCATTGAGCATCGATTTCATTTAAAACAACTGTACACACTATCCCTGTCAGTAAAATCGct                                                                                                                                   <  1:139421/139‑1 (MQ=255)  tCCCTTTTCCATTTATCAAGTTCCTGTTGCCGTTTTAGTCCATCTCTAATTGCATATTTTAATTTTTCTGATAAATGGCATTGAGCATCGATTTCATTTAAAACAACTGTACACACTATCCTTGTCAGTAAAATCGctc                                                                                                                                  >  1:620844/1‑139 (MQ=255)    ccTTTTCCATTTATCAAGTTCCTGTTGCCGTTTTAGTCCATCTCTAATTGCATATTTTAATTTTTCTGATAAATGGCATTGAGCATCGATTTCATTTAAAACAACTGTACACACTATCCCTGTCAGTAAAATCGctcct                                                                                                                                >  2:95289/1‑139 (MQ=255)      ttttCCATTTATCAAGTTCCTGTTGCCGTTTTAGTCCATCTCTAATTGCATATTTTAATTTTTCTGATAAATGGCATTGAGCATCGATTTCATTTAAAACAACTGTACACACTATCCCTGTCAGTAAAATCGCtcctcc                                                                                                                              >  2:615177/1‑139 (MQ=255)                      ttCCTGTTGCCGTTTTAGTCCATCTCTAATTGCATATTTTAATTTTTCTGATAAATGGCATTGAGCATCGATTTCATTTAAAACAACTGTACACACTATCCCTGTCAGTAAAATCGCTCCTCCGACAAGAATTACTGGa                                                                                                              <  2:703197/139‑1 (MQ=255)                           gTTGCCGTTTTAGTCCATCTCTAATTGCATATTTTAATTTTTCTGATAAATGGCATTGAGCATCGATTTCATTTAAAACAACTGTACACACTATCCCTGTCAGTAAAATCGCTCCTCCGACAAGAATTACTGGAAAGcc                                                                                                         >  2:427933/1‑139 (MQ=255)                                    ttAGTCCATCTCTAATTGCATATTTTAATTTTTCTGATAAATGGCATTGAGCATCGATTTCATTTAAAACAACTGTACACACTATCCCTGTCAGTAAAATCGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAac                                                                                                <  1:95289/139‑1 (MQ=255)                                     tAGTCCATCTCTAATTGCATATTTTAATTTTTCTGATAAATGGCATTGAGCCTCGATTTCATTTAAAACAACTGTACACACTATCCCTGTCAGTAAAATCGCTCCTCCGACAAGAATTACTGGTAAGCCAAAGCTAaca                                                                                               <  2:538392/139‑1 (MQ=255)                                        tCCATCTCTAATTGCATATTTTAATTTTTCTGATAAATGGCATTGAGCATCGATTTCATTTAAAACAACTGTACACACTATCCCTGTCAGTAAAATCGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAACACAg                                                                                            <  2:658977/139‑1 (MQ=255)                                             ctctAATTGCATATTTTAATTTTTCTGATAAATGGCATTGAGCATCGATTTCATTTAAAACAACTGTACACACTATCCCTGTCAGTAAAATCGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAACACAGGCaaa                                                                                       <  1:193137/139‑1 (MQ=255)                                                   ttGCATATTTTAATTTTTCTGATAAATGGCATTGAGCATCGATTTCATTTAAAACAACTGTACACACTATCCCTGTCAGTAAAATCGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAACACAGGCAAAAGAAGc                                                                                 <  1:128403/139‑1 (MQ=255)                                                      cATATTTTAATTTTTCTGATAAATGGCATTGAGCATCGATTTCATTTAAAACAACTGTACACACTATCCCTGTCAGTAAAATCGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAACACAGGCAAAAGAAGCCAg                                                                              <  1:136843/139‑1 (MQ=255)                                                      cATATTTTAATTTTTCTGATAAATGGCATTGAGCATCGATTTCATTTAAAACAACTGTACACACTATCCCTGTCAGTAAAATCGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAACACAGGCAAAAGAAGCCAg                                                                              <  1:694404/139‑1 (MQ=255)                                                          ttttAATTTTTCTGATAAATGGCATTGAGCATCGATTTCATTTAAAACAACTGTACACACTATCCCTGTCAGTAAAATCGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAACACAGGCAAAAGAAGCCAGACtt                                                                          >  2:480335/1‑139 (MQ=255)                                                                tttttCTGATAAATGGCATTGAGCATCGATTTCATTTAAAACAACTGTACACACTATCCCTGTCAGTAAAATCGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAACACAGGCAAAAGAAGCCAGACTTCCAATa                                                                    >  1:258021/1‑139 (MQ=255)                                                                     cTGATAAATGGCATTGAGCATCGATTTCATTTAAAACAACTGTACACACTATCCCTGTCAGTAAAATCGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAACACAGGCAAAAGAAGCCAGACTTCCAATAGCGGt                                                               <  1:615177/139‑1 (MQ=255)                                                                     cTGATAAATGGCATTGAGCATCGATTTCATTTAAAACAACTGTACACACTATCCCTGTCAGTAAAATCGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAACACAGGCAAAAGAAGCCAGACTTCCAATAGCGGt                                                               <  1:178961/139‑1 (MQ=255)                                                                             tGGCATTGAGCATCGATTTCATTTAAAACAACTGTACACACTATCCCTGTCAGTAAAATCGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAACACAGGCAAAAGAAGCCAGACTTCCAATAGCGGTTGCAacac                                                       >  1:624702/1‑139 (MQ=255)                                                                                       cATCGATTTCATTTAAAACAACTGTACACACTATCCCTGTCAGTAAAATCGCTCCTCCg                                                                                                                             >  1:201722/1‑59 (MQ=255)                                                                                       cATCGATTTCATTTAAAACAACTGTACACACTATCCCTGTCAGTAAAATCGCTCCTCCg                                                                                                                             <  2:201722/59‑1 (MQ=255)                                                                                         tCGATTTCATTTAAAACAACTGTACACACTATCCCTGTCAGTAAAATCGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAACACAGGCAAAAGAAGCCAGACTTCCAATAGCGGTTGCAACACCACCGGCTATaa                                           <  2:212354/139‑1 (MQ=255)                                                                                          cGATTTCATTTAAAACAACTGTACACACTATCCCTGTCAGTAAAATCGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAACACAGGCAAAAGAAGCCAGACTTCCAATAGCGGTTGCAACACCACCGGCTATAAc                                          >  1:106683/1‑139 (MQ=255)                                                                                          cGATTTCATTTAAAACAACTGTACACACTATCCCTGTCAGTAAAATCGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAACACAGGCAAAAGAAGCCAGACTTCCAATAGCGGTTGCAACACCACCGGCTATAAc                                          >  2:340612/1‑139 (MQ=255)                                                                                              ttCATTTAAAACAACTGTACACACTATCCCTGTCAGTAAAATCGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAACACAGGCAAAAGAAGCCAGACTTCCAATAGCGGTTGCAACACCACCGGCTATAACTGCt                                      <  1:340612/139‑1 (MQ=255)                                                                                                      aaaCAACTGTACACACTATCCCTGTCAGTAAAATCGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAACACAGGCAAAAGAAGCCAGACTTCCAATAGCGGTTGCAACACCACCGGCTATAACTGCTTTGGCcac                              <  2:54040/139‑1 (MQ=255)                                                                                                               tACACACTATCCCTGTCAGTAAAATCGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAACACAGGCAAAAGAAGCCAGACTTCCAATAGCGGTTGCAACACCACCGGCTATAACTGCTTTGGCCACATCCATTGa                     >  2:2675/1‑139 (MQ=255)                                                                                                                      tATCCCTGTCAGTAAAATCGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAACACAGGCAAAAGAAGCCAg                                                                              <  2:580344/75‑1 (MQ=255)                                                                                                                      tATCCCTGTCAGTAAAATCGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAACACAGGCAAAAGAAGCCAg                                                                              >  1:580344/1‑75 (MQ=255)                                                                                                                      tATCCCTGTCAGTAAAATCGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAACACAGGCAAAAGAAGCCAGAc                                                                            >  2:506189/1‑77 (MQ=255)                                                                                                                      tATCCCTGTCAGTAAAATCGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAACACAGGCAAAAGAAGCCAGAc                                                                            <  1:506189/77‑1 (MQ=255)                                                                                                                       aTCCCTGTCAGTAAAATCGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAACACAGGCAAAAGAAGCCAGACTTCCAATAGCGGTTGCAACACCACCGGCTATAACTGCTTTGGCCACATCCATTGAAAAATCGc             >  2:453282/1‑139 (MQ=255)                                                                                                                       aTCCCTGTCAGTAAAATCGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAACACAGGCAAAAGAAGCCAGACTTCCAATAGCGGTTGCAACACCACCGGCTATAACTGCTTTGGCCACATCCATTGAAAAATCGc             >  2:602389/1‑139 (MQ=255)                                                                                                                       aTCCCTGTCAGTAAAATCGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAACACAGGCAAAAGAAGCCAGACTTCCAATAGCGGTTGCAACACCACCGGCTATAACTGCTTTGGCCACATCCATTGAAAAATCGc             >  1:487040/1‑139 (MQ=255)                                                                                                                         cccTGTCAGTAAAATCGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAACACAGGCAAAAGAAGCCAGACTTCCAATAGCGGTTGCAACACCACCGGCTATAACTGCTTTGGCCACATCCATTGAAAAATCGCCa           >  1:527294/1‑139 (MQ=255)                                                                                                                         cccTGTCAGTAAAATCGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAACACAGGCAAAAGAAGCCAGACTTCCAATAGCGGTTGCAACACCACCGGCTATAACTGCTTTGGCCACATCCATTGAAAAATCGCCa           >  2:340020/1‑139 (MQ=255)                                                                                                                           cTGTCAGTAAAATCGCTCCTCCGACAAGAATTACTGGAAAGcc                                                                                                         <  2:147123/43‑1 (MQ=255)                                                                                                                           cTGTCAGTAAAATCGCTCCTCCGACAAGAATTACTGGAAAGcc                                                                                                         >  1:147123/1‑43 (MQ=255)                                                                                                                                aGTAAAATCGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAACACAGGCAAAAGAAGCCAGACTTCCAATAGCGGTTGCAACACCACCGGCTATAACTGCTTTGGCCACATCCATTGAAAAATCGCCaa          <  2:601688/133‑1 (MQ=255)                                                                                                                                aGTAAAATCGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAACACAGGCAAAAGAAGCCAGACTTCCAATAGCGGTTGCAACACCACCGGCTATAACTGCTTTGGCCACATCCATTGAAAAATCGCCaa          >  1:601688/1‑133 (MQ=255)                                                                                                                                aGTAAAATCGCTACTCAAACAACAATGACTGGAAAGCCAAAGCTAACACAGGAAAAAGAAGCCATACATCCAATAGCGGTTGCAACACCACCGGCTATAACTGCTTTGGTGACATCCATTGAAAAATCGCTACGAAAAt    <  2:280587/139‑1 (MQ=255)                                                                                                                                  tAAAATCGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAACACAGGCAAAAGAAGCCAGACTTCCAATAGCg                                                                 <  2:425169/76‑1 (MQ=255)                                                                                                                                  tAAAATCGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAACACAGGCAAAAGAAGCCAGACTTCCAATAGCg                                                                 >  1:425169/1‑76 (MQ=255)                                                                                                                                  tAAAATCGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAACACAGGCAAAAGAAGCCAGACTTCCAATAGCGGTTGCAACACCACCGGCTATAACTGCTTTGGCCACATCCATTGAAAAATCGCCAAGAAAATTa  >  1:157398/1‑139 (MQ=255)                                                                                                                                        |                                                                                                                                     TTCCCTTTTCCATTTATCAAGTTCCTGTTGCCGTTTTAGTCCATCTCTAATTGCATATTTTAATTTTTCTGATAAATGGCATTGAGCATCGATTTCATTTAAAACAACTGTACACACTATCCCTGTCAGTAAAATTGCTCCTCCGACAAGAATTACTGGAAAGCCAAAGCTAACACAGGCAAAAGAAGCCAGACTTCCAATAGCGGTTGCAACACCACCGGCTATAACTGCTTTGGCCACATCCATTGAAAAATCGCCAAGAAAATTA  >  NC_000913/238794‑239061

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑