Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,518,501	C→T	intergenic (‑15/+42)	aroB ← / ← aroK	3‑dehydroquinate synthase/shikimate kinase 1

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,518,501	0	C	T	100.0%	99.5 / NA	30	intergenic (‑15/+42)	aroB/aroK	3‑dehydroquinate synthase/shikimate kinase 1
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (17/13);  total (17/13)

GGCTTTTATACTGCTCGCCGTCAGGGAGGATAACGCTATCGACGTTAACACCCGCCTGTTCAAGTACGCCGCGGACCTTATCGAGATACAGAGGAGCCAGGGTTTCGTTGGTGACCAACATGACCTGCTCGCCCGATTTCAGCGGTAAGAATGAAGCTGGTTCATTAAACAAACCAGATGCGATGGTAATTGGGTAACTACGTTCCCCGAGAGTAACGACAATCCTCTCCATAACGCGACATCCACCTTAATTACTGTACCCGCAGACGAGTGTATATAAAGCCAGAATTAGTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTCTTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGTTTTTTATCACGCTGCGTGCGTGCAAGTTGCTTT  >  NC_000913/3518255‑3518741                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                                 ggCTTTTATACTGCTCGCCGTCAGGGAGGATAACGCTATCGACGTAAACACCCGCCTGTTCAAGTACGCCGCGGACCTTATCGAGATACAGAGGAGCCAGGGTTTCGTTGGTGACCAACATGACCTGCTCGCCCGATTTCAGCGGTAAGAATGAAGCTGGTTCATTAAACAAACCAGATGCGATGGTAATTGGGTAACTACGTTCCCCGAGAGTAACGACAATCCTCTCCATAACGCGACATCCACTTTaa                                                                                                                                                                                                                                              <  1:145487/251‑1 (MQ=255)                       ggggAGGATAACGCTATCGACGTTAACACCCGCCTGTTCAAGTACGCCGCGGACCTTATCGAGATACAGAGGAGCCAGGGTTTCGTTGGTGACCAACATGACCTGCTCGCCCGATTTCAGCGGTAAGAATGAAGCTGGTTCATTAAACAAACCAGATGCGATGGTAATTGGGTAACTACGTTCCCCGAGAGTAACGACAATCCTCTCCATAACGCGACATCCACTTTAATTACTGTACCCGCAGACGAgtg                                                                                                                                                                                                                        <  1:174017/250‑1 (MQ=255)                       aGGGAGGATAACGCTATCGACGTTAACACCCGCCTGTTCAAGTACGCCGCGGACCTTATCGAGATACAGAGGAGCCAGGGTTTCGTTGGTGACCAACATGACCTGCTCGCCCGATTTCAGCGGTAAGAATGAAGCTGGTTCATTAAACAAACCAGATGCGATGGTAATTGGGTAACTACGTTCCCCGAGAGTAACGACAATCCTCTCCATAACGCGACATCCACTTTAATTACTGTACCCGCAGACGAgtg                                                                                                                                                                                                                        >  2:302091/1‑251 (MQ=255)                                                  ccccGCCTGTTCAAGTACGCCGCGGACCTTATCGAGATACAGAGGAGCCAGGGTTTCGTTGGTGACCAACATGACCTGCTCGCCCGATTTCAGCGGTAAGAATGAAGCTGGTTCATTAAACAAACCAGATGCGATGGTAATTGGGTAACTACGTTCCCCGAGAGTAACGACAATCCTCTCCATAACGCGACATCCACTTTAATTACTGTACCCGCAGACGAGTGTATATAAAGCCAGAATTAGTTGCTTTc                                                                                                                                                                                             <  2:71838/250‑1 (MQ=255)                                                                  aCGCCGCGGACCTTATCGAGATACAGAGGAGCCAGGGTTTCGTTGGTGACCAACATGACCTGCTCGCCCGATTTCAGCGGTAAGAATGAAGCTGGTTCATTAAACAAACCAGATGCGATGGTAATTGGGTAACTACGTTCCCCGAGAGTAACGACAATCCTCTCCATAACGCGACATCCACTTTAATTACTGTACCCGCAGACGAGTGTATATAAAGCCAGAATTAGTTGCTTTCCAGCATGTGaataat                                                                                                                                                                              <  1:83656/250‑1 (MQ=255)                                                                           ccactATCGATATGCAGAGGAGCCAGGGCGTTGTTGGTGCCCAACATGACCTGCTCGCTCGATTTCAGAGGTAAGAATGAAGCTGGGTCATTAAACAAACAAGATGCGATGGTAATTGGGTAACTACGTTCCCCGAGAGCAACAACAATCCTCTCCATAACGCGCCATCCACTTTAATTACTGTACCCGAAGCAGCGTGTATATACAGCCAGAATAAGTTGCTTTCGAGAATGTGAATACTATGGTTTGc                                                                                                                                                                     >  2:305376/5‑250 (MQ=255)                                                                                                   aGGGTTTCGTTGGTGACCAACATGACCTGCTCGCCCGATTTCAGCGGTAAGAATGAAGCTGGTTCATTAAACAAACCAGATGCGATGGTAATTGGGTAACTACGTTCCCCGAGAGTAACGACAATCCTCTCCATAACGCGACATCCACTTTAATTACTGTACCCGCAGACGAGTGTATATAAAGCCAGAATTAGTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGatcatc                                                                                                                                             >  1:216176/1‑250 (MQ=255)                                                                                                        ttCGTTGGTGACCAACATGACCTGCTCGCCCGATTTCAGCGGTAAGAATGAAGCTGGTTCATTAAACAAACCAGATGCGATGGTAATTGGGTAACTACGTTCCCCGAGAGTAACGACAATCCTCTCCATAACGCGACATCCACTTTAATTACTGTACCCGCAGACGAGTGTATATAAAGCCAGAATTAGTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGTTCATCAGTAc                                                                                                                                        <  1:12999/250‑1 (MQ=255)                                                                                                                    cAACATGACCTGCTCGCCCGATTTCAGCGGTAAGAATGAAGCTGGTTCATTAAACAAACCAGATGCGATGGTAATTGGGTAACTACGTTCCCCGAGAGTAACGACAATCCTCTCCATAACGCGACATCCACTTTAATTACTGTACCCGCAGACGAGTGTATATAAAGCCAGAATTAGTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTc                                                                                                                           <  1:261469/251‑1 (MQ=255)                                                                                                                    cAACATGACCTGCTCGCCCGATTTCAGCGGTAAGAATGAAGCTGGTTCATTAAACAAACCAGATGCGATGGTAATTGGGTAACTACGTTCCCCGAGAGTAACGACAATCCTCTCCATAACGCGACATCCACTTTAATTACTGTACCCGCAGACGAGTGTATATAAAGCCAGAATTAGTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTc                                                                                                                           >  1:110413/1‑251 (MQ=255)                                                                                                                           aCCTGCTCGCCCGATTTCAGCGGTAAGAATGAAGCTGGTTCATTAAACAAACCAGATGCGATGGTAATTGGGTAACTACGTTCCCCGAGAGTAACGACAATCCTCTCCATAACGCGACATCCACTTTAATTACTGTACCCGCAGACGAGTGTATATAAAGCCAGAATTAGTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAAtc                                                                                                                    <  1:257011/251‑1 (MQ=255)                                                                                                                                       gATTTCAGCGGTAAGAATGAAGCTGGTTCATTAAACAAACCAGATGCGATGGTAATTGGGTAACTACGTTCCCCGAGAGTAACGACAATCCTCTCCATAACGCGACATCCACTTTAATTACTGTACCCGCAGACGAGTGTATATAAAGCCAGAATTAGTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTCTTCATACAGc                                                                                                        >  2:85211/1‑251 (MQ=255)                                                                                                                                                        tGAAGCTGGTTCATTAAACAAACCAGATGCGATGGTAATTGGGTAACTACGTTCCCCGAGAGTAACGACAATCCTCTCCATAACGCGACATCCACTTTAATTACTGTACCCGCAGACGAGTGTATATAAAGCCAGAATTAGTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTCTTCATACAGCGGATTGCGTTCATTGGc                                                                                       >  1:282036/1‑251 (MQ=255)                                                                                                                                                         gAAGCTGGTTCATTAAACAAACCAGATGCGATGGTAATTGGGTAACTACGTTCCCCGAGAGTAACGACAATCCTCTCCATAACGCGACATCCACTTTAATTACTGTACCCGCAGACGAGTGTATATAAAGCCAGAATTAGTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTCTTCATACAGCGGATTGCGTTCATTGGcc                                                                                      >  1:92375/1‑251 (MQ=255)                                                                                                                                                             cTGGTTCATTAAACAAACCAGATGCGATGGTAATTGGGTAACTACGTTCCCCGAGAGTAACGACAATCCTCTCCATAACGCGACATCCACTTTAATTACTGTACCCGCAGACGAGTGTATATAAAGCCAGAATTAGTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTCTTCATACAGCGGATTGCGTTCATTGGCCAACg                                                                                  >  2:305416/1‑251 (MQ=255)                                                                                                                                                                  tCATTAAACAAACCAGATGCGATGGTAATTGGGTAACTACGTTCCCCGAGAGTAACGACAATCCTCTCCATAACGCGACATCCACTTTAATTACTGTACCCGCAGACGAGTGTATATAAAGCCAGAATTAGTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTCTTCATACAGCGGATTGCGTTCATTGGCCAACGCTTc                                                                              <  1:13097/250‑1 (MQ=255)                                                                                                                                                                      tAAACAAACCAGATGCGATGGTAATTGGGTAACTACGTTCCCCGAGAGTAACGACAATCCTCTCCATAACGCGACATCCACTTTAATTACTGTACCCGCAGACGAGTGTATATAAAGCCAGAATTATTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTCTTCCTACATCGGATTGCGGTCATTGGCCACCGCTTCCAGa                                                                          >  1:1138/1‑250 (MQ=255)                                                                                                                                                                      tAAACAAACCAGATGCGATGGTAATTGGGTAACTACGTTCCCCGAGAGTAACGACAATCCTCTCCATAACGCGACATCCACTTTAATTACTGTACCCGCAGACGAGTGTATATAAAGCCAGAATTAGTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTCTTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGa                                                                          >  1:246370/1‑250 (MQ=255)                                                                                                                                                                       aaacaaacCAGATGCGATGGTAATTGGGTAACTACGTTCCCCGAGAGTAACGACAATCCTCTCCATAACGCGACATCCACTTTAATTACTGTACCCGCAGACGAGTGTATATAAAGCCAGAATTAGTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTCTTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAAc                                                                        >  2:116954/1‑251 (MQ=255)                                                                                                                                                                                      gATGGTAATTGGGTAACTACGTTCCCCGAGAGTAACGACAATCCTCTCCATAACGCGACATCCACTTTAATTACTGTACCCGCAGACGAGTGTATATAAAGCCAGAATTAGTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTCTTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGgtgt                                                         >  1:15076/1‑251 (MQ=255)                                                                                                                                                                                            aaTTGGGTAACTACGTTCCCCGAGAGTAACGACAATCCTCTCCATAACGCGACATCCACTTTAATTACTGTACCCGCAGACGAGTGTATATAAAGCCAGAATTAGTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTCTTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAAc                                                   >  2:10467/1‑251 (MQ=255)                                                                                                                                                                                                         cGTTCCCCGAGAGTAACGACAATCCTCTCCATAACGCGACATCCACTTTAATTACTGTACCCGCAGACGAGTGTATATAAAGCCAGAATTAGTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTCTTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACggg                                      >  1:236627/1‑251 (MQ=255)                                                                                                                                                                                                               ccGAGAGTAACGACAATCCTCTCCATAACGCGACATCCACTTTAATTACTGTACCCGCAGACGAGTGTATATAAAGCCAGAATTAGTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTCTTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGtttt                                >  1:20515/1‑251 (MQ=255)                                                                                                                                                                                                                         cGACAATCCTCTCCATAACGCGACATCCACTTTAATTACTGTACCCGCAGACGAGTGTATATAAAGCCAGAATTAGTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGGTCATCAGTACGAATGGTCACGTCGGCAATCTCTTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGTTTTTTATCACGCt                      <  2:216176/251‑1 (MQ=255)                                                                                                                                                                                                                                  tctcCATAACGCGACATCCACTTTAATTACTGTCCCCGCAGACGAGTGTATATAAAGCCAGCATTAGTTGCTTTCCCGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTCTTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGTTTTTTATCACGCTGcgtgcgtg             >  2:151289/1‑251 (MQ=255)                                                                                                                                                                                                                                       aTAACGCGACATCCACTTTAATTACTGTACCCGCAGACGAGTGTATATAAAGCCAGAATTAGTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTCTTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCAcgc                                                                 <  1:65532/194‑1 (MQ=255)                                                                                                                                                                                                                                       aTAACGCGACATCCACTTTAATTACTGTACCCGCAGACGAGTGTATATAAAGCCAGAATTAGTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTCTTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCAcgc                                                                 >  2:65532/1‑194 (MQ=255)                                                                                                                                                                                                                                         aaCGCGACATCCACTTTAATTACTGTACCCGCAGACGAGTGTATATAAAGCCAGAATTAGTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTCTTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGTTTTTTATCACGCTGCGTGCGTGCAAGtt       <  1:251523/250‑1 (MQ=255)                                                                                                                                                                                                                                         aaCGCGACATCCACTTTAATTACTGTACCCGCAGACGAGTGTATATAAAGCCAGAATTAGTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTCTTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGTTTTTTATCACGCTGCGTGCGTGCAAGTTg      <  1:305416/251‑1 (MQ=255)                                                                                                                                                                                                                                             cgACATCCACTTTAATTACTGTACCCGCAGACGAGTGTATATAAAGCCAGAATTAGTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTCTTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGTTTTTTATCACGCTGCGTGCGTGCAAGTTGCttt  <  1:302091/251‑1 (MQ=255)                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                                 GGCTTTTATACTGCTCGCCGTCAGGGAGGATAACGCTATCGACGTTAACACCCGCCTGTTCAAGTACGCCGCGGACCTTATCGAGATACAGAGGAGCCAGGGTTTCGTTGGTGACCAACATGACCTGCTCGCCCGATTTCAGCGGTAAGAATGAAGCTGGTTCATTAAACAAACCAGATGCGATGGTAATTGGGTAACTACGTTCCCCGAGAGTAACGACAATCCTCTCCATAACGCGACATCCACCTTAATTACTGTACCCGCAGACGAGTGTATATAAAGCCAGAATTAGTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTCTTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGTTTTTTATCACGCTGCGTGCGTGCAAGTTGCTTT  >  NC_000913/3518255‑3518741

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑