Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_tpiA	4,110,747	G→T	intergenic (+62/+784)	cdh → / ← yiiQ	CDP‑diacylglycerol phosphotidylhydrolase/DUF1454 family putative periplasmic protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_tpiA	4,110,747	0	G	T	93.0%	115.4 / ‑1.2	43	intergenic (+62/+784)	cdh/yiiQ	CDP‑diacylglycerol phosphotidylhydrolase/DUF1454 family putative periplasmic protein
Reads supporting (aligned to +/- strand):  ref base G (1/2);  new base T (24/16);  total (25/18)
Fisher's exact test for biased strand distribution p-value = 5.62e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

ACAACGAAATCTACTGACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCAATACCCGCCC  >  NC_000913_3_pae_tpiA/4110610‑4110888                                                                                                                                          |                                                                                                                                               acaACGAAATCTACTGACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGGAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCcgcg                                                                                                                                     >  2:413809/1‑149 (MQ=255) acaACGAAATCTACTGACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCcgcg                                                                                                                                     >  1:244310/1‑149 (MQ=255)          tCTACTGACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTc                                                                                                                           <  2:644402/149‑1 (MQ=255)                gACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAAt                                                                                                                     >  2:48353/1‑149 (MQ=255)                   gCTTACCCGTGCTTCAGCCGAGGAAATTCAGGTTCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCTGCCGCGAGCGG‑GTTCGCCAATTCt                                                                                                                  >  2:336944/1‑149 (MQ=255)                      tAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGGGATTTTGCGTTAAGGAGAAGAGTTAAGGAAAGTAAGTGCCGGATATGCAACACGGCACCTGTCAGACTTAAGGCTGCCCCGCAGCG‑GCGGCTTTCGCCAATTCTAAg                                                                                                               >  2:82244/1‑149 (MQ=255)                         ccGTGCTTCAGCCGAGGAAATGCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCGCCTGTCAGCATTAAGGCTGCCACGCCGCGAGCGG‑TTTCGCCAATTCTAAGATc                                                                                                            >  2:568911/1‑149 (MQ=255)                          cGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCACCAATTCTAAGATCt                                                                                                           >  2:263289/1‑149 (MQ=255)                               ttCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGa                                                                                                      >  2:129491/1‑149 (MQ=255)                                    ccGAGGAAATTCGGCATCATCAGTGTGAGATTTGGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑GTTCGCCAATGCTAAGATCTTAAGATATgg                                                                                                 >  2:317966/1‑149 (MQ=255)                                    ccGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATgg                                                                                                 >  2:413019/1‑149 (MQ=255)                                     cGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATggg                                                                                                >  2:349595/1‑149 (MQ=255)                                           aaTTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCtttt                                                                                          <  1:129491/149‑1 (MQ=255)                                              tCAGGATCATCAGTGTAAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGcc                                                                                       <  1:348149/149‑1 (MQ=255)                                                 ggATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTc                                                                                    <  2:446703/149‑1 (MQ=255)                                                           tgtgAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTgcgc                                                                          <  2:512400/149‑1 (MQ=255)                                                             tgAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGAt                                                                                                             <  2:416106/112‑1 (MQ=255)                                                             tgAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGAt                                                                                                             >  1:416106/1‑112 (MQ=255)                                                             ggaaaTTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCtt                                                                        <  1:321600/145‑1 (MQ=255)                                                                gaTTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGcc                                                                     >  1:539144/1‑149 (MQ=255)                                                                         ttAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACt                                                            >  2:275805/1‑149 (MQ=255)                                                                            aGGCGAAGAGTTAAGGAAAGTAAGGGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTccc                                                         <  2:347349/149‑1 (MQ=255)                                                                            aGGCGAAGAGTCAAGGAATGTAAGTGCCGGAGAAGACCCCCCGCGGCTTGCGGGCTTATTTTGGCGGCGCCGCGGGCGG‑TTTTGCCTATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTccc                                                         <  2:449176/149‑1 (MQ=255)                                                                              gCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCt                                                       >  2:392686/1‑149 (MQ=255)                                                                                gAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCg                                                     <  1:349595/149‑1 (MQ=255)                                                                                gAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCGTGCCGGCACCACTCCCCTCg                                                     >  1:14686/1‑149 (MQ=255)                                                                                   gagTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCa                                                                    <  1:547791/131‑1 (MQ=255)                                                                                   gagTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCa                                                                    >  2:547791/1‑131 (MQ=255)                                                                                        aaGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCATTAACGGATGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGt                                             >  1:442266/1‑149 (MQ=255)                                                                                                   gtGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGc                                  <  2:244310/149‑1 (MQ=255)                                                                                                    tGCCGGATATGAAATCCGGCAACTGTCAGACTTAAGGCTGCCCCGCCGCGAACGG‑TGTCGCCAATTGTAAGAACTTAAGATATGGGTATTTTGCCATCACAGCAGCGCATGCCAGAAACGCACCCAGCGTGCCGGGTTTAAACGCGGCt                                 >  2:185254/1‑149 (MQ=255)                                                                                                       cGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCa                              >  2:213429/1‑149 (MQ=255)                                                                                                        ggATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCaa                             <  2:30415/149‑1 (MQ=255)                                                                                                         gATATGAAATCCGCCATCTCTCAGACTTAAGGCTGCCCCGGCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAAc                            <  2:424995/149‑1 (MQ=255)                                                                                                          atatGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACCATCCCCTCTTGCCGAGTTTAAGCGCGGCTTCAACg                           <  2:463431/149‑1 (MQ=255)                                                                                                            atGAAATCCGCCACCCGTCAGAGTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTGTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTc                         <  1:265281/149‑1 (MQ=255)                                                                                                            aggAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGAGCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTc                         <  2:73355/147‑1 (MQ=255)                                                                                                             tGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCAAGTTTAAACGCGGCTTCCACGTcc                        >  1:60186/1‑149 (MQ=255)                                                                                                                          cTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCaa           >  2:555691/1‑149 (MQ=255)                                                                                                                               aGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCAATAccc      <  1:213429/149‑1 (MQ=255)                                                                                                                               aGACTTAAGACTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCAATAccc      >  2:401781/1‑149 (MQ=255)                                                                                                                                 aCTTAAGGCTGCCCCGCCGCGAGAGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCAATAccccc    >  1:562261/1‑147 (MQ=255)                                                                                                                                   ttAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCAATACCCGccc  >  1:640480/1‑149 (MQ=255)                                                                                                                                          |                                                                                                                                               ACAACGAAATCTACTGACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCAATACCCGCCC  >  NC_000913_3_pae_tpiA/4110610‑4110888

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: ‑