Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	576,168	T→C	pseudogene (658/1040 nt)	nmpC ←	DLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	576,168	0	T	C	100.0%	151.0 / NA	42	pseudogene (658/1040 nt)	nmpC	DLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (20/22);  total (20/22)

TCAGCAAATACAGTCATATTCTGGGTTTCAGAATAGGTAGTGGCCAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGTGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCGAAGCCATCACCGTTACCTTCAGTGTAGTTATCGAAATCGCTACGATCGTTTTTGCCTTGGTACTGAGCAGC  >  NC_000913/576020‑576312                                                                                                                                                     |                                                                                                                                                 tCAGCAAATACAGTCATATTCTGGGTTTCAGAATAGGTAGTGGCCAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAgcgt                                                                                                                                                >  2:77781/1‑151 (MQ=255)   aGCAAATACAGTCATATGCTGGGTTTCAGAATAGGTAGTGGCCAGGTAAATGTTGTTAGCGTCGTATTTCAGACCTGCAGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCg                                                                                                                                              >  1:516905/1‑151 (MQ=255)    gCAAATACAGTCATATTCTGGGTTTCAGAATAGGTAGTGGCCAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCgg                                                                                                                                             >  1:86307/1‑151 (MQ=255)      aaaTACAGTCATATTCTGGGTTTCAGAATAGGTAGTGGCCAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGt                                                                                                                                            >  2:566678/1‑150 (MQ=255)       aaTACAGTCATATTCTGGGTTTCAGAATAGGTAGTGGCCAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTAc                                                                                                                                          >  2:507147/1‑151 (MQ=255)          aCAGTCATATTCTGGGTTTCAGAATAGGTAGTGGCCAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGa                                                                                                                                        <  1:343985/150‑1 (MQ=255)           cAGTCATATTCTGGGTTTCAGAATAGGTAGTGGCCAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATc                                                                                                                                      <  2:122964/151‑1 (MQ=255)             gTCATATTCTGGGTTTCAGAATAGGTAGTGGCCAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAg                                                                                                                                    <  2:537294/151‑1 (MQ=255)                 tatTCTGGGTTTCAGAATAGGTAGTGGCCAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGAttt                                                                                                                                >  2:229094/1‑151 (MQ=255)                       gggTTTCAGAATAGGTAGTGGCCAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGc                                                                                                                             <  2:381777/148‑1 (MQ=255)                             cAGAATAGGTAGTGGCCAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATa                                                                                                                          <  2:54085/145‑1 (MQ=255)                             cAGAATAGGTAGTGGCCAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATa                                                                                                                          >  1:54086/1‑145 (MQ=255)                                 aTAGGTAGTGGCCAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCg                                                                                                                <  2:126720/151‑1 (MQ=255)                                 aTAGGTAGTGGCCAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCg                                                                                                                <  2:505851/151‑1 (MQ=255)                                          ggCCAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAAt                                                                                                       >  2:250304/1‑151 (MQ=255)                                            ccAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATcc                                                                                                     <  2:343412/151‑1 (MQ=255)                                              aGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGTATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACGTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCtt                                                                                                   <  2:355878/151‑1 (MQ=255)                                              aGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCtt                                                                                                   <  1:491534/151‑1 (MQ=255)                                               ggTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTc                                                                                                  <  2:308462/151‑1 (MQ=255)                                                    aTGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTAtt                                                                                             >  1:296145/1‑151 (MQ=255)                                                        tgttAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCTTTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTTCACCGATACCGAATCCTTCGTATTCAt                                                                                          <  2:37705/150‑1 (MQ=255)                                                             gCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGt                                                                                      >  2:125350/1‑149 (MQ=255)                                                                 cATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGc                                                                                   >  1:168468/1‑148 (MQ=255)                                                                  atatTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCag                                                                                 >  2:327862/1‑149 (MQ=255)                                                                  atatTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCag                                                                                 >  2:600941/1‑149 (MQ=255)                                                                      ttCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAAc                                                                           >  2:567671/1‑151 (MQ=255)                                                                       tCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAAc                                                                           <  1:61791/150‑1 (MQ=255)                                                                        cAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAAcc                                                                          <  2:508465/150‑1 (MQ=255)                                                                         aGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCg                                                                         >  2:302805/1‑150 (MQ=255)                                                                                   cccAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCGAAGCCATCAcc                                                              <  2:36853/151‑1 (MQ=255)                                                                                          ttCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCGAAGCCATCACCGTTACCt                                                       >  1:401373/1‑151 (MQ=255)                                                                                           tCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCGAAGCCATCACCGTTACCt                                                       <  2:618234/150‑1 (MQ=255)                                                                                                  ttttACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCGAAGCCATCACCGTTACCTTCAgtgt                                                <  2:81937/150‑1 (MQ=255)                                                                                                   tttACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCGAAGCCATCACCGTTACCTTCAGTGTa                                               <  1:17463/150‑1 (MQ=255)                                                                                                   tttACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCGAAGCCATCACCGTTACCTTCAGTGTa                                               <  2:232393/150‑1 (MQ=255)                                                                                                            aGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCGAAGCCATCACCGTTACCTTCAGTGTAGTTATCGaa                                      >  2:39683/1‑150 (MQ=255)                                                                                                               aaaTACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCGAAGCCATCACCGTTACCTTCAGTGTAGTTATCGAAATCg                                  >  2:253065/1‑151 (MQ=255)                                                                                                                      tCAGGAAGAACTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGAATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCGAAGCCATCACCGTTACCTTCAGTGTAGTTATCGAAATCGCTACg                             <  1:139719/149‑1 (MQ=255)                                                                                                                          gaagaaCTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCGAAGCCATCACCGTTACCTTCAGTGTAGTTATCGAAATCGCTACGATCGtt                       <  2:225680/151‑1 (MQ=255)                                                                                                                          gaagaaCTTTCCCTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCGAAGCCATCACCGTTACCTTCAGTGTAGTTATCGAAATCGCTACGATCGtt                       <  2:401377/151‑1 (MQ=255)                                                                                                                                      cTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCGAAGCCATCACCGTTACCTTCAGTGTAGTTATCGAAATCGCTACGATCGTTTTTGCCTTGGt            >  2:501380/1‑150 (MQ=255)                                                                                                                                      cTGCATTAACTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCGAAGCCATCACCGTTACCTTCAGTGTAGTTATCGAAATCGCTACGATCGTTTTTGCCTTGGt            >  1:177915/1‑150 (MQ=255)                                                                                                                                               cTTGAGCGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCGAAGCCATCACCGTTACCTTCAGTGTAGTTATCGAAATCGCTACGATCGTTTTTGCCTTGGTACTGagcagc  >  2:3103/1‑151 (MQ=255)                                                                                                                                                     |                                                                                                                                                 TCAGCAAATACAGTCATATTCTGGGTTTCAGAATAGGTAGTGGCCAGGTAAATGTTGTTAGCGTCATATTTCAGACCTGCGGCCCAAACTTCTGCATTTTTACCGGAAGCAAATACTTCAGGAAGAACTTTCCCTGCATTAACTTGAGTGTCGGTACGATCAGATTTCGCATAAGTTGCACCGATACCGAATCCTTCGTATTCATAGGTAGCAGAGAAACCGAAGCCATCACCGTTACCTTCAGTGTAGTTATCGAAATCGCTACGATCGTTTTTGCCTTGGTACTGAGCAGC  >  NC_000913/576020‑576312

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑