Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_pgi	4,234,667	Δ1 bp	intergenic (‑1434/‑499)	lysC ← / → yjbE	lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_pgi	4,234,666	0	A	.	100.0%	175.8 / NA	39	intergenic (‑1433/‑500)	lysC/yjbE	lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (20/19);  total (20/19)

GTCTATATACGCAGTAGAGATGCACCCCAAGGGCGTTTTATCCTTTTTACGAGATGTGGGCATCGCCTCTGTAAAACTGGCAGAGATTAGAGGCGTAAATCCCCTGGCCACCCCGAGAATAGATGCATTGAAGAG‑GCGCTTGCAGTGAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTATTCGGCAATTAATACATAGC  >  NC_000913_3_pae_pgi/4234519‑4234803                                                                                                                                                     |                                                                                                                                          gTCTATATACGCAGTAGAGATGCACCCCAAGGGCGTTTTATCCTTTTTACGAGATGTGGGCATCGCCTCTGTAAAACTGGCAGAGATTAGAGGCGTAAATCCCCTGGCCACCCCGAGAATAGATGCATTGAAGAG‑GCGCTTGCAGTGat                                                                                                                                          >  1:104468/1‑148 (MQ=255)     atataCGCAGTAGAGATGCACCCCAAGGGCGTTTTATCCTTTTTACGAGATGTGGGCATCGCCTCTGTAAAACTGGCAGAGATTAGAGGCGTAAATCCCCTGGCCACCCCGAGAATAGATGCATTGAAGAG‑GCGCTTGCAGTG‑atcatc                                                                                                                                     >  1:336420/1‑149 (MQ=255)      tataCGCAGTAGAGATGCACCCCAAGGGCGTTTTATCCTTTTTACGAGATGTGGGCATCGCCTCTGTAAAACTGGCAGAGATTAGAGGCGTAAATCCCCTGGCCACCCCGAGAATAGATGCATTGAAGAG‑GCGCTTGCAGTG‑ATCAtcg                                                                                                                                    <  1:479713/149‑1 (MQ=255)           gCAGTAGAGATGCACCCCAAGGGCGTTTTATCCTTTTTACGAGATGTGGGCATCGCCTCTGTAAAACTGGCAGAGATTAGAGGCGTAAATCCCCTGGCCACCCCGAGAATAGATGCATTGAAGAG‑GCGCTTGCAGTG‑ATCATCGTCGat                                                                                                                               <  2:336420/149‑1 (MQ=255)            cacaagagATGCACCCCAAGTGCGTTTTATCCTTTTTACGATATGTGGGCATCGCCTCTGTAAAACTGGCAGAGATTAGAGGCGTAAATCCCCTGGCCACCCCGAGAATAGATGCATTGAAGAG‑GCGCTTGCAGTG‑ATCATCGTCGata                                                                                                                              <  2:18741/145‑1 (MQ=255)                                ggCGTTTTATCCTTTTTACGAGATGTGGGCATCGCCTCTGTAAAACTGGCAGAGATTAGAGGCGTAAATCCCCTGGCCACCCCGAGAATAGATGCATTGAAGAG‑GCGCTTGCAGTG‑ATCATCGTCGATATGTAGGCCGGATAAGGCGtt                                                                                                          >  2:369527/1‑149 (MQ=255)                                     tttATCCTTTTTACGAGATGTGGGCATCGCCTCTGTAAAACTGGCAGAGATTAGAGGCGTAAATCCCCTGGCCACCCCGAGAATAGATGCATTGAAGAG‑GCGCTTGCAGTG‑ATCATCGTCGatat                                                                                                                             >  2:397819/1‑125 (MQ=255)                                     tttATCCTTTTTACGAGATGTGGGCATCGCCTCTGTAAAACTGGCAGAGATTAGAGGCGTAAATCCCCTGGCCACCCCGAGAATAGATGCATTGAAGAG‑GCGCTTGCAGTG‑ATCATCGTCGatat                                                                                                                             <  1:397819/125‑1 (MQ=255)                                       tATCCTTTTTACGAGATGTGGGCATCGCCTCTGTAAAACTGGCAGAGATTAGAGGCGTAAATCCCCTGGCCACCCCGAGAATAGATGCATTGAAGAG‑GCGCTTGCAGTG‑ATCATCGTCGATATGTAGGCCGGATAAGGCGTTCAcgccg                                                                                                   >  1:406805/1‑149 (MQ=255)                                                  cGAGATGTGGGCATCGCCTCTGTAAAACTGGCAGAGATTAGAGGCGTAAATCCCCTGGCCACCCCGAGAATAGATGCATTGAAGAG‑GCGCTTGCAGTG‑ATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAAc                                                                                        <  1:485828/149‑1 (MQ=255)                                                      aTGTGGGCATCGCCTCTGTAAAACTGGCAGAGATTAGAGGCGTAAATCCCCTGGCCACCCCGAGAATAGATGCATTGAAGAG‑GCGCTTGCAGTG‑ATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGAt                                                                                    >  1:427929/1‑149 (MQ=255)                                                       ggtgGGCATCGCGTCTGGAACACTGGCAGCGATGAGATGCGTAAATCCCCTGGCCACCCCGAGAATAGATGCATTGAAGAG‑GCGCTTGCAGTG‑ATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATg                                                                                   <  1:18738/148‑1 (MQ=38)                                                         tgGGCATCGCCTCTGTAAAACTGGCAGAGATTAGAGGCGTAAATCCCCTGGCCACCCCGAGAATAGATGCATTGAAGAG‑GCGCTGGCAGTG‑ATCATCCTCGATATGTAGGCCGGATAAGGCGTTCACGCAGCATCCGGCAACCGATGcc                                                                                 >  2:227929/1‑149 (MQ=255)                                                                         aaaaCTGGCAGAGATTAGAGGCGTAAATCCCCTGGCCACCCCGAGAATAGATGCATTGAAGAG‑GCGCTTGCAGTG‑ATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGAt                                                                                    <  1:449853/130‑1 (MQ=255)                                                                         aaaaCTGGCAGAGATTAGAGGCGTAAATCCCCTGGCCACCCCGAGAATAGATGCATTGAAGAG‑GCGCTTGCAGTG‑ATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGAt                                                                                    >  2:449853/1‑130 (MQ=255)                                                                              tGGCAGAGATTAGAGGCGTAAATCCCCTGGCCACCCCGAGAATAGATGCATTGAAGAG‑GCGCTTGCAGTG‑ATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCt                                                            >  2:80456/1‑149 (MQ=255)                                                                                  agagATTAGAGGCGTAAATCCCCTGGCCACCCCGAGAATAGATGCATTGATGCGCCCGCTT‑CAGTG‑ATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATc                                                        <  1:349748/149‑1 (MQ=25)                                                                                    agaTTAGAGGCGTAAATCCCCTGGCCACCCCGAGAATAGATGCATTGAAGAG‑GCGCTTGCAGTG‑ATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAg                                                      >  2:583924/1‑149 (MQ=255)                                                                                     gaTTAGAGGCGTAAATCCCCTGGCCACCCCGAGAATAGATGCATTGAAGAG‑GCGCTTGCAGTG‑ATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAgg                                                     <  2:406805/149‑1 (MQ=255)                                                                                      aTTAGAGGCGTAAATCCCCTGGCCACCCCGAGAATAGATGCATTGAAGAG‑GCGCTTGCAGTG‑ATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGc                                                    >  1:633738/1‑149 (MQ=255)                                                                                         agagGCGTAAATCCCCTGGCCACCCCGAGAATAGATGCATTGAAGAG‑GCGCTTGCAGTG‑ATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTa                                                 <  1:369527/149‑1 (MQ=255)                                                                                         agagGCGTAAATCCCCTGGCCACCCCGAGAATAGATGCATTGAAGAG‑GCGCTTGCAGTG‑ATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATAAGACGCGACCGCGTCGCATCAGGcatc                                                 <  1:18713/149‑4 (MQ=37)                                                                                             gCGTAAATCCCCTGGCCACCCCGAGAATAGATGCATTGAAGAG‑GCGCTTGGAGTG‑ATCATCGTCGATATGTAGGCCGGATAAGGCGTTCAGGCCCCATCCAGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCTGGCCTACCgg                                             >  2:285092/1‑149 (MQ=37)                                                                                                    tCCCCTGGCCACCCCGAGAATAGATGCATTGAAGAG‑GCGCTTGCAGTG‑ATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGc                                      <  1:80456/149‑1 (MQ=255)                                                                                                        cTGGCCACCCCGAGAATAGATGCATTGAAGAG‑GCGCTTGCAGTG‑ATCATCGTCGATATGTAGGCGGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGt                                            >  1:137530/1‑139 (MQ=255)                                                                                                        cTGGCCACCCCGAGAATAGATGCATTGAAGAG‑GCGCTTGCAGTG‑ATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGt                                            <  2:137530/139‑1 (MQ=255)                                                                                                            ccACCCCGAGAATAGATGCATTGAAGCG‑GCGCTTGCAGTG‑ATCAACGTCGATAGGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGCCGCGCGGCCGTCTTATCAGGCCTACACGTCCATTCCgctcgct                              >  1:306786/1‑143 (MQ=21)                                                                                                              aCCCCGAGAATAGATGCATTGAAGAG‑GCGCTTGCAGTG‑ATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATg                                                                            <  1:327902/101‑1 (MQ=255)                                                                                                              aCCCCGAGAATAGATGCATTGAAGAG‑GCGCTTGCAGTG‑ATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATg                                                                            >  2:327902/1‑101 (MQ=255)                                                                                                                 ccGAGGATAGATGCATTGAGGGG‑GCGCTTGCAGTG‑ATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATc                         <  1:113833/149‑1 (MQ=255)                                                                                                                 ccGAGAATAGATGCATTGAAGAG‑GCGCTTGCAGTG‑ATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATc                         >  1:623858/1‑149 (MQ=255)                                                                                                                   gagaATAGATGCATTGAAGAG‑GCGCTTGCAGTG‑ATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCgg                                                                    <  1:656517/104‑1 (MQ=255)                                                                                                                   gagaATAGATGCATTGAAGAG‑GCGCTTGCAGTG‑ATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCgg                                                                    >  2:656517/1‑104 (MQ=255)                                                                                                                   gagaATAGATGCATTGAAGAG‑GCGCTTGCAGTG‑ATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACAt                          <  2:489277/146‑1 (MQ=255)                                                                                                                   gagaATAGATGCATTGAAGAG‑GCGCTTGCAGTG‑ATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACAt                          >  1:489277/1‑146 (MQ=255)                                                                                                                                ttGAAGAG‑GCGCTTGCAGTG‑ATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATg                                                                            <  1:602271/83‑1 (MQ=255)                                                                                                                                ttGAAGAG‑GCGCTTGCAGTG‑ATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATg                                                                            >  2:602271/1‑83 (MQ=255)                                                                                                                                ttGAAGAG‑GCGCTTGCAGTG‑ATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACa                                               <  1:522572/112‑1 (MQ=255)                                                                                                                                ttGAAGAG‑GCGCTTGCAGTG‑ATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACa                                               >  2:522572/1‑112 (MQ=255)                                                                                                                                      ag‑GCGCTTGCAGTG‑ATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTATTCGGCAATTAATACATa    >  1:293032/1‑149 (MQ=255)                                                                                                                                         gcgcTTGCAGTG‑ATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTATTCGGCAATTAATACATAGc  >  1:56869/1‑149 (MQ=255)                                                                                                                                                     |                                                                                                                                          GTCTATATACGCAGTAGAGATGCACCCCAAGGGCGTTTTATCCTTTTTACGAGATGTGGGCATCGCCTCTGTAAAACTGGCAGAGATTAGAGGCGTAAATCCCCTGGCCACCCCGAGAATAGATGCATTGAAGAG‑GCGCTTGCAGTGAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTATTCGGCAATTAATACATAGC  >  NC_000913_3_pae_pgi/4234519‑4234803

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑