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%	188.4 / NA	58	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 (26/32);  total (26/32)

CTGCTAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGCTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTCCATGTCATAAGTTGTTGCAGACTGACTGCGCGCATTCCGTTGTCAGTTTTCG  >  NC_000913/2334209‑2334466                                                                                                                                |                                                                                                                                   ctgctAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAg                                                                                                                         <  2:1023689/139‑1 (MQ=255)    ctAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGaaa                                                                                                                      >  1:957668/1‑139 (MQ=255)              tgTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAAtt                                                                                                                   <  1:1111308/132‑1 (MQ=255)              tgTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAAtt                                                                                                                   >  2:1111308/1‑132 (MQ=255)              tgTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGa                                                                                                            >  2:714713/1‑139 (MQ=255)                tCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATa                                                                                                          <  2:591841/139‑1 (MQ=255)                       gcaaAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGACACAGGGTCAAGCACGCTGTTATTGCGCCAGAAAATTTAAACGATAAATGCCa                                                                                                   <  2:957668/139‑1 (MQ=255)                          aaaaGAATGTTCCCCCGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATg                                                                                                >  2:1219718/1‑139 (MQ=255)                                  gTTCCCCCGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAAt                                                                                                                    <  2:124160/111‑1 (MQ=255)                                  gTTCCCCCGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAAt                                                                                                                    >  1:124160/1‑111 (MQ=255)                                  gTTCCCCCGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTaaa                                                                                                               >  1:909871/1‑116 (MQ=255)                                  gTTCCCCCGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTaaa                                                                                                               <  2:909871/116‑1 (MQ=255)                                    tCCCCCGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGAt                                                                                      <  2:899496/139‑1 (MQ=255)                                         cGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGATAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGaa                                                                                 >  2:289733/1‑139 (MQ=255)                                          ggCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAAt                                                                                <  2:546845/139‑1 (MQ=255)                                             aGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAAtt                                                                                           >  1:1222967/1‑125 (MQ=255)                                             aGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAAtt                                                                                           <  2:1222967/125‑1 (MQ=255)                                               gcggcgCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTaaa                                                                                                               >  2:689111/1‑103 (MQ=255)                                               gcggcgCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTaaa                                                                                                               <  1:689111/103‑1 (MQ=255)                                                  gcgcATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTaaa                                                                                                               <  2:96806/100‑1 (MQ=255)                                                  gcgcATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTaaa                                                                                                               >  1:96806/1‑100 (MQ=255)                                                         gTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATc                                                                 <  2:239312/139‑1 (MQ=255)                                                          ttGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCg                                                                <  1:714713/139‑1 (MQ=255)                                                              tGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGgtg                                                            <  1:862331/139‑1 (MQ=255)                                                                       gCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTCCAt                                                   >  1:317828/1‑139 (MQ=255)                                                                           atcatcAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTCCATGTCa                                               <  1:289733/139‑1 (MQ=255)                                                                               tcaGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTggg                                                                         >  2:1331861/1‑109 (MQ=255)                                                                               tcaGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTggg                                                                         <  1:1331861/109‑1 (MQ=255)                                                                                 aGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTCCATGTCATAAgtt                                         <  1:1430128/139‑1 (MQ=255)                                                                                   cATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTCCATGTCATAAgttgt                                       <  1:1048360/139‑1 (MQ=255)                                                                                        gCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTcc                                                     <  2:147286/120‑1 (MQ=255)                                                                                        gCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTcc                                                     >  1:147286/1‑120 (MQ=255)                                                                                        gCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTc                                                      <  1:1158039/119‑1 (MQ=255)                                                                                        gCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTc                                                      >  2:1158039/1‑119 (MQ=255)                                                                                             cccTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAAt                                                                                                 <  1:1422362/71‑1 (MQ=255)                                                                                             cccTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAAt                                                                                                 >  2:1422362/1‑71 (MQ=255)                                                                                             cccTGTTCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTCCATGTCATAAGTTGTTGCAgactga                             >  1:1636871/1‑139 (MQ=255)                                                                                                  ttCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAAt                                                                                            <  2:925632/71‑1 (MQ=255)                                                                                                  ttCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAAt                                                                                            >  1:925632/1‑71 (MQ=255)                                                                                                  ttCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGaa                                                                                 <  2:1526904/82‑1 (MQ=255)                                                                                                  ttCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGaa                                                                                 >  1:1526904/1‑82 (MQ=255)                                                                                                  ttCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGtt                                                                            <  2:1387577/87‑1 (MQ=255)                                                                                                  ttCCCACAAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGtt                                                                            >  1:1387577/1‑87 (MQ=255)                                                                                                       acaAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATa                                                                                                          <  2:1144991/52‑1 (MQ=255)                                                                                                       acaAGAGACAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATa                                                                                                          >  1:1144991/1‑52 (MQ=255)                                                                                                            agaCAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTaaa                                                                                                               >  2:1135087/1‑42 (MQ=255)                                                                                                            agaCAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTaaa                                                                                                               <  1:1135087/42‑1 (MQ=255)                                                                                                            agaCAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCg                                                                              <  2:1625648/75‑1 (MQ=255)                                                                                                            agaCAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCg                                                                              >  1:1625648/1‑75 (MQ=255)                                                                                                            agaCAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTcc                                                     <  2:1224753/100‑1 (MQ=255)                                                                                                            agaCAGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTcc                                                     >  1:1224753/1‑100 (MQ=255)                                                                                                                aGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAAt                                                                                            <  1:861530/57‑1 (MQ=255)                                                                                                                aGGGACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAAt                                                                                            >  2:861530/1‑57 (MQ=255)                                                                                                                   gACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGaa                                                                                 <  2:239553/65‑1 (MQ=255)                                                                                                                   gACAAGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGaa                                                                                 >  1:239553/1‑65 (MQ=255)                                                                                                                      aaGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTc                                                      <  2:358133/89‑1 (MQ=255)                                                                                                                      aaGCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTc                                                      >  1:358133/1‑89 (MQ=255)                                                                                                                        gCACGCTGTTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTCCATGTCATAAGTTGTTGCAGACTGACTGCGCGCATTCCGTTGTCAGTTTTCg  <  1:1219718/139‑1 (MQ=255)                                                                                                                                |                                                                                                                                   CTGCTAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGCTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATCGGGTGTCCTTCCATGTCATAAGTTGTTGCAGACTGACTGCGCGCATTCCGTTGTCAGTTTTCG  >  NC_000913/2334209‑2334466

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑