Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	1	1,558,978	C→T	P46P (CCG→CCA)	unknown ←	Phosphoglycerate transport system transcriptional regulatory protein PgtA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	1	1,558,978	0	C	T	100.0%	102.3 / NA	37	P46P (CCG→CCA)	unknown	Phosphoglycerate transport system transcriptional regulatory protein PgtA
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (18/19);  total (18/19)

AAGCGTTATCGACTTGAATAAGTAATTTTTCAGGGGAAACCGGTTTTTCAAAGAAATTTGTCGCCCCTTTCTTGACAGCTTCTACCGCCATGGGAACATCACCATGCCCGGTAATCATAATCACCGGAATTTGGCTATCCATTTCAATCATTCGATCTAATCATCTAATCCTGAAATGCCCAGCAATAATACGTCGCAAATCACAACGCCATACCAATTTTCCGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATACAGAATAGCCTTCTTGTTGTAATAAATCGGCATACGATTCCAAAATATCAAAATCATCATCAATTAATAAAACATTATTCTGATAATTAAACATTATCTACCACCTTAAATTCCAAAATAACCAGCGCATTTTTTGTCAATGTAGAAGCAATTAATAAGTTTCCTTGACATTGTTGCATAATGGATAGACTTATTGAT  >  1/1558756‑1559219                                                                                                                                                                                                                               |                                                                                                                                                                                                                                                  aaGCGTTATCGACTTGAATAAGTAATTTTTCAGGGGAAACCGGTTTTTCAAAGAAATTTGTCGCCCCTTTCTTGACAGCTTCTACCGCCATGGGAACATCACCATGCCCGGTAATCATAATCACCGGAATTTGGCTATCCATTTCAATCATTCGATCTAATCATCTAATCCTGAAATGCCCAGCAATAATACGTCGCAAATCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGtt                                                                                                                                                                                                                       <  1:384619/251‑1 (MQ=255)                      gTAATTTTTCAGGGGAAACCGGTTTTTCAAAGAAATTTGTCGCCCCTTTCTTGACAGCTTCTACCGCCATGGGAACATCACCATGCCCGGTAATCATAATCACCGGAATTTGGCTATCCATTTCAATCATTCGATCTAATCATCTAATCCTGAAATGCCCAGCAATAATACGTCGCAAATCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCa                                                                                                                                                                                                                  >  1:374872/1‑235 (MQ=255)                          tttttCAGGGGAAACCGGTTTTTCAAAGAAATTTGTCGCCCCTTTCTTGACAGCTTCTACCGCCATGGGAACATCACCATGCCCGGTAATCATAATCACCGGAATTTGGCTATCCATTTCAATCATTCGATCTAATCATCTAATCCTGAAATGCCCAGCAATAATACGTCGCAAATCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATACAGAATAGcc                                                                                                                                                                                              <  1:356504/251‑1 (MQ=255)                                  gggAAACCGGTTTTTCAAAGAAATTTGTCGCCCCTTTCTTGACAGCTTCTACCGCCATGGGAACATCACCATGCCCGGTAATCATAATCACCGGAATTTGGCTATCCATTTCAATCATTCGATCTAATCATCTAATCCTGAAATGCCCAGCAATAATACGTCGCAAATCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATACAGAATAGCcttctt                                                                                                                                                                                         <  1:422623/248‑1 (MQ=255)                                  gggAAACCGGTTTTTCAAAGAAATTTGTCGCCCCTTTCTTGACAGCTTCTACCGCCATGGGAACATCACCATGCCCGGTAATCATAATCACCGGAATTTGGCTATCCATTTCAATCATTCGATCTAATCATCTAATCCTGAAATGCCCAGCAATAATACGTCGCAAATCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATACAGAATAGCCTTCttg                                                                                                                                                                                        <  1:806412/249‑1 (MQ=255)                                                                  ccTTTCTTGACAGCTTCTACCGCCATGGGAACATCACCATGCCCGGTAATCATAATCACCGGAATTTGGCTATCCATTTCAATCATTCGATCTAATCATCTAATCCTGAAATGCCCAGCAATAATACGTCGCAAATCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATACAGAATAGCCTTCTTGTTGTAATAAATCGGCATACGATTCCAAAATATCa                                                                                                                                                      >  1:809233/1‑251 (MQ=255)                                                                    tttCTTGACAGCTTCTACCGCCATGGGAACATCACCATGCCCGGTAATCATAATCACCGGAATTTGGCTATCCATTTCAATCATTCGATCTAATCATCTAATCCTGAAATGCCCAGCAATAATACGTCGCAAATCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATAc                                                                                                                                                                                                       <  1:662463/200‑1 (MQ=255)                                                                                        ccATGGGAACATCACCATGCCCGGTAATCATAATCACCGGAATTTGGCTATCCATTTCAATCATTCGATCTAATCATCTAATCCTGAAATGCCCAGCAATAATACGTCGCAAATCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATACAGAATAGCCTTCTTGTTGTAATAAATCGGCATACGATTCCaaaa                                                                                                                                                           >  1:336973/1‑224 (MQ=255)                                                                                              gAACATCACCATGCCCGGTAATCATAATCACCGGAATTTGGCTATCCATTTCAATCATTCGATCTAATCATCTAATCCTGAAATGCCCAGCAATAATACGTCGCAAATCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATACAGAATAGCCTTCTTGTTGTAATAAATCGGCATACGATTCCAAAATATCAAAATCATCATCAATTAATAAAAc                                                                                                                               >  1:251361/1‑246 (MQ=255)                                                                                              gAACATCACCATGCCCGGTAATCATAATCACCGGAATTTGGCTATCCATTTCAATCATTCGATCTAATCATCTAATCCTGAAATGCCCAGCAATAATACGTCGCAAATCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTAGGCAGTTGCAAATACAGAATAGCCTTCTTGTTGTAATAAATCGGCATAc                                                                                                                                                                     >  1:710679/1‑208 (MQ=255)                                                                                                 cATCACCATGCCCGGTAATCATAATCACCGGAATTTGGCTATCCATTTCAATCATTCGATCTAATCATCTAATCCTGAAATGCCCAGCAATAATACGTCGCAAATCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATCCAGAATAGCCTTCTTGTTGTAATAAATCGGCATACGATTCCAAAATATCAAAATCATCATCAATTAATAAAAc                                                                                                                               >  1:449481/1‑243 (MQ=255)                                                                                                          gCCCGGTAATCATAATCACCGGAATTTGGCTATCCATTTCAATCATTCGATCTAATCATCTAATCCTGAAATGCCCAGCAATAATACGTCGCAAATCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAgg                                                                                                                                                                                                                         >  1:175362/1‑144 (MQ=255)                                                                                                          gCCCGGTAATCATAATCACCGGAATTTGGCTATCCATTTCAATCATTCGATCTAATCATCTAATCCTGAAATGCCCAGCAATAATACGTCGCAAATCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATACAGAATAGCCTTCTTGTTGTAATAAATCGGCATACGATTCCAAAATATCAAAATCATCATCAATTAATAAAACATTATTCTGATAATTaa                                                                                                              >  1:862093/1‑251 (MQ=255)                                                                                                            ccGGTAATCATAATCACCGGAATTTGGCTATCCATTTCAATCATTCGATCTAATCATCTAATCCTGAAATGCCCAGCAATAATACGTCGCAAATCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATACAGAATAGCCTTCTTGTTGTAATAAATCGGCATACGATTCCAAAATATCAAAATCATCATCAATTAATAAAACATTATTCTGATAATTAAAc                                                                                                            <  1:641197/251‑1 (MQ=255)                                                                                                                  atcataatcaCCGGAATTTGGCTATCCATTTCAATCATTCGATCTAATCATCTAATCCTGAAATGCCCAGCAATAATACGTCGCAAATCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGt                                                                                                                                                                                                                        <  1:47022/137‑1 (MQ=255)                                                                                                                  atcataatcaCCGGAATTTGGCTATCCATTTCAATCATTCGATCTAATCATCTAATCCTGAAATGCCCAGCAATAATACGTCGCAAATCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATACAGAATAGCct                                                                                                                                                                                             >  1:834136/1‑164 (MQ=255)                                                                                                                   tcataatcaCCGGAATTTGGCTATCCATTTCAATCATTCGATCTAATCATCTAATCCTGAAATGCCCAGCAATAATACGTCGCAAATCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATACAGAATAGCCTTCTTGTTGTAATAAATCGGCATACGATTCCAAAATATCAAAATCATCATCAATTAATAAAACATTATTCTGATAATTAAACATTATc                                                                                                      >  1:733873/1‑250 (MQ=255)                                                                                                                    cataatcaCCGGAATTTGGCTATCCATTTCAATCATTCGATCTAATCATCTAATCCTGAAATGCCCAGCAATAATACGTCGCAAATCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATACAGAATAGCCTTCTTGTTGTAATAAATCGGCATACGATTCCAAAATATCAAAATCATCATCAATtaat                                                                                                                                    <  1:201812/219‑1 (MQ=255)                                                                                                                        atcaCCGGAATTTGGCTATCCATTTCAATCATTCGATCTAATCATCTAATCCTGAAATGCCCAGCAATAATACGTCGCAAATCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATACAGAATAGCCTTCTTGTTGTAATAAATCGGCATACGATTCCAAAATATCAAAATCATCATCAATTAATAAAACATTATTCTGATAATTAAACATTATCTaccac                                                                                                <  1:116524/251‑1 (MQ=255)                                                                                                                                         aTCCATTTCAATCATTCGATCTAATCATCTAATCCTGAAATGCCCAGCAATAATACGTCGCAAATCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATACAGAATAGCCTTCttg                                                                                                                                                                                        <  1:780717/146‑1 (MQ=255)                                                                                                                                                           atctaatcatctaatcCTGAAATGCCCAGCAATAATACGTCGCAAATCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATACAGAATAGCCTTCTTGTTGTAATAAATCGGCATACGATTCCAAAATATCaaaa                                                                                                                                                   >  1:546426/1‑165 (MQ=255)                                                                                                                                                           atctaatcatctaatcCTGAAATGCCCAGCAATAATACGTCGCAAATCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATACAGAATAGCCTTCTTGTTGTAATAAATCGGCATACGATTCCAAAATATCAAAATCATCATCAATTAATAAAAc                                                                                                                               >  1:900887/1‑185 (MQ=255)                                                                                                                                                                    tctaatcCTGAAATGCCCAGCAATAATACGTCGCAAATCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATACAGAATAGCCTTCTTGTTGTAATAAATCGGCATACGATTCCAAAATATCAAAATCATCATCAATTAATAAAACATTATTCTGATAATTAAACATTATCTACCACCTTAAATTCCAAAATAACCAGCGTATTTTTTGTCAATGTAGAAg                                                    <  1:196323/251‑1 (MQ=255)                                                                                                                                                                                aTGCCCAGCAATAATACGTCGCAAATCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATACAGAATAGCCTTCTTGTTGTAATAAATCGGc                                                                                                                                                                         <  1:520114/122‑1 (MQ=255)                                                                                                                                                                                       gCAATAATACGTCGCAAATCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCaaa                                                                                                                                                                                                          >  1:525520/1‑82 (MQ=255)                                                                                                                                                                                       gCAATAATACGTCGCAAATCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATACAGAATAGCCTTCTTGTTGTAATAAATCGGCATACGATTCCAAAATATCAAAATCATCATCAATTAATAAAACATTATTCTGATAATTAAACATTATCTaccacc                                                                                               >  1:673823/1‑189 (MQ=255)                                                                                                                                                                                        cAATAATACGTCGCAAATCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATACAGAATAGCCTTCTTGTTGTAATAAATCGGCATACGATTCCAAAATATCAAAATCATCATCAATTAATAAAACATTATTCTGATAATTAAACATTATCTACCACCTTAAATTCCAAAATAACCAGCGTATTTTTTGTCAATGTAGAAGCAATTAATAAGTTTCCTTGa                                >  1:578002/1‑251 (MQ=255)                                                                                                                                                                                          ataataCGTCGCAAATCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATACAGAATAGCCTTCTTGTTGTAATAAATCGGCATACGATTCCAAAATATCAAAATCATCATCAATTAATAAAACATTATTCTGATAATTAAACATTATCTACCACCTTAAATTCCAAAATAACCAGCGTATTTTTTGTCAATGTAGaa                                                     <  1:737832/228‑1 (MQ=255)                                                                                                                                                                                           taataCGTCGCAAATCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATACAGAATAGCCTTCTTGTTGTAATAAATCGGCATACGATTCCAAAATATCAAAATCATCATCAATTAATAAAACATTATTCTGATAATTAAACATTATCTACCACCTTAAATTCCAAAATAACCAGCGTATTTTTTGTCAATGTAGAAGCAATTAATAAGTTTCCTTGACAt                             <  1:40952/251‑1 (MQ=255)                                                                                                                                                                                           taataCGTCGCAAATCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATACAGAATAGCCTTCTTGTTGTAATAAATCGGCATACGATTCCAAAATATCAAAATCATCATCAATTAATAAAACATTATTCTGATAATTAAACATTATCTACCACCTTAAATTCCAAAATAACCAGCGTATTTTTTGTCAATGTAGAAGCAATTAATAAGTTTCCTTGACAt                             <  1:261453/251‑1 (MQ=255)                                                                                                                                                                                                  tCGCAAATCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATACAGAATAGCCTTCTTGTTGTAATAAATCGGCATACGATTCCAAAATATCaaaa                                                                                                                                                   >  1:159826/1‑126 (MQ=255)                                                                                                                                                                                                  tCGCAAATCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATACAGAATAGCCTTCTTGTTGTAATAAATCGGCATACGATTCCAAAATATCAAAATCATCATCAATTAATAAAACATTATTCTGATAATTAAACAt                                                                                                          >  1:398626/1‑167 (MQ=255)                                                                                                                                                                                                         tCACAACGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATACAGAATAGCCTTCTTGTTGTAATAAATCGGCATACGATTCCAAAATATCAAAATCATCATCAATTAATAAAACATTATTCTGATAATTAAACATTATCTACCACCTTAAATTCCAAAATAACCAGCGTATTTTTTGTCAATGTAGAAGCAATtaata                                           <  1:763912/223‑1 (MQ=255)                                                                                                                                                                                                               cGCCATACCAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATACAGAATAGCCTTCTTGTTGTAATAAATCGGCATACGATTCCAAAATATCAAAATCATCATCAATTAATAAAACATTATTCTGATAATTAAACATTATCTACCACCTTAAATTCCAAAATAACCAGCGTATTTTTTGTCAATGTAGAAGCAATTAATAAGTTTCCTTGACATTGTTGCATAATGGATAGACt         <  1:837162/251‑1 (MQ=255)                                                                                                                                                                                                                      ccAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATACAGAATAGc                                                                                                                                                                                               >  1:788689/1‑62 (MQ=255)                                                                                                                                                                                                                      ccAATTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATACAGAATAGCCTTCTTGTTGTAATAAATCGGCATACGATTCCAAAATATCAAAATCATCATCAATTAATAAAACATTATTCTGATAATTAAACATTATCTACCACCTTAAATTCCAAAATAACCAGCGTATTTTTTGTCAATGTAGAAGCAATTAATAAGTTTCCTTGACATTGTTGCATAATGGATAGACTTATTGAt  <  1:103449/251‑1 (MQ=255)                                                                                                                                                                                                                         aTTTTCTGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATACAGAATAGCCTTCTTGTTGTAATAAATCGGCATACGATTCCAAAATATCAAAATCATCATCAATTAATAAAACATTATTCTGATAATTAAACATTATCTACCACCTTAAATTCCAAAATAACCAGCGTATTTTTTGTCAATGTAGAAGCAATTAATAAGt                                        <  1:178215/210‑1 (MQ=255)                                                                                                                                                                                                                               |                                                                                                                                                                                                                                                  AAGCGTTATCGACTTGAATAAGTAATTTTTCAGGGGAAACCGGTTTTTCAAAGAAATTTGTCGCCCCTTTCTTGACAGCTTCTACCGCCATGGGAACATCACCATGCCCGGTAATCATAATCACCGGAATTTGGCTATCCATTTCAATCATTCGATCTAATCATCTAATCCTGAAATGCCCAGCAATAATACGTCGCAAATCACAACGCCATACCAATTTTCCGGAATTTGATTAATAATCTCTTTAGGTTCGGCAGTTGCAAATACAGAATAGCCTTCTTGTTGTAATAAATCGGCATACGATTCCAAAATATCAAAATCATCATCAATTAATAAAACATTATTCTGATAATTAAACATTATCTACCACCTTAAATTCCAAAATAACCAGCGCATTTTTTGTCAATGTAGAAGCAATTAATAAGTTTCCTTGACATTGTTGCATAATGGATAGACTTATTGAT  >  1/1558756‑1559219

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑