Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,187,588	G→A	pseudogene (162/2439 nt)	yqiG →	pseudogene, fimbrial export usher family,putative membrane, Not classified, putative membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,187,588	0	G	A	100.0%	180.0 / NA	56	pseudogene (162/2439 nt)	yqiG	pseudogene, fimbrial export usher family,putative membrane, Not classified, putative membrane protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (26/30);  total (26/30)

GTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACGCCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAACCTGATCGATGGTTGT  >  NC_000913/3187460‑3187723                                                                                                                                 |                                                                                                                                        gTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCAcc                                                                                                                               <  1:23026/139‑1 (MQ=255)    gAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTg                                                                                                                            <  1:1041098/139‑1 (MQ=255)                                      gTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACAcc                                                                                                                                       <  2:242202/94‑1 (MQ=255)                                      gTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACAcc                                                                                                                                       >  1:242202/1‑94 (MQ=255)                                       tGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCa                                                                                         >  2:402550/1‑139 (MQ=255)                                       tGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCa                                                                                         >  2:666991/1‑139 (MQ=255)                                          aaaCGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGtt                                                                                      <  2:356071/139‑1 (MQ=255)                                              gTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCg                                                                                  <  1:666991/139‑1 (MQ=255)                                              gTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCg                                                                                  <  1:402550/139‑1 (MQ=255)                                                      ttCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCa                                                                          <  1:45522/139‑1 (MQ=255)                                                      ttCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCa                                                                          <  1:473/139‑1 (MQ=255)                                                        cccAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGt                                                                                 >  2:312083/1‑130 (MQ=255)                                                        cccAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGt                                                                                 <  1:312083/130‑1 (MQ=255)                                                        cccAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCaga                                                                        <  2:806779/139‑1 (MQ=255)                                                                gAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTaa                                                                >  2:278750/1‑139 (MQ=255)                                                                         ggCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAAt                                                                                                                   <  1:522406/79‑1 (MQ=255)                                                                         ggCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAAt                                                                                                                   >  2:522406/1‑79 (MQ=255)                                                                              aTTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGa                                                                                                                           <  1:354823/66‑1 (MQ=255)                                                                              aTTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGa                                                                                                                           >  2:354823/1‑66 (MQ=255)                                                                               ttACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGt                                                                                 <  2:609701/107‑1 (MQ=255)                                                                               ttACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGt                                                                                 >  1:609701/1‑107 (MQ=255)                                                                                     gTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACTTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACatta                                                           >  1:335096/1‑123 (MQ=255)                                                                                     gTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACTTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACatta                                                           <  2:335096/123‑1 (MQ=255)                                                                                     gTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGAGACCAGAGCAATTAACATTATTAGGATTTACtgatg                                           >  1:64269/1‑139 (MQ=255)                                                                                       cGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACattat                                                          >  2:790016/1‑122 (MQ=255)                                                                                       cGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACattat                                                          <  1:790016/122‑1 (MQ=255)                                                                                       cGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGaa                                         >  1:183462/1‑139 (MQ=255)                                                                                                   aCTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGt                                                                                                               <  1:299635/57‑1 (MQ=255)                                                                                                   aCTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGt                                                                                                               >  2:299635/1‑57 (MQ=255)                                                                                                   aCTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGaaaaa                             >  1:288867/1‑139 (MQ=255)                                                                                                          aCTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGAt                                                                                                     <  2:986305/60‑1 (MQ=255)                                                                                                          aCTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGAt                                                                                                     >  1:986305/1‑60 (MQ=255)                                                                                                               gATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGAGACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAAc                 <  2:64269/139‑1 (MQ=255)                                                                                                               gATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTaa                                                                <  2:335450/92‑1 (MQ=255)                                                                                                               gATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTaa                                                                >  1:335450/1‑92 (MQ=255)                                                                                                                   aataataaGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCagag                                                                       <  2:440243/81‑1 (MQ=255)                                                                                                                   aataataaGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCagag                                                                       >  1:440243/1‑81 (MQ=255)                                                                                                                       ataaGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAACCTGATCGa         <  2:656874/139‑1 (MQ=255)                                                                                                                        taaGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAc                           >  2:339987/1‑120 (MQ=255)                                                                                                                        taaGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAc                           <  1:339987/120‑1 (MQ=255)                                                                                                                          agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCaa                                                                                               <  1:1002575/50‑1 (MQ=255)                                                                                                                          agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCaa                                                                                               >  2:1002575/1‑50 (MQ=255)                                                                                                                          agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCaga                                                                        >  1:773310/1‑73 (MQ=255)                                                                                                                          agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCaga                                                                        <  2:773310/73‑1 (MQ=255)                                                                                                                          agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAAc                                                               >  1:326356/1‑82 (MQ=255)                                                                                                                          agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAAc                                                               <  2:326356/82‑1 (MQ=255)                                                                                                                          agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGAtt                                                   <  1:558055/94‑1 (MQ=255)                                                                                                                          agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGAtt                                                   >  2:558055/1‑94 (MQ=255)                                                                                                                          agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAAcc                >  2:776561/1‑129 (MQ=255)                                                                                                                          agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAAcc                <  1:776561/129‑1 (MQ=255)                                                                                                                            agGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAACCTGATCGATGgtt    >  2:1034765/1‑139 (MQ=255)                                                                                                                              gACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCa                                                                          <  2:706020/67‑1 (MQ=255)                                                                                                                              gACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTaa                                                                >  2:71586/1‑77 (MQ=255)                                                                                                                              gACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTaa                                                                <  1:71586/77‑1 (MQ=255)                                                                                                                              gACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAg                       <  2:192952/118‑1 (MQ=255)                                                                                                                              gACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAACCTGATCGATGgttgt  >  2:278135/1‑139 (MQ=255)                                                                                                                                 |                                                                                                                                        GTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACGCCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAACCTGATCGATGGTTGT  >  NC_000913/3187460‑3187723

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: ‑