Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,347,069	G→A	*164* (TAG→TAA)	ptsN →	sugar‑specific enzyme IIA component of PTS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,347,069	0	G	A	100.0%	219.8 / NA	69	*164* (TAG→TAA)	ptsN	sugar‑specific enzyme IIA component of PTS
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (36/33);  total (36/33)

CTCTGTCGCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAGTTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGATATGGGTTTTTACTGCGTG  >  NC_000913/3346945‑3347201                                                                                                                             |                                                                                                                                     gtcggcaaccgtgggCGAAAGGTATGGCGGACAACCCCACCTGCCGCCGTTTACGCGCCGCCTAGAGCGATGAACAGCACTATCAAATCAATACTGATAACGAAGGTAATCAGGATGAAGGGTAATTATTCGGTAAGGt                                                                                                                        <  2:322386/126‑1 (MQ=255)    tGTCGCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGtctc                                                                                                                     >  1:184355/1‑139 (MQ=255)            gtggCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGAc                                                                                                             >  2:1258015/1‑139 (MQ=255)            gtggCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGAc                                                                                                             >  2:103501/1‑139 (MQ=255)            gtggCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGAc                                                                                                             >  1:916595/1‑139 (MQ=255)                     cGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTgagg                                                                                                    <  2:936143/139‑1 (MQ=255)                     cGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTgagg                                                                                                    <  1:1579676/139‑1 (MQ=255)                         tGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGaa                                                                                                >  2:147980/1‑139 (MQ=255)                          ggCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGaaa                                                                                               <  1:1097945/139‑1 (MQ=255)                          ggCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGaaa                                                                                               <  1:1258015/139‑1 (MQ=255)                          ggCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGaaa                                                                                               <  1:129245/139‑1 (MQ=255)                                 aaaaCCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACa                                                                                        <  1:103501/139‑1 (MQ=255)                                 aaaaCCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACa                                                                                        <  1:1729693/139‑1 (MQ=255)                                 aaaaCCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACa                                                                                        <  2:916595/139‑1 (MQ=255)                                   aaCCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATg                                                                                      <  2:1507439/139‑1 (MQ=255)                                         cTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGaaa                                                                                               <  1:1689740/124‑1 (MQ=255)                                         cTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGaaa                                                                                               >  2:1689740/1‑124 (MQ=255)                                                 gTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGt                                                                        >  2:150218/1‑139 (MQ=255)                                                  tttACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATg                                                                                                                         <  1:178602/89‑1 (MQ=255)                                                  tttACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATg                                                                                                                         >  2:178602/1‑89 (MQ=255)                                                  tttACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTc                                                                       >  2:1534073/1‑139 (MQ=255)                                                  tttACACGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACa                                                                                        >  1:1715504/1‑122 (MQ=255)                                                  tttACACGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACa                                                                                        <  2:1715504/122‑1 (MQ=255)                                                      cgcgCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTgagg                                                                                                    <  2:204625/106‑1 (MQ=255)                                                      cgcgCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTgagg                                                                                                    >  1:204625/1‑106 (MQ=255)                                                      cgcgCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCg                                                                   >  2:1728132/1‑139 (MQ=255)                                                       gcgcAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCgg                                                                  <  1:1534073/139‑1 (MQ=255)                                                                       tGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGTAGCGTAATTATTCGGTAATGTCTCTTCTAGATGTTGTGAGGAGAAACAGTCCATGGTACTGATGATCGTCAGCGGACGTtcaggttcaggt                                                  >  2:1229416/1‑139 (MQ=255)                                                                       tGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTa                                                                                          >  1:675981/1‑99 (MQ=255)                                                                       tGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTa                                                                                          <  2:675981/99‑1 (MQ=255)                                                                             gCTGTATCAAATCATTACGGATACCGAAGGTACTGCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCt                                            >  2:798406/1‑139 (MQ=255)                                                                                        tCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTgaggag                                                                                                  >  2:1482418/1‑74 (MQ=255)                                                                                        tCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTgaggag                                                                                                  <  1:1482418/74‑1 (MQ=255)                                                                                           ttACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGAc                                                                                                             >  2:1716354/1‑60 (MQ=255)                                                                                           ttACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGAc                                                                                                             <  1:1716354/60‑1 (MQ=255)                                                                                           ttACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCtgcgtgc                              >  1:319615/1‑139 (MQ=255)                                                                                           ttACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCtgcgtgc                              >  2:1260079/1‑139 (MQ=255)                                                                                            tACGGATACCGAAGGTACTCCGGATGAAGCGTAATTa                                                                                                                                   >  1:1436731/1‑37 (MQ=255)                                                                                            tACGGATACCGAAGGTACTCCGGATGAAGCGTAATTa                                                                                                                                   <  2:1436731/37‑1 (MQ=255)                                                                                               ggATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTg                          <  1:798406/139‑1 (MQ=255)                                                                                               ggATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTg                          <  1:1310962/139‑1 (MQ=255)                                                                                                 aTACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGa                        >  1:1038059/1‑139 (MQ=255)                                                                                                   aCCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACgttcaggt                                                        <  1:944281/105‑1 (MQ=255)                                                                                                   aCCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACgttcaggt                                                        >  2:944281/1‑105 (MQ=255)                                                                                                    ccGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGa                     >  2:587767/1‑139 (MQ=255)                                                                                                      gAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGata                   <  2:184355/139‑1 (MQ=255)                                                                                                         ggTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAg                                                                                                               <  2:1702842/44‑1 (MQ=255)                                                                                                         ggTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAg                                                                                                               >  1:1702842/1‑44 (MQ=255)                                                                                                              tCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCtgcgca                               >  2:1391003/1‑117 (MQ=255)                                                                                                              tCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCtgcgca                               <  1:1391003/119‑3 (MQ=255)                                                                                                              tCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGATATGGGtttt           >  1:245182/1‑139 (MQ=255)                                                                                                               ccGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCg                                                                   >  2:1042650/1‑82 (MQ=255)                                                                                                               ccGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCg                                                                   <  1:1042650/82‑1 (MQ=255)                                                                                                               ccGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGATATGGGttttt          >  1:722223/1‑139 (MQ=255)                                                                                                                  gATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGATATGGGTTTTTACt       <  2:722223/139‑1 (MQ=255)                                                                                                                   aTGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCg                                                                   <  2:386791/78‑1 (MQ=255)                                                                                                                   aTGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCg                                                                   >  1:386791/1‑78 (MQ=255)                                                                                                                   aTGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGATATGGGTTTTTACTg      <  1:150218/139‑1 (MQ=255)                                                                                                                    tGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGATATGGGTTTTTACTGc     >  1:1480703/1‑139 (MQ=255)                                                                                                                       aGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTgagg                                                                                                    >  1:1286509/1‑41 (MQ=255)                                                                                                                       aGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTgagg                                                                                                    <  2:1286509/41‑1 (MQ=255)                                                                                                                       aGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGaaa                                                                                               <  2:723934/46‑1 (MQ=255)                                                                                                                       aGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGaaa                                                                                               >  1:723934/1‑46 (MQ=255)                                                                                                                       aGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTaa                                                <  2:655424/93‑1 (MQ=255)                                                                                                                       aGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTaa                                                >  1:655424/1‑93 (MQ=255)                                                                                                                       aGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGATATGGGTTTTTACTGCg    >  2:840829/1‑137 (MQ=255)                                                                                                                       aGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGATATGGGTTTTTACTGCg    <  1:840829/137‑1 (MQ=255)                                                                                                                       aGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGATATGGGTTTTTACTGCGTg  >  2:959948/1‑139 (MQ=255)                                                                                                                       aGCGTAATTATTCGGTAATGTCTCGTTTAGACGCTGTGAGGAGAAACAGTACACGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGATATGGGTTTTTACTGCGTg  >  2:95476/1‑139 (MQ=255)                                                                                                                             |                                                                                                                                     CTCTGTCGCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAGTTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGATATGGGTTTTTACTGCGTG  >  NC_000913/3346945‑3347201

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑