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%	121.1 / NA	40	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 (22/18);  total (22/18)

GAACAGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCCCTGAAG  >  NC_000913/315131‑315365                                                                                                                  |                                                                                                                          gAACAGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAAc                                                                                                  >  1:980688/1‑139 (MQ=255)  aaCAGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCgg                                                                                                                <  2:49960/124‑1 (MQ=255)  aaCAGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCgg                                                                                                                >  1:49960/1‑124 (MQ=255)      gTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAActct                                                                                               <  2:628567/137‑1 (MQ=255)      gTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAActct                                                                                               >  1:628567/1‑137 (MQ=255)       tattatGGCGATGAAGTCGGACTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGacac                                                                                                                    >  2:918699/1‑115 (MQ=255)       tattatGGCGATGAAGTCGGACTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGacac                                                                                                                    <  1:918699/115‑1 (MQ=255)        attatGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCtcagt                                                                                           >  1:194155/1‑139 (MQ=255)            tGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCaga                                                                                       >  2:85026/1‑139 (MQ=255)               cGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGt                                                                                    >  2:940607/1‑139 (MQ=255)                 aTGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCGGTCaga                                                                                       <  1:437766/134‑1 (MQ=255)                 aTGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCGGTCaga                                                                                       >  2:437766/1‑134 (MQ=255)                      gTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTcac                                                                             <  1:962989/139‑1 (MQ=255)                                ttGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACaaaaa                                                                   <  2:980688/139‑1 (MQ=255)                                ttGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACaaaaa                                                                   <  2:599707/139‑1 (MQ=255)                                ttGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACaaaaa                                                                   <  1:85026/139‑1 (MQ=255)                                          tAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAAc                                                         <  1:741641/139‑1 (MQ=255)                                          tAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAAc                                                         <  2:194155/139‑1 (MQ=255)                                             gcgcCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCgg                                                                                                                <  1:1042274/81‑1 (MQ=255)                                             gcgcCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCgg                                                                                                                >  2:1042274/1‑81 (MQ=255)                                             gcgcCAGAAAGACCCGCATGCTATTTCGGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAAGAGTATCAACCAg                                                      >  2:641639/1‑139 (MQ=255)                                                   gAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTaaaaa                                                <  1:477585/139‑1 (MQ=255)                                                           cGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACaaaaa                                                                   >  1:204221/1‑112 (MQ=255)                                                           cGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACaaaaa                                                                   <  2:204221/112‑1 (MQ=255)                                                              aTGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACAcgc                                                                                                                  >  1:532610/1‑62 (MQ=255)                                                              aTGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACAcgc                                                                                                                  <  2:532610/62‑1 (MQ=255)                                                                  tATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCa                                 >  2:1028291/1‑139 (MQ=255)                                                                    tttCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGAc                                                                        <  2:29836/98‑1 (MQ=255)                                                                    tttCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGAc                                                                        >  1:29836/1‑98 (MQ=255)                                                                          ccGAGGTTACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTg                         >  1:352275/1‑139 (MQ=255)                                                                              ggTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCtcagt                                                                                           >  2:57276/1‑69 (MQ=255)                                                                              ggTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCtcagt                                                                                           <  1:57276/69‑1 (MQ=255)                                                                                      ataCGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAGGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTg             <  1:381194/139‑1 (MQ=255)                                                                                              gTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCCCTg     >  2:778983/1‑139 (MQ=18)                                                                                               tGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGAc                                                                        >  1:31357/1‑71 (MQ=25)                                                                                               tGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGAc                                                                        <  2:31357/71‑1 (MQ=255)                                                                                               tGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCCCTGa    >  2:40478/1‑139 (MQ=18)                                                                                               tGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCCCTGa    >  1:937604/1‑139 (MQ=18)                                                                                                 ccTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCCCTGAAg  >  2:805448/1‑139 (MQ=14)                                                                                                 ccTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCCCTGAAg  >  2:946434/1‑139 (MQ=14)                                                                                                                  |                                                                                                                          GAACAGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCCCTGAAG  >  NC_000913/315131‑315365

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑