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%	196.7 / NA	60	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 (27/33);  total (27/33)

TATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACGCCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAACCTGATCGATGG  >  NC_000913/3187454‑3187719                                                                                                                                       |                                                                                                                                    tATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCaa                                                                                                                                 <  2:1421256/139‑1 (MQ=255)  aTGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAAt                                                                                                                                <  1:102898/139‑1 (MQ=255)        ttGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCt                                                                                                                          >  2:831483/1‑139 (MQ=255)        ttGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCt                                                                                                                          >  2:1364592/1‑139 (MQ=255)         tGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCtt                                                                                                                         >  1:1312376/1‑139 (MQ=255)            aTTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGAc                                                                                                                      <  2:1312376/139‑1 (MQ=255)             ttCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCAcc                                                                                                                           <  2:998836/133‑1 (MQ=255)             ttCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCAcc                                                                                                                           >  1:998836/1‑133 (MQ=255)              tCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCt                                                                                                                    <  2:519470/139‑1 (MQ=255)                 acaaAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCa                                                                                                                 <  1:750287/139‑1 (MQ=255)                 acaaAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCa                                                                                                                 <  2:779991/139‑1 (MQ=255)                  caaAGATTTTATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCaa                                                                                                                <  2:608121/139‑1 (MQ=255)                  caaAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCTCTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCaa                                                                                                                <  1:1182616/139‑1 (MQ=255)                  caaAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCaa                                                                                                                <  1:1364592/139‑1 (MQ=255)                  caaAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCaa                                                                                                                <  1:794555/139‑1 (MQ=255)                                 aGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAAt                                                                                                               <  1:219611/125‑1 (MQ=255)                                 aGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAAt                                                                                                               >  2:219611/1‑125 (MQ=255)                                   ccGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATaa                                                                                               <  1:575768/139‑1 (MQ=255)                                           cGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTg                                                                                       >  1:1419816/1‑139 (MQ=255)                                             tGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCaa                                                                                                                <  2:1605402/112‑1 (MQ=255)                                             tGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCaa                                                                                                                >  1:1605402/1‑112 (MQ=255)                                             tGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATg                                                                                                              <  2:831236/114‑1 (MQ=255)                                             tGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATg                                                                                                              >  1:831236/1‑114 (MQ=255)                                                      tAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAAt                                                                                                                                <  1:684472/87‑1 (MQ=255)                                                      tAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAAt                                                                                                                                >  2:684472/1‑87 (MQ=255)                                                             tCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGAt                                                                                                 >  1:428298/1‑111 (MQ=255)                                                             tCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGAt                                                                                                 <  2:428298/111‑1 (MQ=255)                                                              cccAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAAt                                                                                                               <  2:337924/96‑1 (MQ=255)                                                              cccAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAAt                                                                                                               >  1:337924/1‑96 (MQ=255)                                                                      gAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTaa                                                            <  1:831483/139‑1 (MQ=255)                                                                       aaaCTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAAc                                                           <  2:1419816/139‑1 (MQ=255)                                                                       aaaCTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAAc                                                           >  1:42309/1‑139 (MQ=255)                                                                             aTGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAAt                                                                                                                                >  2:37721/1‑64 (MQ=255)                                                                             aTGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAAt                                                                                                                                <  1:37721/64‑1 (MQ=255)                                                                                                          cTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGaaaaaa                        >  1:987586/1‑139 (MQ=255)                                                                                                           tAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAc                       >  2:1200537/1‑139 (MQ=255)                                                                                                             aGCACTCTGATTAATAATAAGAGGACACCAATCCAcc                                                                                                                           >  2:517575/1‑37 (MQ=255)                                                                                                             aGCACTCTGATTAATAATAAGAGGACACCAATCCAcc                                                                                                                           <  1:517575/37‑1 (MQ=255)                                                                                                                  tctGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCaa                                                                                                                <  1:1334062/43‑1 (MQ=255)                                                                                                                  tctGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCaa                                                                                                                >  2:1334062/1‑43 (MQ=255)                                                                                                                  tctGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGtt                                                                                  <  1:1001374/73‑1 (MQ=255)                                                                                                                  tctGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGtt                                                                                  >  2:1001374/1‑73 (MQ=255)                                                                                                                  tctGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTg                                                                                <  1:434107/75‑1 (MQ=255)                                                                                                                  tctGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTg                                                                                >  2:434107/1‑75 (MQ=255)                                                                                                                   ctGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCaaa               >  1:797766/1‑139 (MQ=255)                                                                                                                      aTTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAAcc            <  2:42309/139‑1 (MQ=255)                                                                                                                       ttAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGt                                                                             <  1:1039325/73‑1 (MQ=255)                                                                                                                       ttAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGt                                                                             >  2:1039325/1‑73 (MQ=255)                                                                                                                         aataataaGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGac                                                                          <  1:279044/74‑1 (MQ=255)                                                                                                                         aataataaGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGac                                                                          >  2:279044/1‑74 (MQ=255)                                                                                                                          ataataaGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAAt                                                               >  1:1271274/1‑84 (MQ=255)                                                                                                                          ataataaGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAAt                                                               <  2:1271274/84‑1 (MQ=255)                                                                                                                            aataaGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCag                                                                     >  2:1106321/1‑76 (MQ=255)                                                                                                                            aataaGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCag                                                                     <  1:1106321/76‑1 (MQ=255)                                                                                                                             ataaGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAACCTGATCGa     <  2:987586/139‑1 (MQ=255)                                                                                                                                agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACATCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAACCTGATCGATgg  >  1:393868/1‑139 (MQ=255)                                                                                                                                agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTaa                                                            >  1:1262854/1‑81 (MQ=255)                                                                                                                                agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTaa                                                            <  2:1262854/81‑1 (MQ=255)                                                                                                                                agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACatta                                                       <  2:1058069/86‑1 (MQ=255)                                                                                                                                agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAAGTAACatta                                                       >  1:1058069/1‑86 (MQ=255)                                                                                                                                       |                                                                                                                                    TATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACGCCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAACCTGATCGATGG  >  NC_000913/3187454‑3187719

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑