Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_pgi	1,656,008	Δ1 bp	coding (201/342 nt)	ynfB →	UPF0482 family putative periplasmic protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_pgi	1,656,008	0	C	.	97.8%	205.1 / ‑3.3	46	coding (201/342 nt)	ynfB	UPF0482 family putative periplasmic protein
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base . (22/23);  total (23/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATTGAGCACAACTGTTCATGCCGAAACTAACAAACTGGTGATTGAGTCTGGCGACAGTGCACAAAGCCGCCAGCA‑CGCCGCTATGGAAAAAGAGCAATGGAATGACACGCGCAATCTGCGCCAGAAAGTGAATAAACGCACTGAAAAAGAGTGGGATAAAGCCGACGCCGCTTTTGATAACCGCGATAAATGTGAGCAAAGCGCCAACATCAATGCCTACTGGGAGCCCAATACTTTGCGCTGCCTGGACCGTCGAACTGGCCGCGTTATTACCCCCTAAC  >  NC_000913_3_pae_pgi/1655870‑1656150                                                                                                                                            |                                                                                                                                               aTTGAGCACAACTGTTCATGCCGAAACTAACAAACTGGTGATTGAGTCTGGCGACAGTGCACAAAGCCGCCAGCA‑CGCCGCTATGGAAAAAGAGCAATGGAATGACACGCGCAATCTGCGCCAGAAAGTAAATAAACG‑ACTGAACAaga                                                                                                                                     >  1:663144/1‑149 (MQ=255)     aGCACAACTGTTCATGCCGAAACTAACAAACTGGTGATTGAGTCTGGCGACAGTGCACAAAGCCGCCAGCA‑CGCCGCTATGGAAAAAGAGCAATGGAATGACACGCGCAATCTGCGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTgg                                                                                                                                 <  1:961179/149‑1 (MQ=255)     aGCACAACTGTTCATGCCGAAACTAACAAACTGGTGATTGAGTCTGGCGACAGTGCACAAAGCCGCCAGCA‑CGCCGCTATGGAAAAAGAGCAATGGAATGACACGCGCAATCTGCGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTgg                                                                                                                                 <  2:932493/149‑1 (MQ=255)     aGCACAACTGTCCATGCCGAATGTAACTAACTGGTGATTGAGTCTGGCGCCAGTGCACAAAGCCGCCAGCA‑CGCCGCTATGGAAAAAGAGCAATGGAATGACACGCGCAATCTGCGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTgg                                                                                                                                 <  2:332046/149‑1 (MQ=255)      gCACAACTGCACACTCCCAAACAAACAAACTGAGGATTGAGTCCGGCGACAGTGCACAAAACCGCCAACA‑CGCCGCAAAGAAAAAAGAGCAATGGAATGACACGCGCAATCTTCGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTggg                                                                                                                                <  2:681382/149‑1 (MQ=255)       cacaACTGTTCATGCCGAAACTAACAAACTGGTGATTGAGTCTGGCGACAGTGCACAAAGCCGCCAGCA‑CGCCGCTATGGAAAAAGAGCAATGGAATGACACGCGCAATCTGCGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTGGGa                                                                                                                               <  1:615405/149‑1 (MQ=255)          aaCTGTTCATGCCGAAACTAACAAACTGGTGATTGAGTCTGGCGACAGTGCACAAAGCCGCCAGCA‑CGCCGCTATGGAAAAAGAGCAATGGAATGACACGCGCAATCTGCGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGt                                                                                                                                   <  2:760012/142‑1 (MQ=255)          aaCTGTTCATGCCGAAACTAACAAACTGGTGATTGAGTCTGGCGACAGTGCACAAAGCCGCCAGCA‑CGCCGCTATGGAAAAAGAGCAATGGAATGACACGCGCAATCTGCGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGt                                                                                                                                   >  1:760012/1‑142 (MQ=255)          aaCTGTTCATGCCGAAACTAACAAACTGGTGATTGAGTCTGGCGACAGTGCACAAAGCCGCCAGCA‑CGCCGCTATGGAAAAAGAGCAATGGAATGACACGCGCAATCTGCGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTGGGATaa                                                                                                                            >  2:403158/1‑149 (MQ=255)           aCTGTTCATGCCGAAACTAACAAACTGGTGATTGAGTCTGGCGACAGTGCACAAAGCCGCCAGCA‑CGCCGCTATGGAAAAAGAGCAATGGAATGACACGCGCAATCTGCGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTGGGATaaa                                                                                                                           <  1:670758/149‑1 (MQ=255)                  aTGCCGAAACTAACAAACTGGTGATTGAGTCTGGCGACAGTGCACAAAGCCGCCAGCA‑CGCCGCTATGGAAAAAGAGCAATGGAATGACACGCGCAATCTGCGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTGGGATAAAGCCGAcg                                                                                                                    >  1:408418/1‑149 (MQ=255)                  aTGCCGAAACTAACAAACTGGTGATTGAGTCTGGCGACAGTGCACAAAGCCGCCAGCA‑CGCCGCTATGGAAAAAGAGCAATGGAATGACACGCGCAATCTGCGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTGGGATAAAGCCGAcg                                                                                                                    >  1:717860/1‑149 (MQ=255)                  aTGCCGAAACTAACAAACTGGTGATTGAGTCTGGCGACAGTGCACAAACCCGCCAGCC‑CGCCGCTATCGAAAAAGAGCAATGGAATGACACGCGCAACCTGCGCCAGAAAGTGAATAAACGC‑CTGCAAAAGAGGGGGCTCAACccgccg                                                                                                                    >  2:910254/1‑149 (MQ=255)                            tAACAAACTGGTGATTGAGTCTGGCGACAGTGCACAAAGCCGCCAGCA‑CGCCGCTATGGAAAAAGAGCAATGGAATGACACGCGCAATCTGCGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTGGGATAAAGCCGACGCCGCTTTTGa                                                                                                          >  2:317300/1‑149 (MQ=255)                              aCAAACTGGTGATTGAGTCTGGCGACAGTGCACAAAGCCGCCAGCA‑CGCCGCTATGGAAAAAGAGCAATGGAATGACACGCGCAATCTGCGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTGGGATAAAGCCGACGCCGCCTTTGATa                                                                                                        >  1:963541/1‑149 (MQ=255)                                        gATTGAGTCTGGCGACAGTGCACAAAGCCGCC‑GCAGTTGTGTTATGGAAAAAGAGCAATGGAATAACACGCGCAATCTGAGCCAGAAAGTGAATCAACG‑ACTGAAAAAGGGTGGGATAAAGCCGACGCCCCTATTAATACCCACGGTaa                                                                                              >  2:229751/1‑149 (MQ=255)                                              gTCTGGCGACAGTGCACAAAGCCGCCAGCA‑CGCCGCTATGGAAAAAGAGCAATGGAATGACACGCGCAATCTGCGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTGGGATAAAGCCGACGCCGCTTTTGATAACCGCGATAAATGTGa                                                                                        <  1:317300/149‑1 (MQ=255)                                              ctCTGGCGACAGTGCAAAAAGCCGACAGCA‑CGCCGCTAGGGAAAAAGAGCAAGGGAATTACACGCGCAATCTGCGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTGGGATAAAGCCGACGCCGCTTTTGATAACCGCGATAAATGTGa                                                                                        <  2:68761/148‑1 (MQ=255)                                                   gCGACAGTGCACAAAGCCGCCAGCA‑CGCCGCTATGGAAAAAGAGCAATGGAATGACACGCGCAATCTGCGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTGGGATAAAGCCGCCGCCGCTTTTGATAACCGCGATAAAAGTGAGCaaa                                                                                   >  2:588471/1‑149 (MQ=255)                                                   gCGACAGTGCACAAAGCCGCCAGCA‑CGCCGCTATGGAAAAAGAGCAATGGAATGACACGCGCAATCTGCGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTGGGATAAAGCCGACGCCGCTTTTGATAACCGCGATAAATGTGAGCaaa                                                                                   >  2:59418/1‑149 (MQ=255)                                                     gACAGTGCACAAAGCCGCCAGCA‑CGCCGCTATGGAAAAAGAGCAATGGAATGACACGCGCAATCTGCGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTGGGATAAAGCCGACGCCGCTTTTGATAACCGCGATAAATGTGAgatcgga                                                                                 >  1:646976/1‑143 (MQ=255)                                                          tGCACAAAGCCGCCAGCA‑CGCCGCTATGGAAAAAGAGCAATGGAATGACACGCGCAATCTGCGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTGGGATAAAGCCGACGCCGCTTTTGCTAACGGCGATAAATGTGAGCAAAGCGCCaa                                                                            >  1:1033630/1‑149 (MQ=255)                                                             acaAAGCCGCCAGCA‑CGCCGCTATGGAAAAAGAGCAATGGAATGACACGCGCAATCTGCGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTGGGATAAAGCCGACGCCGCTTTTGATAACCGCAATAAATGTGAGCAAAGCGCCAACAt                                                                         >  2:81552/1‑149 (MQ=255)                                                               aaaGCCGCCAGCA‑CGCCGCTATGGAAAAAGAGCAATGGAATGACACGCGCAATCTGCGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTGGGATAAAGCCGACGCCGCTTTTGATAACCGCGAAAAATGTGAGCAAAGCGCCAACATCa                                                                       >  1:691446/1‑149 (MQ=255)                                                                aaGCCGCCAGCA‑CGCCGCTATGGAAAAAGAGCAATGGAATTACACGCGCAATCTGCGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTGGGATAAAGCCGACGCCGCTTTTGATAACCGCGATAAATGTGAGCAAAGCGCCAACATCaa                                                                      <  1:685477/149‑1 (MQ=255)                                                                   ccgccAGCA‑CGCCGCTATGGAAAAAGAGCAATGGAATGACACGCGCAATCTGCGCCAGAAAGTGAATAAACG‑ACTGAAAGAGAGTGGGATAAAGCCGACGCCGCTTTTGATAACCGCGATAAATGTGAGCAAAGCGCCAACATCAATGc                                                                   <  1:883281/149‑1 (MQ=255)                                                                          taaagccgcGATGAAAAAAGAGCAAGGGAATGACACGCGTAATCAGTGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTGGGATAAAGCCGACGCCGCTTTTGATAACCGCGATAAATGTGAGCAAAGCGCCAACATCAATGCCTACTg                                                             <  2:57479/145‑1 (MQ=255)                                                                             cggcggtATGGAAAAAGAGCAATGGAATGACACGCGCAATCTGCGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTGGGATATAGCCGACGCCGCTTTTGATAACCGCGATAAATGTGAGCAAAGCGCCAACATCAATGCCTACTGGGa                                                          <  2:348047/143‑1 (MQ=255)                                                                              gccgcTATGGAAAAAGAGCAATGGAATGACACGCGCAATCTGCGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTGGGATAAAGCCGACGCCGCTTTTGATAACCGCGATAAATGTGAGCAAAGCGCCAACATCAATGCCTACTGGGAg                                                         <  1:580709/149‑1 (MQ=255)                                                                                  ccaTGGAAAAAGAGCAATGGAATGACACGCGCAATCTGCGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTGGGATAAAGCCGACGCCGCTTTTGATAACCGCGATAAATGTGAGCAAAGCGCCAACATCAATGCCTACTGGGAGCCCa                                                     <  1:555645/147‑1 (MQ=255)                                                                                         aaaaGAGCAATGGAATGACACGCGCAATCTGCGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTGGGATAAAGCCGACGCCGCTTTTGATAACCGCGATAAATGTGAGCAAAGCGCCAACATCAATGCCTACTGGGAGCCCAAGACttt                                              >  2:378962/1‑149 (MQ=255)                                                                                                     gAATGACACGCGCAATCTGCGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTGGGATTAAGCCGACGCCGCTTTTGATAACCGCGATAAATGTGAGCAAAGCGCCAACATCAATGCCTACTGGGAGCCCAATACTTTGCTCTGCCTGGa                                  <  1:425433/149‑1 (MQ=255)                                                                                                     gAATGACACGCGCAATCTGCGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTGGGATAAAGCCGACGCCGCGTTTGATAACCGCGCCAAATGTGAGCAAAGCGCCAACATCAATGCCTACTGGGAGCCCAATACTTTGCGCTGCCTgaa                                  >  2:326975/1‑147 (MQ=255)                                                                                                      aaTGACACGCGCAATCTGCGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTGGGATAAAGCCGACGCCGCTTTTGATAACCGCGATAAATGTGAGCAAAGCGCCAACATCAATGCCTACTg                                                             >  1:430155/1‑121 (MQ=255)                                                                                                      aaTGACACGCGCAATCTGCGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTGGGATAAAGCCGACGCCGCTTTTGATAACCGCGATAAATGTGAGCAAAGCGCCAACATCAATGCCTACTg                                                             <  2:430155/121‑1 (MQ=255)                                                                                                       aTGACACGCGCACTTCGCACCAGAAAGTGAATAAACG‑ACTGAAAAAGAGGGGGATAAAGCCGACGCCGCTTTTGATAACCGCGATAAATGTGAGCAAAGCGCCAACATCAATGCCTACTGGTAGCCCAATACTTTGCGCTGCCTGGAcc                                <  2:1033630/149‑1 (MQ=255)                                                                                                       aTGACACGCGCAATCTGCGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTGGGATAAAGCCGACGCCGCTTTTGATAACCGCGATAAATGTGAGCAAAGCGCCAACATCAATGCCTACTGGGAGCCCAATACTTTGCGCTGCCTGGAcc                                >  2:594875/1‑149 (MQ=255)                                                                                                        tGACACGCGCAATCTGCGCCAGAAAGTGAGTAAACG‑ACTGAAAAAGAGTGGGATAAAGCCGACGCCGCTTTTGATCACCGCGATAAATGCGAGCAAAGCGCCAGCATCAATGCCTACTGGGAGTCCAAGACTTTACGCTGCGTGGACCg                               >  1:1033850/1‑149 (MQ=255)                                                                                                          acacGCGCAATCTGAGCCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTGGGATAAAGCCGTCGCTGCTTTTGATAACCGCGATAAATGTGAGCAAAGCGCCAACATCAATGCCTACTGGGATCCCAGTACTTTGCGCTGCCTGGACCGTc                             <  2:970796/149‑1 (MQ=255)                                                                                                                       gcgcCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTGGGATAAAGCCGACGCCGCTTTTGATAACCGCGATAAATGTGAGCAAAGCGCCAACATCAATGCCTACTGGGAGCCCAATACTTTGCGCTGCCTGGACCGTCGAACTGGCCGCGt                <  1:378962/149‑1 (MQ=255)                                                                                                                         gcCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTGGGATAAAGCCGACGCCGCTTTTGATAACCGCGATAAATGTGAGCAAAGCGCCAACATCAATGCCTACTGGGAGCCCAATACTTTGCGCTGCCTGGACCGTCGAACTg                       <  2:578476/140‑1 (MQ=255)                                                                                                                         gcCAGAAAGTGAATAAACG‑ACTGAAAAAGAGTGGGATAAAGCCGACGCCGCTTTTGATAACCGCGATAAATGTGAGCAAAGCGCCAACATCAATGCCTACTGGGAGCCCAATACTTTGCGCTGCCTGGACCGTCGAACTg                       >  1:578476/1‑140 (MQ=255)                                                                                                                             gAAAGTGAATAAACG‑ACTGAAAAAGAGTGGGATAATGCCGACGCCGCTTTTGATAACCGCGATAAATGTGAGCAAAGCGCCAACATCAATGCCTACTGGGAGCCCAATACTTTGCGCTGCCTGGACCGTCGAACTGGCCGCGTTATTAc          <  1:910254/149‑1 (MQ=255)                                                                                                                             gAAAGTGAATAAACG‑ACTGAAAAAGAGTGGGATAAAGCCGACGCCGCTTTTGATAACCGCGATAAATGTGAGCAAAGCGCAAACATCAATGCCTCCTGGGAGCCCAATCCTTTGCGCTGCCTGGACCGTCGCACTGGCCGCGTTATTAc          >  1:360513/1‑149 (MQ=255)                                                                                                                                    aaTAAACG‑ACTGAAAAAGAGTGGGATAAAGCCGACGCCGCTTTTGATAACCGCGATAAATGTGAGCAAAGCGCCAACATCAATGCCTACTGGGAGCCCAATACTTTGCGCTGCCTGGACCGTCGAACTGGCCGCGTTATTACCCCCTaa   >  2:223382/1‑149 (MQ=255)                                                                                                                                     aTAAACG‑ACTGAAAAAGAGTGGGATAAAGCCGACGCCGCTTTTGATAACCGCGATAAATGTGAGCAAAGCGCCAACATCAATGCCTACTGGGAGCCCAATACTTTGCGCTGCCTGGACCGTCGAACTGGCCGCGTTATTACCCCCTAAc  <  1:44000/149‑1 (MQ=255)                                                                                                                                            |                                                                                                                                               ATTGAGCACAACTGTTCATGCCGAAACTAACAAACTGGTGATTGAGTCTGGCGACAGTGCACAAAGCCGCCAGCA‑CGCCGCTATGGAAAAAGAGCAATGGAATGACACGCGCAATCTGCGCCAGAAAGTGAATAAACGCACTGAAAAAGAGTGGGATAAAGCCGACGCCGCTTTTGATAACCGCGATAAATGTGAGCAAAGCGCCAACATCAATGCCTACTGGGAGCCCAATACTTTGCGCTGCCTGGACCGTCGAACTGGCCGCGTTATTACCCCCTAAC  >  NC_000913_3_pae_pgi/1655870‑1656150

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑