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%	191.4 / NA	62	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 (33/29);  total (33/29)

TTGGCGCAAGCCTGATGTATGAACAGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCCCTGAAGC  >  NC_000913/315111‑315366                                                                                                                                      |                                                                                                                           ttGGCGCAAGCCTGATGTATGAACAGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGac                                                                                                                       <  2:1379416/139‑1 (MQ=255)  tGGCGCAAGCCTGATGTATGAACAGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGaca                                                                                                                      <  2:1015358/139‑1 (MQ=255)   ggCGCAAGCCTGATGTATTAACAGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCAAGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGacac                                                                                                                     <  2:1597618/139‑1 (MQ=255)   ggCGCAAGCCTGATGTATGAACAGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGacac                                                                                                                     <  2:1485751/139‑1 (MQ=255)    gcgcAAGCCTGATGTATGAACAGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACAcg                                                                                                                    >  2:678600/1‑139 (MQ=255)            cTGATGTATGAACAGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAg                                                                                                            <  1:852342/139‑1 (MQ=255)                  tATGAACAGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTa                                                                                                      <  2:424132/139‑1 (MQ=255)                    tGAACAGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTaaa                                                                                                    >  1:358366/1‑139 (MQ=255)                         aGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGacac                                                                                                                     <  2:786884/117‑1 (MQ=255)                         aGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGacac                                                                                                                     >  1:786884/1‑117 (MQ=255)                         aGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACtctc                                                                                               >  2:197672/1‑139 (MQ=255)                                     aTGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGa                                                                                   >  1:825690/1‑139 (MQ=255)                                     aTGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGa                                                                                   >  1:1588462/1‑139 (MQ=255)                                     aTGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGa                                                                                   >  1:849587/1‑139 (MQ=255)                                          gTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACAcgcg                                                                                                                  >  2:1534002/1‑103 (MQ=255)                                          gTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACAcgcg                                                                                                                  <  1:1534002/103‑1 (MQ=255)                                          gTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTcac                                                                              <  2:1588462/139‑1 (MQ=255)                                               gCTGTTTGCTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTTTACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGAc                                                                         <  2:1004370/139‑1 (MQ=255)                                                    ttGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACaaaaa                                                                    <  2:1333478/139‑1 (MQ=255)                                                           aGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATc                                                             <  2:849587/139‑1 (MQ=255)                                                             aTAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCtcagtc                                                                                           >  1:851632/1‑107 (MQ=255)                                                             aTAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCtcagtc                                                                                           <  2:851632/107‑1 (MQ=255)                                                             aTAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCaa                                                           >  2:1180244/1‑139 (MQ=255)                                                                 gcgcCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACaaaaa                                                                    <  2:1601855/126‑1 (MQ=255)                                                                 gcgcCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACaaaaa                                                                    >  1:1601855/1‑126 (MQ=255)                                                                 gcgcCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAg                                                       >  2:501793/1‑139 (MQ=255)                                                                  cgcCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTCACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCtcagtc                                                                                           <  2:743609/102‑1 (MQ=255)                                                                  cgcCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTAACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCtcagtc                                                                                           >  1:743609/1‑102 (MQ=255)                                                                       gAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACaaaaa                                                                    <  1:1036172/120‑1 (MQ=255)                                                                       gAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTGACCCAGAAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACaaaaa                                                                    >  2:1036172/1‑120 (MQ=255)                                                                       gAAAGACCCGCATGCTATTTCTGCCGAGGAGACCTATACGCCAGTACCTCTTTCCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTaaaaa                                                 >  2:957258/1‑139 (MQ=255)                                                                             cccGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCg                                           >  1:460744/1‑139 (MQ=255)                                                                                 cATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTa                                                                                                      >  1:833396/1‑76 (MQ=255)                                                                                 cATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTa                                                                                                      >  2:434603/1‑76 (MQ=255)                                                                                 cATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTa                                                                                                      <  1:434603/76‑1 (MQ=255)                                                                                 cATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTa                                                                                                      <  2:833396/76‑1 (MQ=255)                                                                                  aTGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAActc                                                                                                 >  1:231923/1‑80 (MQ=255)                                                                                  aTGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAActc                                                                                                 <  2:231923/80‑1 (MQ=255)                                                                                      tATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCa                                  <  1:197672/139‑1 (MQ=255)                                                                                              ccGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGaca                                                                                                                      <  2:473520/47‑1 (MQ=255)                                                                                              ccGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGaca                                                                                                                      >  1:473520/1‑47 (MQ=255)                                                                                              ccGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTg                          >  1:454618/1‑139 (MQ=255)                                                                                                gAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGaa                        >  2:1443776/1‑139 (MQ=255)                                                                                                             cGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAg           >  1:480727/1‑139 (MQ=255)                                                                                                             cGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAg           >  1:460099/1‑139 (MQ=255)                                                                                                                cAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGAc                                                                         <  2:519154/74‑1 (MQ=255)                                                                                                                cAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGAc                                                                         >  1:519154/1‑74 (MQ=255)                                                                                                                cAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGccc        >  2:843239/1‑139 (MQ=25)                                                                                                                cAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTACCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTg              <  2:750910/133‑1 (MQ=255)                                                                                                                cAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTACCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTg              >  1:750910/1‑133 (MQ=255)                                                                                                                 aGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCCCt       <  2:460099/139‑1 (MQ=21)                                                                                                                  gTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTa                                                                                                      >  2:1078235/1‑43 (MQ=255)                                                                                                                  gTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTa                                                                                                      <  1:1078235/43‑1 (MQ=255)                                                                                                                  gTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAActc                                                                                                 <  2:1216974/48‑1 (MQ=255)                                                                                                                  gTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAActc                                                                                                 >  1:1216974/1‑48 (MQ=255)                                                                                                                   tGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAActc                                                                                                 <  2:1530704/47‑1 (MQ=255)                                                                                                                   tGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAActc                                                                                                 >  1:1530704/1‑47 (MQ=255)                                                                                                                   tGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCCCTGa     >  1:1168258/1‑139 (MQ=18)                                                                                                                     ccTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACAt                                                                            <  1:815487/66‑1 (MQ=16)                                                                                                                     ccTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACAt                                                                            >  2:815487/1‑66 (MQ=16)                                                                                                                     ccTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCCCTGAAg   >  1:1648127/1‑139 (MQ=14)                                                                                                                      ctctTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCCCTGAAGc  <  2:1648127/139‑1 (MQ=11)                                                                                                                                      |                                                                                                                           TTGGCGCAAGCCTGATGTATGAACAGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCCCTGAAGC  >  NC_000913/315111‑315366

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: ‑