Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,334,336	C→T	pseudogene (67/4605 nt) *208* (TAG→TAA)	yfaS ← yfaT ←	pseudogene, bacterial alpha2‑macroglobulin YfaS variant family, putative membrane protein DUF1175 family protein, putative host defense protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,334,336	0	C	T	100.0%	156.4 / NA	49	pseudogene (67/4605 nt) *208* (TAG→TAA)	yfaS yfaT	pseudogene, bacterial alpha2‑macroglobulin YfaS variant family, putative membrane protein DUF1175 family protein, putative host defense protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (22/27);  total (22/27)

TGCTAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGCTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTCCATGTCATAAGTTGTTGCAGACTGACTGCGCGCATTCCGTTGTCAGTTTTCGTGGCG  >  NC_000913/2334210‑2334471                                                                                                                               |                                                                                                                                        tgctAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGa                                                                                                                             >  1:62545/1‑139 (MQ=255)   ctAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGaaa                                                                                                                           >  2:395408/1‑139 (MQ=255)            ctgTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACg                                                                                                                  >  2:552994/1‑139 (MQ=255)             tgTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGa                                                                                                                 >  2:121121/1‑139 (MQ=255)                   caagcaaAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATg                                                                                                           <  1:121121/139‑1 (MQ=255)                      gcaaAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCa                                                                                                        <  2:373674/139‑1 (MQ=255)                           aaGAATGTTCCCCCGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGaa                                                                                                   <  2:187638/139‑1 (MQ=255)                            aGAATGTTCCCCCGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGaaa                                                                                                  >  1:681127/1‑139 (MQ=255)                              aaTGTTCCCCCGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAAtt                                                                                                <  2:681127/139‑1 (MQ=255)                              aaTGTTCCCCCGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAAtt                                                                                                <  1:1112588/139‑1 (MQ=255)                              aaTGTTCCCCCGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAAtt                                                                                                <  2:62545/139‑1 (MQ=255)                                 gTTCCCCCGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTggg                                                                                             >  2:688392/1‑139 (MQ=255)                                        cGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAAt                                                                                                 >  1:1018247/1‑128 (MQ=255)                                        cGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAAt                                                                                                 <  2:1018247/128‑1 (MQ=255)                                              gcggcgCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTg                                                                                         >  2:1208111/1‑130 (MQ=255)                                              gcggcgCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTg                                                                                         <  1:1208111/130‑1 (MQ=255)                                                ggcgCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTggg                                                                              <  2:667744/139‑1 (MQ=255)                                                       aGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTg                                                                                         <  2:777941/121‑1 (MQ=255)                                                       aGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAAAGCCAATGAAATTGGGATTg                                                                                         >  1:777941/1‑121 (MQ=255)                                                        gTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATc                                                                      <  1:846628/139‑1 (MQ=255)                                                        gTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATc                                                                      <  2:643885/139‑1 (MQ=255)                                                                aaggaagCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTcc                                                              <  1:688392/139‑1 (MQ=255)                                                                                  cATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTCCATGTCATAAgttgt                                            <  1:1104689/139‑1 (MQ=255)                                                                                    ttAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTCCATGTCATAAGttgttg                                          <  1:395408/139‑1 (MQ=255)                                                                                     tAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGAt                                                                                                                <  2:442505/68‑1 (MQ=255)                                                                                     tAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGAt                                                                                                                >  1:442505/1‑68 (MQ=255)                                                                                       gCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTcc                                                          <  2:280372/120‑1 (MQ=255)                                                                                       gCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTcc                                                          >  1:280372/1‑120 (MQ=255)                                                                                            cccTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAAt                                                                                                 >  1:1200506/1‑76 (MQ=255)                                                                                            cccTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAAt                                                                                                 <  2:1200506/76‑1 (MQ=255)                                                                                            cccTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTggg                                                                              <  2:785951/95‑1 (MQ=255)                                                                                            cccAGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTggg                                                                              >  1:785951/1‑95 (MQ=255)                                                                                                 ttCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTaaa                                                                                                                    >  1:795084/1‑52 (MQ=255)                                                                                                 ttCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTaaa                                                                                                                    <  2:795084/52‑1 (MQ=255)                                                                                                 ttCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTcc                                                          >  2:1173556/1‑110 (MQ=255)                                                                                                 ttCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTcc                                                          <  1:1173556/110‑1 (MQ=255)                                                                                                  tCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTCCATGTCATAAGTTGTTGCAGACTGACTgcgc                            >  1:913074/1‑139 (MQ=255)                                                                                                           agaCAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTggg                                                                              >  1:509133/1‑80 (MQ=255)                                                                                                           agaCAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTggg                                                                              <  2:509133/80‑1 (MQ=255)                                                                                                           agaCAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTCCATGTCATAAg                                                >  2:1062453/1‑110 (MQ=255)                                                                                                           agaCAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTCCATGTCATAAg                                                <  1:1062453/110‑1 (MQ=255)                                                                                                               aGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTCCa                                                         <  1:105294/97‑1 (MQ=255)                                                                                                               aGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTCCa                                                         >  2:105294/1‑97 (MQ=255)                                                                                                                    cAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCa                                                                                                        <  2:476352/45‑1 (MQ=255)                                                                                                                    cAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCa                                                                                                        >  1:476352/1‑45 (MQ=255)                                                                                                                      aGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATcc                                                                         <  2:1072505/74‑1 (MQ=255)                                                                                                                      aGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATcc                                                                         >  1:1072505/1‑74 (MQ=255)                                                                                                                         aCGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTCCATGTCATAAGTTGTTGCAGACTGACTGCGCGCATTCCGTTGTCAGTTTTCGTg     >  1:51526/1‑139 (MQ=255)                                                                                                                          cGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTCCATGTCATAAGTTGTTGCAGACTGACTGCGCGCATTCCGTTGTCAGTTTTCGTgg    <  2:928165/139‑1 (MQ=255)                                                                                                                           gctgttATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTCCATGTCATAAGTTGTTGCAGactgactg                               >  2:2697/1‑111 (MQ=255)                                                                                                                           gctgttATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTCCATGTCATAAGTTGTTGCAGactgactg                               <  1:2697/111‑1 (MQ=255)                                                                                                                            ctgttATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTCCATGTCATAAGTTGTTGCAGACTGACTGCGCGCATTCCGTTGTCAGTTTTCGTGgcg  >  2:245355/1‑139 (MQ=255)                                                                                                                               |                                                                                                                                        TGCTAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGCTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTCCATGTCATAAGTTGTTGCAGACTGACTGCGCGCATTCCGTTGTCAGTTTTCGTGGCG  >  NC_000913/2334210‑2334471

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: ‑