Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,419,403	C→T	pseudogene (297/960 nt)	yhdW →	pseudogene, ABC transporter periplasmic binding protein family,putative transport, Not classified, putative periplasmic binding transport protein, periplasmic‑binding component of ABC superfamily

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,419,403	0	C	T	100.0%	179.6 / NA	57	pseudogene (297/960 nt)	yhdW	pseudogene, ABC transporter periplasmic binding protein family,putative transport, Not classified, putative periplasmic binding transport protein, periplasmic‑binding component of ABC superfamily
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (32/25);  total (32/25)

TACCCCGCTCACTGCAAAAGAACGCTTCACCGCTTTACAGTCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGCGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTCAGGCGGGTACTGATACCGAACTCAACGTCGCCGACTACTTCAA  >  NC_000913/3419283‑3419537                                                                                                                         |                                                                                                                                       taCCCCGCTCACTGCAAAAGAACGCTTCACCGCTTTACAGTCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGc                                                                                                                      >  1:720029/1‑139 (MQ=255) taCCCCGCTCACTGCAAAAGAACGCTTCACCGCTTTACAGTCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGc                                                                                                                      >  1:279486/1‑139 (MQ=255)   ccccGCTCACTGCAAAAGAACGCTTCACCGCTTTACAGTCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCAt                                                                                                                    <  1:399284/139‑1 (MQ=255)    cccGCTCACTGCAAAAGAACGCTTCACCGCTTTACAGTCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCAtt                                                                                                                   >  1:376350/1‑139 (MQ=255)         tCACTGCAAAAGAACGCTTCACCGCTTTACAGTCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCtt                                                                                                              >  2:819063/1‑139 (MQ=255)         tCACTGCAAAAGAACGCTTCACCGCTTTACAGTCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCtt                                                                                                              >  1:646365/1‑139 (MQ=255)           aCTGCAAAAGAACGCTTCACCGCTTTACAGTCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACtt                                                                                                                                 >  2:832720/1‑118 (MQ=255)           aCTGCAAAAGAACGCTTCACCGCTTTACAGTCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACtt                                                                                                                                 <  1:832720/118‑1 (MQ=255)            cTGCAAAAGAACGCTTCACCGCTTTACAGTCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGc                                                                                                                      >  2:327776/1‑128 (MQ=255)            cTGCAAAAGAACGCTTCACCGCTTTACAGTCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGc                                                                                                                      <  1:327776/128‑1 (MQ=255)             tGCAAAAGAACGCTTCACCGCTTTACAGTCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCa                                                                                                                                    >  1:337916/1‑113 (MQ=255)             tGCAAAAGAACGCTTCACCGCTTTACAGTCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTg                                                                                                          >  2:151236/1‑139 (MQ=255)             tGCAAAAGAACGCTTCACCGCTTTACAGTCAGGGGAGGTGGATTTGCGCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCa                                                                                                                                    <  2:337916/113‑1 (MQ=255)              gCAAAAGAACGCTTCACCGCTTTACAGTCAGGGGAGGTGGATTTGCTCTCCCGT‑ATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGAc                                                                                                        >  2:103534/1‑139 (MQ=255)                aaaaGAACGCTTCACCGCTTTACAGTCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACg                                                                                                       <  1:363174/139‑1 (MQ=255)                  aaGAACGCTTCACCGCTTTACAGTCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCa                                                                                                     >  2:1043470/1‑139 (MQ=255)                   aGAACGCTTCACCGCTTTACAGTCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCAc                                                                                                    >  1:694375/1‑139 (MQ=255)                       cGCTTCACCGCTTTACAGTCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCTCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACtt                                                                                                                                 >  2:77843/1‑106 (MQ=255)                       cGCTTCACCGCTTTACAGTCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACtt                                                                                                                                 <  1:77843/106‑1 (MQ=255)                       cGCTTCACCGCTTTACAGTCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCa                                                                                                     <  1:907384/134‑1 (MQ=255)                       cGCTTCACCGCTTTACAGTCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCa                                                                                                     >  2:907384/1‑134 (MQ=255)                                       aGTCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAg                                                                                >  1:140051/1‑139 (MQ=255)                                         tCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAgcg                                                                              >  2:664746/1‑139 (MQ=255)                                                  gTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTacga                                                                                                                          <  1:731387/86‑1 (MQ=255)                                                  gTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTacga                                                                                                                          >  2:731387/1‑86 (MQ=255)                                                  gTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAAc                                                                     >  2:246746/1‑139 (MQ=255)                                                            tctcCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGgcgc                                                           >  2:968029/1‑139 (MQ=255)                                                               cccGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTAc                                                        >  2:187275/1‑139 (MQ=255)                                                               cccGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTAc                                                        <  1:968029/139‑1 (MQ=255)                                                               cccGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTAc                                                        <  1:1043470/139‑1 (MQ=255)                                                                         gACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTAtt                                              <  2:694375/139‑1 (MQ=255)                                                                          aCCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCTCTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTAc                                                        <  2:768213/128‑1 (MQ=255)                                                                          aCCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTAc                                                        >  1:768213/1‑128 (MQ=255)                                                                          aCCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTc                                             >  1:120697/1‑139 (MQ=255)                                                                          aCCTGGACTTCATCTCGCGATGCCGGGATGGGAATAGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACg                                                                                                       >  2:770313/1‑81 (MQ=255)                                                                          aCCTGGACTTCATCTCGCGATGCCGGGATGGGAATAGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACg                                                                                                       <  1:770313/81‑1 (MQ=255)                                                                            cTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCAGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTCAg                                           >  1:9472/1‑139 (MQ=255)                                                                             tGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTCAgg                                          <  2:501326/139‑1 (MQ=255)                                                                             tGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTCAgg                                          <  2:279486/139‑1 (MQ=255)                                                                             tGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTCAgg                                          <  1:819063/139‑1 (MQ=255)                                                                               gACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTCAGGCg                                        <  1:151236/139‑1 (MQ=255)                                                                                    cATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGa                                                                           >  1:1065429/1‑99 (MQ=255)                                                                                    cATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGa                                                                           <  2:1065429/99‑1 (MQ=255)                                                                                         cgcgATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACg                                                                                                       >  2:594282/1‑66 (MQ=255)                                                                                         cgcgATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACg                                                                                                       <  1:594282/66‑1 (MQ=255)                                                                                         cgcgATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTCAg                                           <  2:83120/126‑1 (MQ=255)                                                                                         cgcgATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTCAg                                           >  1:83120/1‑126 (MQ=255)                                                                                              tGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGa                                                                 >  2:420430/1‑99 (MQ=255)                                                                                              tGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGa                                                                 <  1:420430/99‑1 (MQ=255)                                                                                                      tGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTCAGGCGGGTACTGATACCGAACTCAACGt                 >  2:519728/1‑139 (MQ=255)                                                                                                             ggCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTCAGGCGGGTACTGATACCGAACTCAACGTCGCCGac          <  2:720029/139‑1 (MQ=255)                                                                                                             ggCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTCAGGCGGGTACTGATACCGAACTCAACGTCGCCGac          <  2:646365/139‑1 (MQ=255)                                                                                                             ggCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTCAGGCGGGTACTGATACCGAACTCAACGTCGCCGac          <  1:103534/139‑1 (MQ=255)                                                                                                               cATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTCAGGCGGGTACTGATACCGAACTCAACGTCGCCGacta        >  2:95218/1‑139 (MQ=255)                                                                                                                  ttACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTAc                                                        >  2:617038/1‑88 (MQ=255)                                                                                                                  ttACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTAc                                                        <  1:617038/88‑1 (MQ=255)                                                                                                                     ccGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTCAGGCGGGTACTGATACCGAACTCAACGTCGCCGACTACTTCaa  >  1:227129/1‑139 (MQ=255)                                                                                                                         |                                                                                                                                       TACCCCGCTCACTGCAAAAGAACGCTTCACCGCTTTACAGTCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGCGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTCAGGCGGGTACTGATACCGAACTCAACGTCGCCGACTACTTCAA  >  NC_000913/3419283‑3419537

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: ‑