Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	315,244	G→A	intergenic (+16/‑47)	eaeH → / → insE1	pseudogene, attaching and effacing protein homology,factor, Not classified/IS3 transposase A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	315,244	0	G	A	100.0%	175.6 / NA	57	intergenic (+16/‑47)	eaeH/insE1	pseudogene, attaching and effacing protein homology,factor, Not classified/IS3 transposase A
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (29/28);  total (29/28)

TTGGCGCAAGCCTGATGTATGAACAGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCCC  >  NC_000913/315111‑315360                                                                                                                                      |                                                                                                                     ttGGCGCAAGCCTGATGTATGAACAGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGac                                                                                                                 <  1:244591/139‑1 (MQ=255)    gcgcAAGCCTGATGTATGAACAGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAACGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACAcg                                                                                                              <  2:953469/139‑1 (MQ=255)     cgcAAGCCTGATGTATGAACAGTATTATGGCGATGAAGTCGTGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACAcgc                                                                                                             <  2:905063/139‑1 (MQ=255)                  tATGAACAGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTa                                                                                                <  1:1251509/139‑1 (MQ=255)                    tGAACAGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTaaa                                                                                              >  2:1027754/1‑139 (MQ=255)                       aCAGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAActc                                                                                           <  1:1507156/139‑1 (MQ=255)                        cAGTATTATGGCGATGAAGTCGGGCTGTTTGCTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAActct                                                                                          <  2:1475130/139‑1 (MQ=255)                                tGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAACGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGc                                                                                                          >  1:985589/1‑115 (MQ=255)                                tGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGc                                                                                                          <  2:985589/115‑1 (MQ=255)                                tGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCaga                                                                                  >  2:145342/1‑139 (MQ=255)                                     aTGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGa                                                                             >  2:1218264/1‑139 (MQ=255)                                       gAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCtcag                                                                                       >  1:127318/1‑127 (MQ=255)                                       gAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCtcag                                                                                       <  2:127318/127‑1 (MQ=255)                                          gTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTcac                                                                        <  1:145342/139‑1 (MQ=255)                                                   tttGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAActc                                                                                           >  2:812108/1‑111 (MQ=255)                                                   tttGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAActc                                                                                           <  1:812108/111‑1 (MQ=255)                                                    ttGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGGGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACaaaaa                                                              >  2:850716/1‑139 (MQ=255)                                                            gATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCa                                                      <  2:1030938/139‑1 (MQ=255)                                                             aTAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCaa                                                     >  2:1038369/1‑139 (MQ=255)                                                                 gcgcCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGAc                                                                   <  1:713074/121‑1 (MQ=255)                                                                 gcgcCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGAc                                                                   >  2:713074/1‑121 (MQ=255)                                                                 gcgcCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAg                                                 >  2:1298597/1‑139 (MQ=255)                                                                      aGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGa                                                                             >  2:499803/1‑106 (MQ=255)                                                                      aGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGa                                                                             <  1:499803/106‑1 (MQ=255)                                                                      aGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACaaaaa                                                              <  2:297564/121‑1 (MQ=255)                                                                      aGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACaaaaa                                                              >  1:297564/1‑121 (MQ=255)                                                                      aGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTaaaa                                            >  2:1277211/1‑139 (MQ=255)                                                                       gAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTaaaaa                                           <  1:1027754/139‑1 (MQ=255)                                                                        aaaGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTaaaaaa                                          <  2:755122/139‑1 (MQ=255)                                                                            aCCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCtcagtcag                                                                                   >  1:911794/1‑94 (MQ=255)                                                                            aCCCGCATGCTATTGCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCtcagtcag                                                                                   <  2:911794/94‑1 (MQ=255)                                                                             cccGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCtcagt                                                                                      <  1:836076/90‑1 (MQ=255)                                                                             cccGCATGCTATTTCTGCAGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCtcagt                                                                                      >  2:836076/1‑90 (MQ=255)                                                                                 cATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAAc                                                    >  1:637194/1‑120 (MQ=255)                                                                                 cATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAAc                                                    <  2:637194/120‑1 (MQ=255)                                                                                              ccGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGt                                                                                                 <  1:830071/62‑1 (MQ=255)                                                                                              ccGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGt                                                                                                 >  2:830071/1‑62 (MQ=255)                                                                                              ccGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTg                    >  2:14996/1‑139 (MQ=255)                                                                                              ccGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGT‑AAAAACCCCGGAAAAAAGAATCGCCTGa                   >  2:1343783/1‑139 (MQ=17)                                                                                               cGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACaaa                                                                >  1:1147919/1‑94 (MQ=255)                                                                                               cGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACaaa                                                                <  2:1147919/94‑1 (MQ=255)                                                                                                   gTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAAttt               <  1:1298597/139‑1 (MQ=255)                                                                                                      aCCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGc            >  2:168012/1‑139 (MQ=255)                                                                                                          ataCGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTg        <  1:1038369/139‑1 (MQ=255)                                                                                                             cGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAg     >  2:748603/1‑139 (MQ=255)                                                                                                                cAGTGCCTCTTACCCAGCAATAATGGATACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATc                                                       >  2:900219/1‑86 (MQ=255)                                                                                                                cAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATc                                                       <  1:900219/86‑1 (MQ=255)                                                                                                                cAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCg             <  2:234386/128‑1 (MQ=25)                                                                                                                cAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCg             >  1:234386/1‑128 (MQ=25)                                                                                                                cAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGccc  >  2:172354/1‑139 (MQ=25)                                                                                                                cAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGccc  >  2:1486188/1‑139 (MQ=25)                                                                                                                  gTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAActct                                                                                          >  2:160159/1‑49 (MQ=255)                                                                                                                  gTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAActct                                                                                          <  1:160159/49‑1 (MQ=255)                                                                                                                   tGCCTCTTACCCAGCAATAATGGACATGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACaaaaa                                                              >  2:1276264/1‑76 (MQ=11)                                                                                                                   tGCCTCTTACCCAGCAATAATGGACATGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACaaaaa                                                              <  1:1276264/76‑1 (MQ=11)                                                                                                                   tGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTcaca                                                                       <  2:1249893/67‑1 (MQ=255)                                                                                                                   tGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTcaca                                                                       >  1:1249893/1‑67 (MQ=255)                                                                                                                                      |                                                                                                                     TTGGCGCAAGCCTGATGTATGAACAGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCCC  >  NC_000913/315111‑315360

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: ‑