Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,209,412	T→C	pseudogene (208/501 nt)	stfE ←	pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,209,412	0	T	C	100.0%	186.6 / NA	49	pseudogene (208/501 nt)	stfE	pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (27/22);  total (27/22)

CCATATTTCATCAAAATAGAAATTAATCGTTGCATCAGTCACAATCGTGGATCTTGACGGTAATCCATGAGCATGATCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGTATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAATTTATTTGTCGGATAAGCCTTTGCCAGTTCCGGGTATTCTTCAGCAGAAAAAGCGGCACCATTGCATTTCAGC  >  NC_000913/1209293‑1209542                                                                                                                        |                                                                                                                                   ccATATTTCATCAAAATAGAAATTAATCGTTGCATCAGTCACAACCGTGGATCTTGACGGTAATCCATGAGCATGATCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCcccg                                                                                                                        >  2:986823/1‑132 (MQ=255) ccATATTTCATCAAAATAGAAATTAATCGTTGCATCAGTCACAACCGTGGATCTTGACGGTAATCCATGAGCATGATCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCcccg                                                                                                                        <  1:986823/132‑1 (MQ=255)    tatTTCATCATAATAGAAATTAATCGTTGCATCAGTCACAATCGTGGATCTTGACGGTAATCCATGAGCATGATCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATcc                                                                                                              >  2:853375/1‑139 (MQ=255)    tatTTCATCAAAATAGAAATTAATCGTTGCATCAGTCACAATCGTGGATCTTGACGGTAATCCATGAGCATGATCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATcc                                                                                                              >  1:325654/1‑139 (MQ=255)    tatTTCATCAAAATAGAAATTAATCGTTGCATCAGTCACAATCGTGGATCTTGACGGTAATCCATGAGCATGATCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATcc                                                                                                              >  2:101535/1‑139 (MQ=255)    tatTTCATCAAAATAGAAATTAATCGTTGCATCAGTCACAATCGTGGATCTTGACGGTAATCCATGAGCATGATCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATcc                                                                                                              >  2:555180/1‑139 (MQ=255)    tatTTCATCAAAATAGAAATTAATCGTTGCATCAGTCACAATCGTGGATCTTGACGGTAATCCATGAGCATGATCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATcc                                                                                                              >  2:429123/1‑139 (MQ=255)           tcaAAATAGAAATTAATCGTTGCATCAGTCACAATCGTGGATCTTGACGGTAATCCATGAGCATGATCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGc                                                                                                          >  1:37943/1‑136 (MQ=255)           tcaAAATAGAAATTAATCGTTGCATCAGTCACAATCGTGGATCTTGACGGTAATCCATGAGCATGATCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGc                                                                                                          <  2:37943/136‑1 (MQ=255)               aaTAGAAATTAATCGTTGCATCAGTCACAATCGTGGATCTTGACGGTAATCCATGAGCATGATCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAAt                                                                                                   >  1:817289/1‑139 (MQ=255)                    aaaTTAATCGTTGCATCAGTCACAATCGTGGATCTTGACGGTAATCCATGAGCATGATCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACt                                                                                              <  2:636136/139‑1 (MQ=255)                         aaTCGTTGCATCAGTCACAATCGTGGATCTTGACGGTAATCCATGAGCATGATCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTcacca                                                                                         <  2:817289/139‑1 (MQ=255)                           tCGTTGCATCAGTCACAATCGTGGATCTTGACGGTAATCCATGAGCATGATCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACg                                                                                       >  1:550596/1‑139 (MQ=255)                                  aTCAGTCACAATCGTGGATCTTGACGGTAATCCATGAGCATGATCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCa                                                                                <  2:807911/139‑1 (MQ=255)                                      gTCACAATCGTGGATCTTGACGGTAATCCATGAGCATGATCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACt                                                                                              >  2:996631/1‑121 (MQ=255)                                      gTCACAATCGTGGATCTTGACGGTAATCCATGAGCATGATCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATAAATCCCCCGCCCGTCATCCAAGCCACGAATAAACt                                                                                              <  1:996631/121‑1 (MQ=255)                                           aaTCGTGGATCTTGACGGTAATCCATGAGCATGATCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAattta                                                                       >  2:768671/1‑139 (MQ=255)                                           aaTCGTGGATCTTGACGGTAATCCATGAGCATGATCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAattta                                                                       >  2:979102/1‑139 (MQ=255)                                                     cTTGACGGTAATCCATGAGCATGATCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAATTTATTTGTCGGAt                                                             <  1:979102/139‑1 (MQ=255)                                                       tGACGGTAATCCATGAGCATGATCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAATTTATTTGTCGGATaa                                                           >  1:1016416/1‑139 (MQ=255)                                                              aacccATGAGCATGATCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAATTTATTTg                                                                   <  1:46628/121‑1 (MQ=255)                                                              aacccATGAGCATGATCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAATTTATTTg                                                                   >  2:46628/4‑124 (MQ=255)                                                               aTCCATGAGCATGATCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAATTTATTTGTCGGATAAGCCTTTGc                                                   <  1:229126/139‑1 (MQ=255)                                                               aTCCATGAGCATGATCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAATTTATTTGTCGGATAAGCCTTTGc                                                   <  1:853375/139‑1 (MQ=255)                                                                   aTGAGCATGATCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAATTTATTTGTCGGATAAGCCTTTGCCAGt                                               <  2:325654/139‑1 (MQ=255)                                                                     gAGCATGATCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATcccc                                                                                                                          >  1:330268/1‑62 (MQ=255)                                                                     gAGCATGATCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATcccc                                                                                                                          <  2:330268/62‑1 (MQ=255)                                                                           gATCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAATTTATTTGTCGGATAAGCCTTTGCCAGTTCCGGGTa                                       <  2:550596/139‑1 (MQ=255)                                                                           gATCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAATTTATTTGTCGGATAAGCCTTTGCCAGTTCCGGGTa                                       <  2:583333/139‑1 (MQ=255)                                                                              cctccGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAATTTATTTGTCGGATAAGCCTTTGCCAGTTCCGGGTAttc                                    >  1:253738/1‑139 (MQ=255)                                                                                tccGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAATTTATTTg                                                                   <  2:96137/106‑1 (MQ=255)                                                                                tccGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAATTTATTTg                                                                   >  1:96137/1‑106 (MQ=255)                                                                                tccGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAATTTATTTGTCGGATAAGCCTTTGCCAGTTCCGGGTAttctt                                  >  2:111459/1‑139 (MQ=255)                                                                                tccGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAATTTATTTGTCGGATAAGCCTTTGCCAGTTCCGGGTAttctt                                  <  2:253738/139‑1 (MQ=255)                                                                                       cATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTca                                                                                            <  2:821132/74‑1 (MQ=255)                                                                                       cATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTca                                                                                            >  1:821132/1‑74 (MQ=255)                                                                                       cATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTca                                                                                            >  2:983872/1‑74 (MQ=255)                                                                                       cATACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTca                                                                                            <  1:983872/74‑1 (MQ=255)                                                                                        aTACCCCTGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAATTTATTTGTCGGATAAGCCTTTGCCAGTTCCGGGTATTCTTCAGCAGaa                          >  2:10653/1‑139 (MQ=255)                                                                                               tGAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAATTTATTTGTCGGATAAGCCTTTGCCAGTTCCGGGTATTCTTCAGCAGAAAAAGCgg                   <  1:101535/139‑1 (MQ=255)                                                                                                gAATACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAATTTATTTGTCGGATAAGCCTTTGCCAGTTCCGGGTATTCTTCAGCAGAAAAAGCGGc                  <  1:555180/139‑1 (MQ=255)                                                                                                 aaTACTTAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAATTTATTTATCGGATAAGCCTTTGCCAGTTCCGGGTATTCTTCAGCAGAAAAAGCGGCa                 <  2:1022136/139‑1 (MQ=255)                                                                                                      ttAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAATTTATTTGTCGGATAAGCCTTTGCCAGTTCCGGGTATTCTTCAGCAGAAAAAGCGGCACCAtt            >  2:876141/1‑139 (MQ=255)                                                                                                      ttAAAATAGAGCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAATTTATTTGTCGGATAAGCCTTTGCCAGTTCCGGGTATTCTTCAGCAGAAAAAGCGGCACCAtt            >  2:958903/1‑139 (MQ=255)                                                                                                               agCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTc                                                                                             <  2:874851/49‑1 (MQ=255)                                                                                                               agCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTc                                                                                             >  1:874851/1‑49 (MQ=255)                                                                                                               agCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAATTTATTTGTCGGATAAGCCTTTGCCAGTTCCTGGTATTCTTCAGCAGAAAAAGCGGCACCATTGCATTTcag   >  2:345454/1‑139 (MQ=255)                                                                                                               agCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAATTTATTTGTCGGATAAGCCTTTGCCAGTTCCGGGTATTCTTCAGCAGAAAAAGCGGCACCATTGCATTTcag   >  2:179893/1‑139 (MQ=255)                                                                                                                gCGACCTGCATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAATTTATTTGTCGGATAAGCCTTTGCCAGTTCCGGGTATTCTTCAGCAGAAAAAGCGGCACCATTGCATTTcagc  >  1:359153/1‑139 (MQ=255)                                                                                                                        |                                                                                                                                   CCATATTTCATCAAAATAGAAATTAATCGTTGCATCAGTCACAATCGTGGATCTTGACGGTAATCCATGAGCATGATCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGTATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAATTTATTTGTCGGATAAGCCTTTGCCAGTTCCGGGTATTCTTCAGCAGAAAAAGCGGCACCATTGCATTTCAGC  >  NC_000913/1209293‑1209542

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: ‑