Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP006881	2,185,916	C→G	S395S (TCG→TCC)	U712_10955 ←	3‑phosphoshikimate 1‑carboxyvinyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP006881	2,185,916	0	C	G	100.0%	165.0 / NA	51	S395S (TCG→TCC)	U712_10955	3‑phosphoshikimate 1‑carboxyvinyltransferase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base G (17/34);  total (17/34)

GCATTCTGCACAAAAAATCCTGAAGGAAAATCTTCAGGATTTGTTTGAAAGCTTATTTAAATGCTCGAAAAAGGTTGGATAAGAAACGTGAATGGCATCTGTCTGCTCAATTTCAATTGGCTCTTCAGTTATACACGAAGCGATACCAAGCATCATTCCGATTCGATGATCTCCATGGCTGGACACTGTTGCGCCGCCTCTCAGTGTTTGCTTGCCATAAACCTTCATTCCATCTGCTGTCGGTTCAATCTCAGCACCT  >  CP006881/2185781‑2186039                                                                                                                                        |                                                                                                                            atgatCTGCATAAAAAATCCTGAAGTAAAA‑CTTCAGGATTTTTTCGAAAGCTTATTTAAATGCTCGAAGAAGGTTGGATAAGAAACGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAg                                                                                                                         >  3:287422/5‑139 (MQ=255) atgatCTGCATAAAAAATCCTGAAGTAAAA‑CTTCAGGATTTTTTCGAAAGCTTATTTAAATGCTCGAAGAAGGTTGGATAAGAAACGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAg                                                                                                                         >  3:281509/5‑139 (MQ=255)  tgatCTGCATAAAAAATCCTGAAGTAAAA‑CTTCAGGATTTTTTCGAAAGCTTATTTAAATGCTCGAAGAAGGTTGGATAAGAAACGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAg                                                                                                                         <  7:210510/135‑1 (MQ=255)  tgatCTGCATAAAAAATCCTGAAGTAAAA‑CTTCAGGATTTTTTCGAAAGCTTATTTAAATGCTCGAAGAAGGTTGGATAAGAAACGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAg                                                                                                                         <  6:228438/135‑1 (MQ=255)  tgatCTGCATAAAAAATCCTGAAGTAAAA‑CTTCAGGATTTTTTCGAAAGCTTATTTAAATGCTCGAAGAAGGTTGGATAAGAAACGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAg                                                                                                                         <  4:157767/135‑1 (MQ=255)  tgatCTGCATAAAAAATCCTGAAGTAAAA‑CTTCAGGATTTTTTCGAAAGCTTATTTAAATGCTCGAAGAAGGTTGGATAAGAAACGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAg                                                                                                                         <  8:250184/135‑1 (MQ=255)  tgatCTGCATAAAAAATCCTGAAGTAAAA‑CTTCAGGATTTTTTCGAAAGCTTATTTAAATGCTCGAAGAAGGTTGGATAAGAAACGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAg                                                                                                                         <  3:315626/135‑1 (MQ=255)       tGCATAAAAAATCCTGAAGTAAAA‑CTTCAGGATTTTTTCGAAAGCTTATTTAAATGCTCGAAGAAGGTGGGATAAGAAACGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATAc                                                                                                                   >  3:82397/1‑139 (MQ=255)         cataaaaatTTCTGAATTAAAA‑CTTCAGGATTTTTTCGAAAGCTTATTTAAATGCTCTAAGAAGGTTGGATATGAATCGTGAATGGCATGCGTGTGCTCGATTTCAATCGGCTGCTCCGTTATACAGGAAGCAATAcc                                                                                                                  <  1:153485/135‑1 (MQ=255)         cataaaaaaTCCTGAAGTAAAA‑CTTCAGGATTTTTTCGAAAGCTTATTTAAATGCTCGAAGAAGGTTGGATAAGAAACGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATAcc                                                                                                                  >  1:153181/4‑138 (MQ=255)         cataaaaaaTCCTGAAGTAAAA‑CTTCAGGATTTTTTCGAAAGCTTATTTAAATGCTCGAAGAAGGTTGGATAAGAAACGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATAcc                                                                                                                  <  7:123030/135‑1 (MQ=255)         cataaaaaaTCCTGAAGTAAAA‑CTTCAGGATTTTTTCGAAAGCTTATTTAAATGCTCGAAGAAGGTTGGATAAGAAACGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATAcc                                                                                                                  >  5:37440/4‑138 (MQ=255)         cataaaaaaTCCTGAAGTAAAA‑CTTCAGGATTTTTTCGAAAGCTTATTTAAATGCTCGAAGAAGGTTGGATAAGAAACGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATAcc                                                                                                                  <  3:348155/135‑1 (MQ=255)         cataaaaaaTCCTGAAGTAAAA‑CTTCAGGATTTTTTCGAAAGCTTATTTAAATGCTCGAAGAAGGTTGGATAAGAAACGTGAATGGCATCAGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATACCa                                                                                                                 <  3:248194/136‑1 (MQ=255)         cataaaaaaTCCTGAA‑GTAAATCTTCAGGATTTTTTCGTTAGCTTATTTAAATGCTCGAAGAAGGTTGGATAAGAAACGTGAATGTCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATAcc                                                                                                                  <  2:67735/135‑1 (MQ=255)                        aagtaaaaCTTCAGGATTTTTTCGAAAGCTTATTTAAATGCTCGAAGAAGGTTGGATAAGAAACGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATACCAAGCATCATTCCg                                                                                                     <  3:207313/133‑1 (MQ=255)                         agtaaaaCTTCAGGATTTTTTCGAAAGCTTATTTAAATGCTCGAAGAAGGTTGGATAAGAAACGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATACCAAGCATCATTCCGAtt                                                                                                  <  4:220739/136‑1 (MQ=255)                             aaacTTCAGGATTTTTTCGAAAGCTTATTTAAATGCTCGAAGAAGGTTGGATAAGAAACGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATACCAAGCATCATTCCGATTCgat                                                                                              >  6:128842/4‑139 (MQ=255)                                  tCAGGATTTTTTCGAAAGCTTATTTAAATGCTCGAAGAAGGTTGGATAAGAAACGTGAATGGCATCCGAGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATACCAAGCATCATTCCGATTCGATGAtct                                                                                         >  7:99958/1‑139 (MQ=255)                                    aGGATTTTTTCGAAAGCTTATTTAAATGCTCGAAGAAGGTTGGATAAGAAACGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATACCAAGCATCATTCCGATTCGATGAtctc                                                                                        <  6:37440/138‑1 (MQ=255)                                     ggATTTTTTCGAAAGCTTATTTAAATGCTCGAAGAAGGTTGGATAAGAAACGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATACCAAGCATCATTCCGATTCGATGATCTccg                                                                                      <  2:235710/139‑2 (MQ=255)                                              cgAAAGCTTATTTAAATGCTCGAAGAAGGTTGGATAAGAAACGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATACCAAGCATCATTCCGATTCGATGATCTCCGTGGCTGGa                                                                              <  7:199228/137‑1 (MQ=255)                                              cgAAAGCTTATTTAAATGCTCGAAGAAGGTTGGATAAGAAACGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATACCAAGCATCATTCCGATTCGATGATCTCCGTGGCTGGa                                                                              <  8:370249/137‑1 (MQ=255)                                              cgAAAGCTTATTTAAATGCTCGAAGAAGGTTGGATAAGAAACGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATACCAAGCATCATTCCGATTCGATGATCTCCGTGGCTGGa                                                                              <  7:428395/137‑1 (MQ=255)                                                        tttAAATGCTCGAAGAAGGTTGGATAAGAAAAGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGAAATAACAAGCATCATTCCGATTCGATTATCTCCGTGGCTGGACACTgcagctc                                                                   <  3:120465/139‑7 (MQ=255)                                                                 tCGAAGAAGGTTGGATAAGAAACGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATACCAAGCATCATTCCGATTCGATGATCTCCGTGGCTGGACACTGCAGCGCCGCCtttc                                                           >  2:14393/1‑138 (MQ=255)                                                                          gTTGGATAAGAAACGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATACCAAGCATCATTCCGATTCGATGATCTCCGTGGCTGGACACTGCAGCGCCGCCTTTCAACGTttgtt                                                 >  3:201102/1‑137 (MQ=255)                                                                          gTTGGATAAGAAACGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATACCAAGCATCATTCCGATTCGATGATCTCCGTGGCTGGACACTGCAGCGCCGCCTTTCAACGTttgtt                                                 <  4:82397/139‑3 (MQ=255)                                                                          gTTGGATAAGAAACGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATACCAAGCATCATTCCGATTCGATGATCTCCGTGGCTGGACACTGCAGCGCCGCCTTTCAACGTttgtt                                                 <  1:14393/139‑3 (MQ=255)                                                                              gATAAGAAACGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATACCAAGCATCATTCCGATTCGATGAtctc                                                                                        <  5:232981/96‑1 (MQ=255)                                                                              gATAAGAAACGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATACCAAGCATCATTCCGATTCGATGAtctc                                                                                        >  6:232981/1‑96 (MQ=255)                                                                               aTAAGAAACGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATACCAAGCATCATTCCGATTCGATGATCTCCGTGGCTGGACACTGCAGCGCCGCCTTTCAACGTTTGTTTGCCa                                            <  2:316471/139‑1 (MQ=255)                                                                                  atataCGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATACCAAGCATCATTCCGATTCGATGATCTCCGTGGCTGGACACTGCAGCGCCTCCTTTCAACGTTTGTTTGACATa                                          <  3:343508/134‑1 (MQ=255)                                                                                  aGAAACGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATACCAAGCATCATTCCGATTCGATGATCTCCGTGGCTGGACACTGCAGCGCCGCCTTTCAACGTTTGTTTGCCATa                                          <  7:49515/138‑1 (MQ=255)                                                                                  aGAAACGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATACCAAGCATCATTCCGATTCGATGATCTCCGTGGCTGGACACTGCAGCGCCGCCTTTCAACGTTTGTTTGCCATa                                          <  5:128842/138‑1 (MQ=255)                                                                                  aGAAACGTGAATCGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATACCAAGCATCATTCCGATTCGATGATCTCCGTGGCTGGACACTGCAGCGCCGCCTTTCAACGTTTGTTTGCCATa                                          <  4:429507/138‑1 (MQ=255)                                                                                   gAAACGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATACCAAGCATCATTCCGATTCGATGATCTCCGTGGCTGGACACTGCAGCGCCGCCTGTCAACGTTTGTTTGCCATaaa                                        >  4:94415/1‑139 (MQ=255)                                                                                      aCGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATACCAAGCATCATTCCGATTCGATGATCTCCGTGGCTGGACACTGCAGCGCCGCCTTTCAACGTTTGTTTGCCATAAACCt                                     <  4:281509/139‑1 (MQ=255)                                                                                      aCGTGAATGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATACCAAGCATCATTCCGATTCGATGATCTCCGTGGCTGGACACTGCAGCGCCGCCTTTCAACGTTTGTTTGCCATAAACCt                                     <  4:287422/139‑1 (MQ=255)                                                                                           aaTGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATACCAAGCATCATTCCGATTCGATGATCTCCGTGGCTGGACACTGCAGCGCCGCCtttc                                                           <  8:70007/112‑1 (MQ=255)                                                                                           aaTGGCATCCGTGTGCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATACCAAGCATCATTCCGATTCGATGATCTCCGTGGCTGGACACTGCAGCGCCGCCtttc                                                           >  7:70007/1‑112 (MQ=255)                                                                                                     gtgtgCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATACCAAGCATCATTCCGATTCGATGATCTCCGTGGCTGGACACTGCAGCGCCGCcttt                                                            >  4:374271/4‑99 (MQ=255)                                                                                                     gtgtgCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATACCAAGCATCATTCCGATTCGATGATCTCCGTGGCTGGACACTGCAGCGCCGCcttt                                                            <  3:374271/98‑3 (MQ=255)                                                                                                      tgtgCTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATACCAAGCATCATTCCGATTCGATGATCTCCGTGGCTGGACACTGCAGCGCCGCCTTTCAACGTTTGTTTGCCATAAACCTTCATTCCATCTGCTGt                     <  6:349229/137‑1 (MQ=255)                                                                                                          cTCGATTTCAATCGGCTCCTCCGTTATACAGGAAGCAATACCAAGCATCATTCCGATTCGATGATCTCCGTGGCTGGACACTGCAGCGCCGCCTTTCAACGTTTGTTTGCCATAAACCTTCATTCCATCTGCTGTCGGt                 >  5:314198/1‑139 (MQ=255)                                                                                                                  caatcGGCTCCTCCGTTATACAGGAAGCAATACCAAGCATCATTCCGATTCGATGATCTCCGTGGCTGGACACTGCAGCGCCGCCTTTCAACGTTTGTTTGCCATAAACCTTCATTCCATCTGCTGTCGGTTCAAttt          >  7:319080/1‑136 (MQ=255)                                                                                                                  caatcGGCTCCTCCGTTATACAGGAAGCAATACCAAGCATCATTCCGATTCGATGATCTCCGTGGCTGGACACTGCAGCGCCGCCTTTCAACGTTTGTTTGCCATAAACCTTCATTCCATCTGCTGTCGGTTCAAttt          >  4:34871/1‑136 (MQ=255)                                                                                                                       ggCTCCTCCGTTATACAGGAAGCAATACCAAGCATCATTCCGATTCGATGATCTCCGTGGCTGGACACTGCAGCGCCGCCTTTCAACGTTTGTTTGCCATAAACCTTCATTCCATCTGCTGTCGGTTCAATTTCAGCAc    <  2:153181/139‑1 (MQ=255)                                                                                                                       ggCTCCTCCGTTATAACGGAAGCAATACCAAGCATCATTCCGATTCGATGATCTCCGTGGCTGGACACTGCAGCGCCGCCTTTCAACGTTTGTTTGCCATAAACCTTCATTCCATCTGCTGTCGGTTCAATTTCAGCAc    <  8:392068/139‑1 (MQ=255)                                                                                                                                 ttATACAGGAAGCAATACCAAGCATCATTCCGATTCGATGATCTCCGTGGCTGGACACTGCAGCGCCGCCTTTCAACGTTTGTTTGCCATAAACCTTCATTCCATCTGCTGTCGGTTCAATTTCAGCAccc  >  2:370813/1‑130 (MQ=255)                                                                                                                                 ttATACAGGAAGCAATACCAAGCATCATTCCGATTCGATGATCTCCGTGGCTGGACACTGCAGCGCCGCCTTTCAACGTTTGTTTGCCATAAACCTTCATTCCATCTGCTGTCGGTTCAATTTCAGCAccc  <  1:370813/131‑2 (MQ=255)                                                                                                                                        |                                                                                                                            GCATTCTGCACAAAAAATCCTGAAGGAAAATCTTCAGGATTTGTTTGAAAGCTTATTTAAATGCTCGAAAAAGGTTGGATAAGAAACGTGAATGGCATCTGTCTGCTCAATTTCAATTGGCTCTTCAGTTATACACGAAGCGATACCAAGCATCATTCCGATTCGATGATCTCCATGGCTGGACACTGTTGCGCCGCCTCTCAGTGTTTGCTTGCCATAAACCTTCATTCCATCTGCTGTCGGTTCAATCTCAGCACCT  >  CP006881/2185781‑2186039

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑