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%	176.6 / NA	55	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 (25/30);  total (25/30)

TGGGGTGCCTTTGCCTTTATCTCTGACAGAGATAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCTATATCTACTATTATGTCGCCTGAA  >  NC_000913/1426153‑1426410                                                                                                                                        |                                                                                                                           tGGGGTGCCTTTGCCTTTATCTCTGACAGAGATAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAattg                                                                                                                         >  1:775038/1‑139 (MQ=255)    ggTGCCTTTGCCTTTATCTCTGACAGAGATAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTa                                                                                                                      <  2:1487435/139‑1 (MQ=255)    ggTGCCTTTGCCTTTATCTCTGACAGAGATAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTa                                                                                                                      <  1:1276560/139‑1 (MQ=255)    ggTGCCTTTGCCTTTATCTCTGACAGAGATAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTa                                                                                                                      <  2:274611/139‑1 (MQ=255)      tgcctttgccttTATCTCTGACAGAGATAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAAt                                                                                                                    <  2:1589759/139‑1 (MQ=255)              cctttATCTCTGACAGAGATAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTaca                                                                                                            <  2:309916/139‑1 (MQ=255)                tttATCTCTGACAGAGATAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACAct                                                                                                          <  2:1366439/139‑1 (MQ=255)                tttATCTCTGACAGAGATAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACAct                                                                                                          <  2:775038/139‑1 (MQ=255)                tttATCTCTGACAGAGATAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACAct                                                                                                          <  2:561601/139‑1 (MQ=255)                      tctGACAGAGATAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTa                                                                                                    <  1:111897/139‑1 (MQ=255)                        tGACAGAGATAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAAt                                                                                                                    >  2:1544280/1‑121 (MQ=255)                        tGACAGAGATAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAAt                                                                                                                    <  1:1544280/121‑1 (MQ=255)                        tGACAGAGATAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACa                                                                                                  >  2:591276/1‑139 (MQ=255)                            agagATAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAgaga                                                                                              >  1:1510746/1‑139 (MQ=255)                              agaTAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGAtg                                                                                            >  1:1004438/1‑139 (MQ=255)                              agaTAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGAtg                                                                                            >  2:437572/1‑139 (MQ=255)                                aTAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACag                                                                                                 <  2:997185/132‑1 (MQ=255)                                aTAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACag                                                                                                 >  1:997185/1‑132 (MQ=255)                                          atTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATgg                                                                                      <  1:1464075/133‑1 (MQ=255)                                          atTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATgg                                                                                      >  2:1464075/1‑133 (MQ=255)                                              aGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTttaat                                                                            >  2:800284/1‑139 (MQ=255)                                              aGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGGGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTttaat                                                                            >  2:434083/1‑139 (MQ=255)                                                    tCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATc                                                                      >  1:1065613/1‑139 (MQ=255)                                                         cGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCgatga                                                                 <  1:675766/139‑1 (MQ=255)                                                                gattgaGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTacaat                                                                                                          >  2:1582320/1‑89 (MQ=255)                                                                gattgaGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACAct                                                                                                          >  2:1302546/1‑91 (MQ=255)                                                                gattgaGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACAct                                                                                                          <  1:1302546/91‑1 (MQ=255)                                                                gattgaGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACAct                                                                                                          <  1:1582320/91‑1 (MQ=255)                                                                     aGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTa                                                                                                                      <  2:63243/74‑1 (MQ=255)                                                                     aGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTa                                                                                                                      >  1:63243/1‑74 (MQ=255)                                                                     aGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTa                                                                                                              >  2:165451/1‑82 (MQ=255)                                                                     aGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTa                                                                                                              <  1:165451/82‑1 (MQ=255)                                                                     aGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGgaga                                                     >  1:618778/1‑139 (MQ=255)                                                                     aGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGgaga                                                     <  1:591276/139‑1 (MQ=255)                                                                      gcgcGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGaa                                                    >  1:1303706/1‑139 (MQ=255)                                                                        gcgATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGaaaa                                                  >  1:148263/1‑139 (MQ=255)                                                                                        aGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAattgt                                                                                                                        >  2:917001/1‑53 (MQ=255)                                                                                        aGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAattgt                                                                                                                        <  1:917001/53‑1 (MQ=255)                                                                                        aGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTa                                                                                                    <  1:1245074/73‑1 (MQ=255)                                                                                        aGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTa                                                                                                    >  2:1245074/1‑73 (MQ=255)                                                                                             tCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATc                             <  2:618778/139‑1 (MQ=255)                                                                                                ttGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCt                          <  2:148263/139‑1 (MQ=255)                                                                                                ttGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCt                          <  2:1303706/139‑1 (MQ=255)                                                                                                 tGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCta                         >  2:1396254/1‑139 (MQ=255)                                                                                                  gCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCtat                        <  1:1396254/139‑1 (MQ=255)                                                                                                     cTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTCCAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCTATATc                     <  2:1004438/139‑1 (MQ=255)                                                                                                      tGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACAct                                                                                                          >  1:1209547/1‑53 (MQ=255)                                                                                                      tGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACAct                                                                                                          <  2:1209547/53‑1 (MQ=255)                                                                                                        gATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTa                                                                                                              >  2:756985/1‑47 (MQ=255)                                                                                                        gATGACCAGTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTa                                                                                                              <  1:756985/47‑1 (MQ=255)                                                                                                                gTATTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCTATATCTACTATTATGt          >  2:1098399/1‑139 (MQ=255)                                                                                                                       cAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACag                                                                                                 <  1:1378020/45‑1 (MQ=255)                                                                                                                       cAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACag                                                                                                 >  2:1378020/1‑45 (MQ=255)                                                                                                                        aGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAACATTGCGTGGCCTCGTAATCGCTATATCTACTATTATGTCGCCTGaa  <  1:437572/139‑1 (MQ=255)                                                                                                                          gAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGc                                      <  2:1297991/101‑1 (MQ=255)                                                                                                                          gAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGc                                      >  1:1297991/1‑101 (MQ=255)                                                                                                                                tgtgtgtAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCTATATCTACTATTATGt          >  2:325172/1‑123 (MQ=255)                                                                                                                                tgtgtgtAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCTATATCTACTATTATGt          <  1:325172/123‑1 (MQ=255)                                                                                                                                        |                                                                                                                           TGGGGTGCCTTTGCCTTTATCTCTGACAGAGATAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCTATATCTACTATTATGTCGCCTGAA  >  NC_000913/1426153‑1426410

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: ‑