Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,112,442	T→G	pseudogene (479/867 nt)	yghF ←	putative type II secretion system C‑type protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,112,442	0	T	G	100.0%	157.9 / NA	44	pseudogene (479/867 nt)	yghF	putative type II secretion system C‑type protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (25/19);  total (25/19)

GCCAGTGCCTGACGCACGGCAGCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGTCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCAGACTCAGACGCTCTATTTTTCC  >  NC_000913/3112364‑3112518                                                                               |                                                                             gCCAGTGCCTGACGCACGGCAGCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCa                                                                            >  2:570729/1‑81 (MQ=255) gCCAGTGCCTGACGCACGGCAGCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCa                                                                            >  2:570728/1‑81 (MQ=255) gCCAGTGCCTGACGCACGGCAGCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCa                                                                            >  1:570731/1‑81 (MQ=255)       gCCTGACGCACGGCAGCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACg                                                                      >  1:570720/1‑81 (MQ=255)        ccTGACGCACGGCAGCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACgg                                                                     <  2:570670/81‑1 (MQ=255)          tGACGCACGGCAGCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCt                                                                   >  2:570742/1‑81 (MQ=255)           gACGCACGGCAGCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCtt                                                                  >  2:570727/1‑81 (MQ=255)            aCGCACGGCAGCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCtt                                                                  <  2:570671/80‑1 (MQ=255)              gCACGGCAGCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCttttt                                                               >  1:570721/1‑81 (MQ=255)                   gCAGCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTttgttg                                                          <  1:570672/81‑1 (MQ=255)                   gCAGCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTttgttg                                                          >  1:570733/1‑81 (MQ=255)                    cAGCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTgg                                                         <  1:570673/81‑1 (MQ=255)                    cAGCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTgg                                                         >  1:570695/1‑81 (MQ=255)                     aGCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGt                                                        >  2:570739/1‑81 (MQ=255)                      gCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTc                                                       <  2:570674/81‑1 (MQ=255)                        cGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTca                                                      >  1:570723/1‑80 (MQ=255)                           gATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAg                                                   >  2:570722/1‑80 (MQ=255)                            aTCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGc                                                  >  1:570738/1‑80 (MQ=255)                                 aaCTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGt                                            >  1:570732/1‑81 (MQ=255)                                 aaCTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGt                                            >  1:570734/1‑81 (MQ=255)                                   cTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTg                                           >  1:570749/1‑80 (MQ=255)                                          acTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTc                                   >  2:570747/1‑81 (MQ=255)                                          acTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTc                                   <  1:570675/81‑1 (MQ=255)                                           cTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTcc                                  <  2:570676/81‑1 (MQ=255)                                            tGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCct                                 >  1:570754/1‑81 (MQ=255)                                              aCAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCctct                               >  2:570677/1‑81 (MQ=255)                                                 gcagGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCtcttct                            <  2:570678/81‑1 (MQ=255)                                                  cagGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTg                           >  1:570753/1‑81 (MQ=255)                                                  cagGCTCAGCAACAGCTTGCTTAGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTg                           <  1:570679/81‑1 (MQ=255)                                                   agGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGc                          >  1:570748/1‑81 (MQ=255)                                                   agGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGc                          <  1:570680/81‑1 (MQ=255)                                                     gCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCa                        <  1:570681/81‑1 (MQ=255)                                                      cTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCAg                       <  2:570683/81‑1 (MQ=255)                                                      cTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCAg                       <  1:570682/81‑1 (MQ=255)                                                         aGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCAGAc                     <  1:570684/80‑1 (MQ=255)                                                          gCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCAGACTc                   <  2:570685/81‑1 (MQ=255)                                                          gCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCAGACTc                   <  1:570686/81‑1 (MQ=255)                                                               aGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCAGACTCAGACg              <  2:570687/81‑1 (MQ=255)                                                                gcttgcttTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCAGACTCAGACGc             >  1:570745/1‑81 (MQ=255)                                                                  ttgctttgctTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCAGACTCAGACGctc           >  2:570741/1‑81 (MQ=255)                                                                    gctttgcttCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCAGACTCAGACGctct          <  2:570688/80‑1 (MQ=255)                                                                          cttCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCAGACTCAGACGCTCTATTTTTc   <  2:570689/81‑1 (MQ=255)                                                                          cttCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCAGACTCAGACGCTCTATTTTTc   >  2:570760/1‑81 (MQ=255)                                                                           ttCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCAGACTCAGACGCTCTATTTTTcc  >  1:570750/1‑81 (MQ=255)                                                                               |                                                                             GCCAGTGCCTGACGCACGGCAGCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGTCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCAGACTCAGACGCTCTATTTTTCC  >  NC_000913/3112364‑3112518

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑