Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	178,003	C→A	12.6%	intergenic (+1811/‑23)	cap5C → / → cap5E	capsular polysaccharide biosynthesis protein Cap5C/capsular polysaccharide biosynthesis protein Cap5E

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	178,003	0	C	A	12.6%	160.4 / 2.8	55	intergenic (+1811/‑23)	cap5C/cap5E	capsular polysaccharide biosynthesis protein Cap5C/capsular polysaccharide biosynthesis protein Cap5E
Reads supporting (aligned to +/- strand):  ref base C (28/19);  new base A (2/6);  total (30/25)
Fisher's exact test for biased strand distribution p-value = 1.23e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGAGGTTCATCCTGAACAAGTATTTGAAAAAATTTATCGTGGCAAAGTACAACATATGAAATGTAATGAAGTTGAAGCGATTATTCAAGACATCGTCAATGACTTTAGTAAAGAAAAAATTATTAACTATGCCAATGGCAAAAAGGGAGATAATTATGTTCGA‑TGACAAAATTTTATTAATTACTGGGGGCACAGGATCATTCGGTAATGCTGTTATGAAACAGTTTTTAGATTCTAATATTAAAGAAATTCGTATTTTTTCA  >  CP000730/177871‑178133                                                                                                                                     |                                                                                                                                    tGAGGTGCAACCTGAACAAGTATTTGAAAAAATTTATCGTGGCAAAGTACAACATATGAAATGTAATGAAGTTGAAGCGATTATTCAAGACATCGTCAATGACTTTAGTAAAGACAAAATTATTAACTATGCCAATGGcga                                                                                                                             >  1:419212/1‑139 (MQ=255)  gAGGTTCATCCTGAACAAGTATTTGAAAAAATTTATCGTGGCAAAGTACAACATATGAAATGTAATGAAGTTGAAGCGATTATTCAAGACATCGTCAATGACTTTAGTAAAGAAAAAATTATTAACTATGCCAATGGCaaa                                                                                                                            >  2:53512/1‑141 (MQ=255)  gAGGTTCATCCTGAACAAGTATTTGAAAAAATTTATCGTGGCAAAGTACAACATATGAAATGTAATGAAGTTGAAGCGATTATTCAAGACATCGTCAATGACTTTAGTAAAGAAAAAATTATTAACTATGCAAATGGCaaa                                                                                                                            >  2:450415/1‑141 (MQ=255)  gAGGTTCATCCTGAACAAGTATTTGAAAAAATTTATCGTGGCAAAGTACAACATATGAAATGTAATGAAGTTGAAGCGATTATTCAAGACATCGTCAATGACTTTAGTAAAGAAAAAATTATTAACGATTCCAATGGCaaa                                                                                                                            >  2:197947/1‑141 (MQ=255)  gAGGTTCAGCCTGAACAAGTATTTGAAAAAATTTATCGTGACAAAGTACAACATATGAAATGTAATGAAGTTGAAGCGATTATTCAAGACATCGTCAATGACTTTAGTAAAGAAAAAATTATTAACTATGCCAATGGCaaa                                                                                                                            <  1:46970/141‑1 (MQ=255)     gTTCATCCTGAAAAAGTAATTGAAAAAATTTATCGTGGCAAAGTACAACATATGAAATGTAATGAAGTTGAAGCGATTATTCAAGACATCGTCAATGACTATAGTAAAGAAAAAATTATTAACTATGCCAATGGCAAAAAg                                                                                                                         <  2:479221/141‑1 (MQ=255)       tCATCCTGAACAAGTATTTGAAAAAATTTATCGTGGCAAAGTACAACATATGAAATGTAATGAAGTTGAAGCGATTATTCAAGACATCGTCAATGACTTTAGTAAAGAAAAAAGTATTAACTATGCCAATGGCAAAAAggg                                                                                                                       >  2:57541/1‑141 (MQ=255)         aTCCTGAACAATTATTTGAAAAAATTTATCTTGGAAAAGTACAACATATGAAACGTAATAAAGCTGAAGTGATTGCATTAGACATCGTAAATGACTTTAGTAAAGAAAAAATTATTAACTATGCCAATGGCAAAAAGGgag                                                                                                                     <  2:344587/141‑1 (MQ=255)           ccTGAACAAGTATTTCAAAAAATTTATCGTGGCAAAGTACAACATATGAAATGTAATGAAGTTGAAGCGATTATTCAAGACATCGTCAATGACTTTAGTAAAGAAAAAATTATTAACTATTCCAATGGCAAAAAGGGAGAt                                                                                                                   <  1:346278/141‑1 (MQ=255)           ccTGAACAAGGATTTGAAAAAATTTATCGTGGCAAAGTACAACATATGAAATGTAATGAAGTTGAAGCGATTATTCAAGACATCGTCAATGACTTTAGTAAAGAAAAAATTATTAACTATGCCAATGGCAAAAAGGGAGAt                                                                                                                   <  1:451434/141‑1 (MQ=255)              gAACAAGTATTTGAAAAAATTTATCGTGGCAAAGTACAACATATGAAATGTAATGAAGTTGAAGCGATTATTCAAGACATCGTCAATGACTTTAGTAAAGAAAAAATTATTAACTATGCCAATGGCAAAAAGGGAGATAAt                                                                                                                <  1:321882/141‑1 (MQ=255)               aaCAAGTATTTGAAAAAATTTAACGAGGGAAAGTACAACATATGAAATGTAATGAAGTTGAAGCGATTATTCAAGACATCGGCAATGAATTTAGTAAAGAAAAAATTATTAACTAAAAAAAAAAAAAAAAGGGAGATAAtt                                                                                                               <  2:450083/141‑1 (MQ=255)                 cAAGTATTTGAAAAAATTTATCGTGGCAAAGTACAACATATGAAATGTAATGAAGTTGAAGCGATTATTCAAGACATCGTCAATGACTTTAGTAAAGAAAAAATTATTAACTATGCCAATGGCAAAAAGCGAGATAATTAt                                                                                                             <  1:83368/141‑1 (MQ=255)                   aGTATTTGAAAAAATTTATCGTGGCAAAGTACAACATATGAAATGTAATGAAGTTGAAGCGATTATTCAAGACATCGTCAATGACTTTAGTAAAGAAAAAATTATTAACTATGCCAATGGCAAAAAGGGAGATAATTATGt                                                                                                           >  2:146689/1‑141 (MQ=255)                   aGTATTTGAAAAAATTTATCGTGGCAAAGTACAACATATGAAATGTAATGAAGTTGAAGCGATTATTCAAGACATCGTCAATGACTTTAGTAAAGAAAAAATTATTAACTATGCCAATGGC‑AAAAGGGAGATAATTATGtt                                                                                                          >  2:468217/1‑141 (MQ=255)                      aTTTGAAAAAATTTATCGTGGCAAAGTACAACATATGAAATGTAATGAAGTTGAAGCGATTATTCAAGACATCGTCAATGACTTTAGTAAAGAAAAAATTATTAACTATGCCAATGGCAAAAAGGGAGATAATTATGTTcc                                                                                                        >  2:423770/1‑140 (MQ=255)                           aaaaaaTTTATCGTGGCAAAGTACAACTTATGAAATGTAATTAAGTTGAAGCGATTATTCAAGGCATCGTCAATGACTTTAGTAAAGAAAGAATTATTAACTATGCCAATGGCATAAAGGATGATAATTTTGTTCAA‑TGaa                                                                                                  >  2:479256/1‑140 (MQ=255)                           aaaaaaTTTATCGTGGCAAAGTACAACATATGAAATGTAATGAAGTTGAAGCGATTATTCAAGACATCGTCAATGACTTTAGTAAAGAAAAAATTATTAACTATGCCAATGGCAAAAAGGGAGATAATTATGTTCGA‑TGAc                                                                                                  >  2:83952/1‑141 (MQ=255)                             aaaaTTTATCGTGGCAAAGTACAACATATGAAATGTAATGAAGTTGAAGCGATTATTCAAGACATCGTCAATGACTTTAGTAAAGAAAAAATTATTAACTATGCCAATGGCAAAAAGGGAGATAATTATGTTCGA‑TGACaa                                                                                                >  1:279834/1‑141 (MQ=255)                                atttaagttGGTAAAGAAAAACATATGAAATGTAATGAAGATGAAGCGAGTATTCAAGACATCGCCAATGAATTTAGTAAAGAAAAAATTATTAACTAAAAAAAAAAAAAAAAGGGAGATAATTATGTTCGA‑TGACAAAAt                                                                                             <  2:350844/133‑1 (MQ=255)                                   tATCGTGGCAAAGTACAACATATGAAATGTAATGAAGTTGAAGCGATTATTCAATACATCTTCAATGACTTTAGTAAAGAAAAAATTATTAACTATGACCATGGCAAAAAGGGAGATAATTATGTTCGA‑TGACAAAAtttt                                                                                          >  2:64499/1‑141 (MQ=255)                                   tATCGTGGCAAAGTACAACATATGAAATGTAATGAAGTTGAAGCGATTATTCAAGACATCGTCAATGACTTTAGTAAAGAAAAAATTATTAACTATGCCAATGGCAAAAAGGGAGATAATTATGTTCGA‑TGACAAAAtttt                                                                                          <  1:17616/141‑1 (MQ=255)                                      cGTGGCAAAGTACAACATATGAAATGTAATGACGGTGAAGCGATTATTCAAGACATCGTCAATGACTTTAGTAAAGAAAAAATTATTAACTATGCCAATGGCAAAAAGGGAGATAATTATGTTCGA‑TGACAAAATTttatt                                                                                       <  1:530905/141‑1 (MQ=255)                                      cGTGGCAAAGTACAACATATGAAATGTAAGGAAGTTGACGCGCATCAACGGGGCAGCGTTAATGACTTTAGTAAAGAAAAAATTATTAACTATGCCAATGGCAAAAAGGGAGATAATTATGTTCGA‑TGACAAAATTttatt                                                                                       <  1:469083/141‑1 (MQ=255)                                         ggCAAAGTACAACATATGAAATGTAATGAAGTTGAAGCGATTATTCAAGACATCGTCAATGACTTTAGTAAAGAAAAAATTATTAACTATGCCAATGGCAAAAAGGGAGATAATTATGTTCGA‑TGACAAAATTTTattaat                                                                                    <  1:322626/141‑1 (MQ=255)                                                tACAACATATGAAATGTAATGAAGTTGAAGCGATTATTCAAGACATCGTCAATGACTTTAGTAAAGAAAAAATTATTAACTATGCCAATGGCAAAAAGGGAGATAATTATGTTCGA‑TGAAAAAATTTTATTAATTACTggg                                                                             >  1:479327/1‑141 (MQ=255)                                                  aaacaAATGAAAAGGAATGAAGTTGAAACGATTATTCAAGACATCGTCAATTAATTTAGTAAAGAAAAAATTATTAATTAAAAAAAAAGAAAAAAGGGAGATAATTATGTTCGA‑TGACAAAATTTTATTAATTACTggggg                                                                           <  2:64150/140‑1 (MQ=255)                                                            aaTGTAATGAAGTTGAAGCGATTATTCAAGACATCGTCAATGACTTTGGTAAAGAAAAAATTATTAACTATGCCAATGGCAAAAAGGGAGATAATTATGTTCGA‑TGACAAAATTTTTTTAATTACTGGGGGCACGGGATCa                                                                 >  1:261362/1‑141 (MQ=255)                                                            aaTGTAATGAAGTTGAAGCGATTATTCAAGACATCGTCAATGACTTGAGTAAAGAAAAAATTAGTAACTATGCCAATGGCAAAAAGGGAGATGATTATGTTCTA‑TGACAAAATTTTATTAATTACTGGGGGCACAGGATCa                                                                 <  2:168240/141‑1 (MQ=255)                                                              tGTAATGAAGTTGAAGCGATTATTCAAGACATCGTCAATGACTTTAGTAAAGAAAAAATTATTAACTATGCCAATGGCAAAAAGGGAGATAATTATGTTCGA‑TGACAAAATTTTATTAATTACTGGGGGCACAGGATCAtt                                                               <  2:354440/141‑1 (MQ=255)                                                                tAATGAAGTTGAAGCGATTATTCAAGCCATCGTCAATGACTTTAGTAAAGAAAAAATTATTAACTAAAAAAAAGAAAAAAAGGGAGATAATTATGTTCGA‑TGACAAAATTTTATTAATTACTGGGGGCACAGGATCATTCg                                                             <  2:524704/141‑1 (MQ=255)                                                                 aaTGAAGTTGAAGCGATTATTCAAGACATCGTCAATGACTTTAGTAAAGAAAAAATTATTAACTATGCCAATGGCAAAAAGGGAGATAATTATGTTCGA‑TGACAAAATTTTATTAATTACTGGGGGCACAGGATCATTCgg                                                            >  1:19954/1‑141 (MQ=255)                                                                  atgaagagaaaGCGATTATACAAGACAACGACAATGAATAAAGTAAAGAAAAAATTATTAACTAAAAAAAAAAAAAAAAGGGAGATAATTATGTTCGA‑TGACAAAATTTTATTAATTACTGGGGGCACAGGATCATTCGGt                                                           <  2:479868/132‑1 (MQ=255)                                                                  aTGAAGTTGAAGCGATTATTCAAGACATCGTCAATGACTGTAGTAAAGAAAAAATTATTAACTATGCCAATGGCAAAAAGGGAGATAATTATGTTCGA‑TGACAAAATTTTATTAATTACTGGGGGCACAGGATCATTCGGt                                                           <  2:369124/141‑1 (MQ=255)                                                                          taaGCGATTATTCAAGACATCGTCAATGACTTTAGTAAAGAAAAAATTATTAACTATGCCAATGGCAAAAAGGGAGATAATTATGTTCGA‑TGACAAAATTTTATTAATTACTGGGGGCACAGGATCATTCGGTAATGCTGt                                                   >  2:211893/2‑141 (MQ=255)                                                                            ggCGTTTTTTCAAGACATCGTCAATGACTTTAGTAAAGAAAAAATTATTAACTATGCCAATGGCATAAAGGGAGATAATTATGTTCGA‑TGACAAAATTTTATTAATTAATGGGGGCACAGGGTAATTCGGTAATgttgttt                                                 >  2:67896/2‑140 (MQ=255)                                                                             gCGATTATTCAAGACATCGTCAATGACTTTAGTAAAGAAAAAATTATTAACTATGCCAATGGCAAAGAAGGAGATAATTATG‑TCGATTGCCTTAATTTTATTAATTACTGGTGGCACAGGATCATTCGGTAATGCTGTTAt                                                >  1:108195/1‑141 (MQ=255)                                                                                 ttattCAAGACATCGTCAATGACTTTAGTAAAGAAAAAATTATTAACTATGCAAATGGCAAAAAGGGAGATAATTATGTTCGC‑TGACAAAATTTTATTAATTATTGGGGGCACAGGATAATACGGTAATGCGGTTATGaaa                                            >  2:214963/1‑141 (MQ=255)                                                                                    ttCAAGACATCGTCAATGACTTTAGTAAAGAAAAAATTATTAACTATGCCAATGGCAAAAAGGGAGATAATTATGTTCGA‑TGACAAAATTTTATTAATTACTGGGGGCACAGGATCATTCGGGAATGCAGTTAGGAACCAg                                         >  1:468086/1‑141 (MQ=255)                                                                                      cAAGACATCGTCAATGACTTTAGTAAAGAAAAAATTATTAACTATGCCAATGGCAAAAAGGGAGATAATTATGTTCGA‑TGACAAAATTTTATTAATTACTGGGGGCACAGGATCATTCGGTAATGCTGTTATGAAACAGtt                                       <  1:354596/141‑1 (MQ=255)                                                                                        aGACATCGTCAATGACTTTAGTAAAGAAAAAATTATTAACTATGCCAATGGCAAAAAGGGAGATAATTATGTTCGA‑TGACAAAATTTTATTAATTACTGGGGGCACAGGATCATTCGGTAATGCTGTTATGAGACAGtttt                                     >  1:243115/1‑141 (MQ=255)                                                                                        aGACATAGTCAAAGACTTTAGTAAAGAAAAAATTATTAACTAAAAAAAAAAAAAAAAGGGAGATAATTATGTTCGA‑TGACAAAATTTTATTAATTACTGGGGGCACAGGATCATTCGGTAATGCTGTTATGAAACAGtttt                                     <  2:133163/141‑1 (MQ=255)                                                                                         gACATCGTCAATGACTTTAGTAAAGAAAAAATTATTAACTATGCCAATGGCAAAAAGGGAGATAATTATGTTCGA‑TGACAAAATTTTATTAATTACTGGGGGCACAGGATCATTCGGTAATGCTGTTATGAAACAGttttt                                    <  1:527287/141‑1 (MQ=255)                                                                                         gACATCGTCAATGACTTTAGTAAAGAAAAAATTATTAACTATGCCAATGGCAAAAAGGGAGATAATTATGTTCGA‑TGACAAAATTTTATTAATTACTGGGGGCACAGGATCATTCGGTAATGCTGTTATGAAACAGttttt                                    <  1:146689/141‑1 (MQ=255)                                                                                               gTCAATGACTTTAGTAAAGAAAAAATTATTAACTATGCCAATGGCAAAAAGGGAGATAATTATGTTCGA‑TGACAAAATTTTATTAATTACTGGGGGCACAGGATCATTCGGTAATGCTGTTATGAAACAGTTTTTAGAtac                              >  2:567910/1‑139 (MQ=255)                                                                                                 cAATGACTTTAGTAAAGAAAAAATTATTAACTATGCCAATGGCAAAAAGGGAGATAATTATGTTCGA‑TGACAAAATTTTATTAATTACTGGGGGCACAGGATCATTCGGTAATGCTGTTATGAAACAGTTTTTAGATTCTa                            >  2:36716/1‑141 (MQ=255)                                                                                                   aTGACTTTAGTAAAGAAAAAATTATTAACTATGCCAATGGCAAAAAGGGAGATAATTATGTTCGA‑TGACAAAATTTTATTAATTACTGGGGGCACAGGATCATTCGGTAATGCTGTTATGAAACAGTTTTTAGATTCTAat                          >  1:405478/1‑141 (MQ=255)                                                                                                               aaGAAAAAATTATTAACTATGCCAATGGCAAAAAGGGAGATAATTATGTTCGA‑TGACAAAATTTTATTAATTACTGGGGGCACAGGATCATTCGGTAATGCTGTTATGAAACAGTTTTTAGATTCTAATATTAAAGAAAtt              >  2:273541/1‑141 (MQ=255)                                                                                                                    aaaaTTATTAACTATGCCAATGGCAAAAAGGGAGATAATTATGTTCGA‑TGACAAAATTTTATTAATTACTGGGGGCACAGGATCATTCGGTAATGCTGTTATGAAACAGTTTTTAGATTCTAATATTAAAGAAATTCGTAt         >  1:396154/1‑141 (MQ=255)                                                                                                                    aaaaTTATTAACTATGCCAATGGCAAAAAGGGAGATAATTATGTTCGA‑TGACAAAATTTTATTAATTACTGGGGGCACAGGATCATTCGGTAATGCTGTTATGAAACAGTTTTTAGATTCTAATATTAAAGAAATTCGTAt         <  2:279834/141‑1 (MQ=255)                                                                                                                    aaaaTTATTAACTATGCCAATGGCAAAAAGGGAGATAATTATGTTCGA‑TGACAAAATTTTATTAATTACTGGGGGCACAGGATCATTCGGTAATGCTGTTATGAAACAGTTTTTAGATTCTAATATTAAAGAAATTCGTAt         >  2:39231/1‑141 (MQ=255)                                                                                                                    aaaaTTATTAACTATGCCAATGGCAAAAAGGGAGATAATTATGTTCGA‑TGACAAAATTTTATTAATTACTGGGGGCACAGGATCATTCGGTAATGCTGTTATGAAACAGTTTTTAGATTCTAATATTAAAGAAATTCGTAt         >  2:365021/1‑141 (MQ=255)                                                                                                                     aaaTTATTAACTATGCCAATGGCAAAAAGGGAGATAATTATGTTCGA‑TGACAAAATTTTATTAATTACTGGGGGCACAGGATCATTCGGTAATGCTGTTATGAAACAGTTTTTAGATTCTAATATTAAAGAAATTCGTAtt        >  2:286450/1‑141 (MQ=255)                                                                                                                     aaaTTATTAACTATGCCAATGGCAAAAAGGGAGATAATTATGTTCGA‑TGACAAAATTTTATTAATTACTGGGGGCACAGGATCATTCGGTAATGCTGTTATGAAACAGTTTTTAGATTCTAATATTAAAGAAATTCGTAtt        <  2:243115/141‑1 (MQ=255)                                                                                                                           ttaACTATGCCAATGGCAAAAAGGGAGATAATTATGTTCGA‑TGACAAAATTTTATTAATTACTGGGGGCACAGGATCATTCGGTAATGCTGTTATGAAACAGTTTTTAGATTCTAATATGAAAGAAATTCGTAttttttaa  >  1:551522/1‑139 (MQ=255)                                                                                                                                     |                                                                                                                                    TGAGGTTCATCCTGAACAAGTATTTGAAAAAATTTATCGTGGCAAAGTACAACATATGAAATGTAATGAAGTTGAAGCGATTATTCAAGACATCGTCAATGACTTTAGTAAAGAAAAAATTATTAACTATGCCAATGGCAAAAAGGGAGATAATTATGTTCGA‑TGACAAAATTTTATTAATTACTGGGGGCACAGGATCATTCGGTAATGCTGTTATGAAACAGTTTTTAGATTCTAATATTAAAGAAATTCGTATTTTTTCA  >  CP000730/177871‑178133

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: ‑