Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,426,288	G→A	intergenic (+206/‑166)	ydaY → / → tmpR	pseudogene, Rac prophage,Phage or Prophage Related/Rac prophage, pseudogene, tail protein family,Phage or Prophage Related, putative alpha helix protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,426,288	0	G	A	100.0%	212.1 / NA	67	intergenic (+206/‑166)	ydaY/tmpR	pseudogene, Rac prophage,Phage or Prophage Related/Rac prophage, pseudogene, tail protein family,Phage or Prophage Related, putative alpha helix protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (31/36);  total (31/36)

GGTGCCTTTGCCTTTATCTCTGACAGAGATAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCTATATCTACTATTATGTCGC  >  NC_000913/1426156‑1426405                                                                                                                                      |                                                                                                                      ggTGCCTTTGCCTTTATCTCTGACAGAGATAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTa                                                                                                                 >  2:640732/1‑139 (MQ=255)   tgcctttgccttTATCTCTGACAGAGATAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAAt                                                                                                               <  2:1488817/139‑1 (MQ=255)      ctttgcctttATCTCTGACAGAGATAAATGAATATTTAGCCACTCATCCGGTATAGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTTCAGGGGCAGTGTGTGTAATTGTTAATTa                                                                                                             >  2:1010648/1‑139 (MQ=255)           cctttATCTCTGACAGAGATAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTaca                                                                                                       <  1:1251314/139‑1 (MQ=255)           cctttATCTCTGACAGAGATAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTaca                                                                                                       <  1:28661/139‑1 (MQ=255)                   tctGACAGAGATAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTa                                                                                               <  1:715279/139‑1 (MQ=255)                           agaTAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTa                                                                                                                 >  2:586342/1‑113 (MQ=255)                           agaTAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTa                                                                                                                 <  1:586342/113‑1 (MQ=255)                           agaTAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACa                                                                                             <  1:476991/133‑1 (MQ=255)                           agaTAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACa                                                                                             >  2:476991/1‑133 (MQ=255)                                  tGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGgt                                                                                <  2:566823/139‑1 (MQ=255)                                   gAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGgtg                                                                               >  1:412279/1‑139 (MQ=255)                                      tatTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCt                                                                            >  2:619582/1‑139 (MQ=255)                                       atTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTaca                                                                                                       <  2:1197772/111‑1 (MQ=255)                                       atTTAGCCACTCATCCGGTATCGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTaca                                                                                                       >  1:1197772/1‑111 (MQ=255)                                           aGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTttaat                                                                       >  2:421532/1‑139 (MQ=255)                                                   aTCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACActc                                                                                                    >  1:993900/1‑102 (MQ=255)                                                   aTCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACActc                                                                                                    <  2:993900/102‑1 (MQ=255)                                                      cGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCgatga                                                            <  1:619582/139‑1 (MQ=255)                                                            tgattgaGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTcc                                                      <  2:803489/139‑1 (MQ=255)                                                                 gaGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGgag                                                 >  1:382625/1‑139 (MQ=255)                                                                  aGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTaca                                                                                                       <  1:643552/84‑1 (MQ=255)                                                                  aGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTaca                                                                                                       >  2:643552/1‑84 (MQ=255)                                                                  aGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGgaga                                                <  1:640732/139‑1 (MQ=255)                                                                   gcgcGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTaa                                                                                                                <  1:710035/74‑1 (MQ=255)                                                                   gcgcGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTaa                                                                                                                >  2:710035/1‑74 (MQ=255)                                                                   gcgcGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGaa                                               >  1:63220/1‑139 (MQ=255)                                                                   gcgcGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGaa                                               >  2:1165304/1‑139 (MQ=255)                                                                   gcgcGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGaa                                               >  1:322540/1‑139 (MQ=255)                                                                        aTGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTa                                                                                                         <  2:1445136/76‑1 (MQ=255)                                                                        aTGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTa                                                                                                         >  1:1445136/1‑76 (MQ=255)                                                                        aTGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGAtgtg                                                                                     >  2:638570/1‑96 (MQ=255)                                                                        aTGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGAtgtg                                                                                     <  1:638570/96‑1 (MQ=255)                                                                                      gTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGt                            >  2:632684/1‑139 (MQ=255)                                                                                       tGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTa                                                                                                         >  1:211656/1‑61 (MQ=255)                                                                                       tGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTa                                                                                                         <  2:211656/61‑1 (MQ=255)                                                                                       tGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTCAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTa                           >  1:914137/1‑139 (MQ=255)                                                                                        gATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTaa                          <  2:382625/139‑1 (MQ=255)                                                                                        gATCTTTGCACTCGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCCGGAGAAAAGCATTGCGTGGCCTCGTaa                          <  2:914137/139‑1 (MQ=255)                                                                                           cTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCg                       <  2:63220/139‑1 (MQ=255)                                                                                             ttGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCt                     <  1:632684/139‑1 (MQ=255)                                                                                             ttGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCt                     <  2:274831/139‑1 (MQ=255)                                                                                                cACTCGATGACCAGTATTTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCTTGGCCTCGTAATCGCtat                   <  1:1010648/139‑1 (MQ=255)                                                                                                  cTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCTATATc                <  1:421532/139‑1 (MQ=255)                                                                                                     gATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCt                     >  1:200684/1‑131 (MQ=255)                                                                                                     gATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCt                     <  2:200684/131‑1 (MQ=255)                                                                                                     gATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCTATATctac             >  1:729042/1‑139 (MQ=255)                                                                                                          ccAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAAt                                                                  <  1:104024/81‑1 (MQ=255)                                                                                                          ccAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAAt                                                                  >  2:104024/1‑81 (MQ=255)                                                                                                             gTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCTATATCTACTATTATGt     <  1:1165304/139‑1 (MQ=255)                                                                                                               a‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTa                                                                                                         >  2:1348862/1‑37 (MQ=255)                                                                                                               a‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTa                                                                                                         <  1:1348862/37‑1 (MQ=255)                                                                                                               a‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTttaat                                                                       >  2:743761/1‑71 (MQ=255)                                                                                                               a‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTttaat                                                                       <  1:743761/71‑1 (MQ=255)                                                                                                               a‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCg                                     >  2:1386112/1‑105 (MQ=255)                                                                                                               a‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCg                                     <  1:1386112/105‑1 (MQ=255)                                                                                                               a‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCtat                   >  1:1069362/1‑123 (MQ=255)                                                                                                               a‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCtat                   <  2:1069362/123‑1 (MQ=255)                                                                                                                 ttttCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCTATATCTACTATTATGTCGc  <  2:729042/139‑1 (MQ=255)                                                                                                                         aGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTc                                                                             >  1:897683/1‑56 (MQ=255)                                                                                                                         aGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTc                                                                             <  2:897683/56‑1 (MQ=255)                                                                                                                         aGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTg                                                    >  1:173520/1‑81 (MQ=255)                                                                                                                         aGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTg                                                    <  2:173520/81‑1 (MQ=255)                                                                                                                              tgtgtgtAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTa                           >  2:72261/1‑101 (MQ=255)                                                                                                                              tgtgtgtAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTa                           <  1:72261/101‑1 (MQ=255)                                                                                                                                  tgtAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCt                     <  2:724689/103‑1 (MQ=255)                                                                                                                                  tgtAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCt                     >  1:724689/1‑103 (MQ=255)                                                                                                                                      |                                                                                                                      GGTGCCTTTGCCTTTATCTCTGACAGAGATAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCTATATCTACTATTATGTCGC  >  NC_000913/1426156‑1426405

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑