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%	179.5 / 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 (28/29);  total (28/29)

TTGGCGCAAGCCTGATGTATGAACAGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCCCT  >  NC_000913/315111‑315361                                                                                                                                      |                                                                                                                      ttGGCGCAAGCCTGATGTATGAACAGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGac                                                                                                                  <  2:255416/139‑1 (MQ=255)  tGGCGCAAGCCTGATGTATGAACAGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGaca                                                                                                                 <  2:233129/139‑1 (MQ=255)       cAAGCCTGATGTATGAACAGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCgg                                                                                                            <  1:902613/139‑1 (MQ=255)                    tGAACAGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTaaa                                                                                               >  2:994834/1‑139 (MQ=255)                     gAACAGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAAc                                                                                              >  2:1527994/1‑139 (MQ=255)                         aGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACtctc                                                                                          >  2:457681/1‑139 (MQ=255)                           tattatGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGGCCTATACGCCAGTGCCTCTTACCCAGCAATAATGGaca                                                                                                                 <  2:29206/114‑1 (MQ=255)                           tattatGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGGCCTATACGCCAGTGCCTCTTACCCAGCAATAATGGaca                                                                                                                 >  1:29206/1‑114 (MQ=255)                                  gCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAgg                                                                                 >  2:9004/1‑139 (MQ=255)                                   cGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGacac                                                                                                                >  2:59467/1‑107 (MQ=255)                                   cGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGacac                                                                                                                <  1:59467/107‑1 (MQ=255)                                     aTGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGacac                                                                                                                <  1:109589/105‑1 (MQ=255)                                     aTGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGacac                                                                                                                >  2:109589/1‑105 (MQ=255)                                     aTGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGaca                                                                                                                 <  1:1161493/104‑1 (MQ=255)                                     aTGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGaca                                                                                                                 >  2:1161493/1‑104 (MQ=255)                                     aTGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACAcgc                                                                                                              >  1:218513/1‑107 (MQ=255)                                     aTGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACAcgc                                                                                                              <  2:218513/107‑1 (MQ=255)                                     aTGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAActc                                                                                            <  1:196447/125‑1 (MQ=255)                                     aTGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAActc                                                                                            >  2:196447/1‑125 (MQ=255)                                     aTGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGa                                                                              >  1:86701/1‑139 (MQ=255)                                          gTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTcac                                                                         <  1:9004/139‑1 (MQ=255)                                               gCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGAc                                                                    <  1:1527994/139‑1 (MQ=255)                                               gCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGAc                                                                    <  2:15450/139‑1 (MQ=255)                                                    ttGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACaaaaa                                                               <  1:597046/139‑1 (MQ=255)                                                            gATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCa                                                       <  1:909821/139‑1 (MQ=255)                                                             aTAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCaa                                                      >  2:283208/1‑139 (MQ=255)                                                                          aGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAAcc                                         <  1:914766/139‑1 (MQ=255)                                                                               cGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTa                                                                                                 >  2:703220/1‑78 (MQ=255)                                                                               cGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTa                                                                                                 <  1:703220/78‑1 (MQ=255)                                                                                 cATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGac                                                                                                                  <  1:1058851/59‑1 (MQ=255)                                                                                 cATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGac                                                                                                                  >  2:1058851/1‑59 (MQ=255)                                                                                   tGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGac                                                                                                                  >  1:329411/1‑57 (MQ=255)                                                                                   tGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGac                                                                                                                  <  2:329411/57‑1 (MQ=255)                                                                                        cttCTGCCGAGGTGACCTATACGCCAGTG‑CTCTTACCCAGCAATAATGGACACGCGGCTa                                                                                                         >  2:426897/2‑60 (MQ=25)                                                                                        cttCTGCCGAGGTGACCTATACGCCAGTG‑CTCTTACCCAGCAATAATGGACACGCGGCTa                                                                                                         <  1:426897/59‑1 (MQ=255)                                                                                           cTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGc                        <  2:86701/139‑1 (MQ=255)                                                                                              ccGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTg                     >  2:876053/1‑139 (MQ=255)                                                                                              ccGAGGTGACCTATACGCCAGAACCTCTTAACCAGCAGTGATGGCAACACGCCTAAGTAAGGAAACTCCCGGTTACCGGTGATTCACATGAAAAAAACGGTTTGTACCAGTAAAAAACCCCGTCACTAGCATTccacga                     >  2:732252/1‑134 (MQ=9)                                                                                               cGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACCAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGa                    >  1:1431798/1‑139 (MQ=255)                                                                                                gAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGaa                   >  2:764791/1‑139 (MQ=255)                                                                                                      aCCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCtcagtca                                                                                     <  2:777859/67‑1 (MQ=255)                                                                                                      aCCTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCtcagtca                                                                                     >  1:777859/1‑67 (MQ=255)                                                                                                        cTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAAc                                                     >  1:398108/1‑97 (MQ=255)                                                                                                        cTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAAc                                                     <  2:398108/97‑1 (MQ=255)                                                                                                        cTATACGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAg           >  2:506100/1‑139 (MQ=255)                                                                                                          ataCGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTg         <  1:717454/139‑1 (MQ=255)                                                                                                          ataCGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTg         <  1:876053/139‑1 (MQ=255)                                                                                                             cGCCAGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAg      >  1:518218/1‑139 (MQ=255)                                                                                                                 aGTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCCCt  <  1:291612/139‑1 (MQ=21)                                                                                                                  gTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGAc                                                                    <  2:851436/72‑1 (MQ=255)                                                                                                                  gTGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGAc                                                                    >  1:851436/1‑72 (MQ=255)                                                                                                                   tGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTaaa                                                                                               <  2:56492/44‑1 (MQ=255)                                                                                                                   tGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTaaa                                                                                               >  1:56492/1‑44 (MQ=255)                                                                                                                   tGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACt                                                                            >  1:1235029/1‑63 (MQ=255)                                                                                                                   tGCCTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACt                                                                            <  2:1235029/63‑1 (MQ=255)                                                                                                                     ccTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTg         >  2:420291/1‑128 (MQ=14)                                                                                                                     ccTCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTg         <  1:420291/128‑1 (MQ=14)                                                                                                                                      |                                                                                                                      TTGGCGCAAGCCTGATGTATGAACAGTATTATGGCGATGAAGTCGGGCTGTTTGGTAAAGATAAGCGCCAGAAAGACCCGCATGCTATTTCTGCCGAGGTGACCTATACGCCAGTGCCTCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCCCT  >  NC_000913/315111‑315361

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑