Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 189,365 A→G 16.7% Y409C (TAT→TGT)  cap5O → capsular polysaccharide biosynthesis protein Cap5O

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730189,3650AG16.7% 80.6 / 10.4 36Y409C (TAT→TGT) cap5Ocapsular polysaccharide biosynthesis protein Cap5O
Reads supporting (aligned to +/- strand):  ref base A (13/17);  new base G (3/3);  total (16/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01

GACGCATCGCTAGTATTGATTTTAAGTGACCACTCAGAATTTAAAAATTTATCGGACAGTCATTTTGATAAAATGAAGCATAAAGTGATTTTTGATACAAAAAATGTTGTGAAATCATCATTTGAAGATGTATCGTATTATAATTATGGCAATATATTTAATTTTATCGACAAATAAAATGTGTCAAACTAGGGCATACATGATTAAGGAAAGATAAGCTGTCATGTGTTTGAACTTCAGAGAGGATAATGTTATGAAAAAAATTATGGTTATTTTCGGT  >  CP000730/189226‑189505
                                                                                                                                           |                                                                                                                                            
gACGCATCGCTAGTATTGATTTTAAGTGACCACTCAGAATTTAAAAATTTATCGGACAGTCATTTTGATAAAATGAAGCATAAAGTGATTTTTTTTTTTTTTTTTTTTGTGAAATCATCATTTGAAGATGTATCGtattat                                                                                                                                             >  2:243179/1‑141 (MQ=255)
gACGCATCGCTAGTATTGATTTTAAGTGACCACTCAGAATTTAAAAATTTATCGGACAGTCATTTTGATAAAATGAAGCATAAAGTGATTTTTGATACAAAAAATGTTGTGAAATCATCATTTGAAGATGTATCGtattat                                                                                                                                             >  1:216364/1‑141 (MQ=255)
    cATCGCTAGTATTGATTTTAAGTGACCACTCAGAATTTAAAAATTTATCGGACAGTCATTTTGATAAAATGAAGCATAAAGTGATTTTTGATACAAAAAATGTTGTGAAATCATCATTTGAAGATGTATCGTATTGTAAtt                                                                                                                                         >  1:228387/1‑141 (MQ=255)
    cATCGCTAGTATTGATTTTAAGTGACCACTCAGAATTTAAAAATTTATCGGACAGTCATTTTGATAAAATGAAGCATAAAGTGATTTTTGATACAAAAAATGTTGTGAAATCATCATTTGAAGATGTATCGTATTGTAAtt                                                                                                                                         >  1:96969/1‑141 (MQ=255)
    cATCGCTAGTATTGATTTTAAGTGACCACTCAGAATTTAAAAATTTATCGGACAGTCATTTTGATAAAATGAAGCATAAAGTGATTTTTGATACAAAAAATGTTGTGAAATCATCATTTGAAGATGTATCGTATTATAAtt                                                                                                                                         >  2:88289/1‑141 (MQ=255)
    cATCGCTAGTATTGATTTTAAGTGACCACTCAGAATTTAAAAATTTATCGGACAGTCATTTTGATAAAAGGAAGCAGAAAGTGATTTTTGATACAAAAAATGTTGTGAAATCATCATTTGAAGATGTATCGTATTGTAAtt                                                                                                                                         >  1:389270/1‑141 (MQ=255)
               ttGATTTTAAGTGAGAACGCAGAATTTAAAAATTTATCGGACAGTCATTTTGATAAAATGAAGCATAAAGTGATTTTTGATACAAAAAATGTTGTGAAATCATCATTTGAAGATGTATCGTATTATAATTATGGCAatata                                                                                                                              >  1:109595/1‑141 (MQ=255)
               ttGATTTTAAGTGACCACTCAGAATTTAAAAATTTATCGTACAGTCATTCAGATAAGAAGTTGTAGAAAGAGATGTTGGAGCCGAAATATGATGTAAAATCATCATTTGAAGATGTATCGTATTATAATTATGGCAatata                                                                                                                              >  1:90962/1‑141 (MQ=255)
                 gATTTTCAGTGACCACTCAGAATTTAAAAATTTATCGGACAGTCATTTTGATAAAATGAAGCATAAAGTGATTTTTGATACAACACATGTTGTGCAATCATCATTTGAAGATGTATCGTATTATAATTATGGCCATATAtt                                                                                                                            <  2:114861/141‑1 (MQ=255)
                 gATTTTAAGTGACCACTCAGAATTTAAAAATTTATCGGACAGTCATTTTGATAAAATGAAGCATAAAGTGATTTTTGATACAAAAAATGTTGTGAAATCATCATTTGAAGATGTATCGTATTATAATTATGGCAATATAtt                                                                                                                            <  2:362063/141‑1 (MQ=255)
                     ttAAGTGACCACTCAGAATTTAAAAATTTATCGGACAGTCATTTTGATAAAATGAAGCATAAAGTGATTTTTGATACAAAAAATGTTGTGAAATCATCATTTGAAGATGTATCGTATTATAATTATGGCAATATATTTAAt                                                                                                                        <  2:90710/141‑1 (MQ=255)
                       aaGTGACCACTCAGAATTTAAAAATTTATCGGACAGTCATTTTGATAAAATGAAGCATAAAGTGATTTTTGATACAAAAAATGTTGTGAAATCATCATTTGAAGATGTATCGTATTATAATTATGGCAATATATTTAAttt                                                                                                                      <  1:40732/141‑1 (MQ=255)
                          tGACCACTCAGAATTTAAAAATTTATCGGACAGTCATTTTGATAAAATGAAGCATAAAGTGATTTTTGATACAAAAAATGTTGTGAAATCATCATTTGAAGATGTATCGTATTATAATTATGGCAATATATTTAATTTTAt                                                                                                                   >  1:84046/1‑141 (MQ=255)
                             ccACTCAGAATTTAAAAATTTATCGGACAGTCATTTTGATAAAATGAAGCATAAAGTGATTTTTGATACAAAAAATGTTGTGAAATCATCATTTGAAGATGTATCGTATTATAATTATGGCAATATATTTAATTTTATCGa                                                                                                                >  1:255879/1‑141 (MQ=255)
                             ccACTCAGAATTTAAAAATTTATCGGACAGTCATTTTGATAAAATGAAGCATAAAGTGATTTTTGATACAAAAAATGTTGTGAAATCATCATTTGAAGATGTATCGTATTATAATTATGGCAATATATTTAATTTTATCGa                                                                                                                >  1:15598/1‑141 (MQ=255)
                                cTCAGAATTTAAAAATTTATCGGACAGTCATTTTGATAAAATGAAGCATAAAGTGATTTTTGATACAAAAAATGTTGTGAAATCATCATTTGAAGATGTATCGTATTATAATTATGGCAATATATTTAATTTTATCGACaa                                                                                                             <  1:456174/141‑1 (MQ=255)
                                cTCAGAATTTAAAAATTTATCGGACAGTCATTTTGATAAAATGAAGCATAAAGTGATTTTTGATACAAAAAATGTTGTGAAATCATCATTTGAAGATGTATCGTATTATAATTATGGCAATATATTTAATTTTATCGACaa                                                                                                             >  2:297469/1‑141 (MQ=255)
                                cTCAGAATTTAAAAATTTATCGGACAGTCATTTTGATAAAATGAAGCATAAAGTGATTTTTGATACAAAAAATGTTGTGAAATCATCATTTGAAGATGTATCGTATTATAATTATGGCAATATATTTAATTTTATCGACaa                                                                                                             <  1:89957/141‑1 (MQ=255)
                                cTCAGAATTTAAAAATTTATCGGACAGTCATTTTGATAAAATGAAGCATAAAGTGATTTTTGATACAAAAAATGTTGTGAAATCATCATTTGAAGATGTATCGTATTATAATTATGGCAATATATTTAATTTTATCGACaa                                                                                                             <  1:90125/141‑1 (MQ=255)
                                       tttAAAAATTTATCGGACAGTCATTTTGATAAAATGAAGCATAAAGTGATTTTTGATACAAAAAATGTTGTGAAATCATCATTTGAAGATGTATCGTATTATAATTATGGCAATATATTTAATTTTATCGACAAATAAAAt                                                                                                      <  2:183228/141‑1 (MQ=255)
                                                           tCATTTTGATAAAATGAAGCATAAAGTGATTTTTGATACAAAAAATGTTGTGAAATCATCATTTGAAGATGTATCGTATTATAATTATGGCAATATATTTAATTTTATCGACAAATAAAATGTGTCAAACTAGGGCATACa                                                                                  <  1:88289/141‑1 (MQ=255)
                                                              ttttGATAAAATGAAGCATAAAGTGATTTTTGATACAAAAAATGTTGTGAAATCATCATTTGAAGATGTATCGTATTATAATTATGGCAATATATTTAATTTTATCGACAAATAAAATGTGTCAAACTAGGGCATACATGa                                                                               <  1:61348/141‑1 (MQ=255)
                                                                    tAAAATGAAGCATAAAGTGATTTTTGATACAAAAAATGTTGTGAAATCATCATTTGAAGATGTATCGTATTATAATTATGGCAATATATTTAATTTTATCGACAAATAAAATGTGTCAAACTAGGGCATACATGATTAAgg                                                                         >  1:24249/1‑141 (MQ=255)
                                                                      aaaTGAAGCATAAAGTGATTTTTGATACAAAAAATGTTGTGAAATCATCATTTGAAGATGTATCGTATTATAATTATGGCAATATATTTAATTTTATCGACAAATAAAATGTGTCAAACTAGGGCATACATGATTAAGGaa                                                                       >  2:182152/1‑141 (MQ=255)
                                                                          gAAGCATAAAGTGATTTTTGATACAAAAAATGTTGTGAAATCATCATTTGAAGATGTATCGTATTATAATTATGGCAATATATTTAATTTTATCGACAAATAAAATGTGTCAAACTAGGGCATACATGATTAAGGAAAGAt                                                                   >  2:42256/1‑141 (MQ=255)
                                                                          gAAGCATAAAGTGATTTTTGATACAAAAAATGTTGTGAAATCATCATTTGAAGATGTATCGTATTATAATTATGGCAATATATTTAATTTTATCGACAAATAAAATGTGTCAAACTAGGGCATACATGATTAAGGAAAGAt                                                                   >  2:311659/1‑141 (MQ=255)
                                                                          gAAGCATAAAGTGATTTTTGATACAAAAAATGTTGTGAAATCATCATTTGAAGATGTATCGTATTATAATTATGGCAATATATTTAATTTTATCGACAAATAAAATGTGTCAAACTAGGGCATACATGATTAAGGAAAGAt                                                                   >  2:74502/1‑141 (MQ=255)
                                                                                    gTGATTTTTGATACAAAAAATGTTGTGAAATCATCATTTGAAGATGTATCGTATTGTAATTATGGCAATATATTTAATTTTATCGACAGATAAAATGTGTCAAACTAGGGCATACATGATTAAGGAAAGATAAGCTGTCAt                                                         <  2:96969/141‑1 (MQ=255)
                                                                                    gTGATTTTTGATACAAAAAATGTTGTGAAATCATCATTTGAAGATGTATCGTATTGTAATTATGGCAATATATTTAATTTTATCGACAAATAAAATGTGTCAAACTAGGGCATACATGATTAAGGAAAGATAAGCTGTCAt                                                         <  2:389270/141‑1 (MQ=255)
                                                                                    gTGATTTTTGATACAAAAAATGTTGTGAAATCATCATTTGAAGATGTATCGTATTGTAATTATGGCAATATATTTAATTTTATCGACAAATAAAATGTGTCAAACTAGGGCATACATGATTAAGGAAAGATAAGCTGTCAt                                                         <  2:228387/141‑1 (MQ=255)
                                                                                             gATACAAAAAATGTTGTGAAATCATCATTTGAAGATGTATCGTATTATAATTATGGCAATATATTTAATTTTATCGACAAATAAAATGTGTCAAACTAGGGCATACATGATTAAGGAAAGATAAGCTGTCATGTGTTTGaa                                                >  1:316419/1‑141 (MQ=255)
                                                                                             gATACAAAAAATGTTGTGAAATCATCATTTGAAGATGTATCGTATTATAATTATGGCAATATATTTAATTTTATCGACAAATAAAATGTGTCAAACTAGGGCATACATGATTAAGGAAAGATAAGCTGTCATGTGTTTGaa                                                <  1:298102/141‑1 (MQ=255)
                                                                                                                   catcatTTGAAGATGTATCGTATTATAATTATGGCAATATATTTAATTTTATCGACAAATAAAATGTGTCAAACTAGGGCATACATGATTAAGGAAAGATAAGCTGTCATGTGTTTGAACTTCAGAGAGGATAATGTTATg                          <  1:297469/141‑1 (MQ=255)
                                                                                                                     tcatTTGAAGATGTATCGTATTATAATTATGGCAATATATTTAATTTTATCGACAAATAAAATGTGTCAAACTAGGGCATACATGATTAAGGAAAGATAAGCTGTCATGTGTTTGAACTTCAGAGAGGATAATGTTATGaa                        <  1:422000/141‑1 (MQ=255)
                                                                                                                     tcatTTGAAGATGTACCGTATTATAATTATGGCAATATATTTAATTTTATCGACAAATAAAATGTGTCAAACTAGGGCATACATGATTAAGGAAAGATAAGCTGTCATGTGTTTGAACTTCAGAGAGGATAATGTTATGaa                        <  1:327626/141‑1 (MQ=255)
                                                                                                                        tttGAAGATGTATCGTATTATAATTATGGCAATATATTTAATTTTATCGACAAATAAAATGTGTCAAACTAGGGCATACATGATTAAGGAAAGATAAGCTGTCATGTGTTTGAACTTCAGAGAGGATAATGTTATGaaaaa                     <  2:165600/141‑1 (MQ=255)
                                                                                                                                   aTCGTATTATAATTATGGCAATATATTTAATTTTATCGACAAATAAAATGTGTCAAACTAGGGCATACATGATTAAGGAAAGATAAGCTGTCATGTGTTTGAACTTCAGAGAGGATAATGTTATGAAAAAAATTATGGTTa          <  1:25867/141‑1 (MQ=255)
                                                                                                                                   aTCGTATTATAATTATGGCAATATATTTAATTTTATCGACAAATAAAATGTGTCAAACTAGGGCATACATGATTAAGGAAAGATAAGCTGTCATGTGTTTGAACTTCAGAGAGGATAATGTTATGAAAAAAATTATGGTTa          <  1:25832/141‑1 (MQ=255)
                                                                                                                                           ataATTATGGCAATATATTTAATTTTATCGACAAATAAAATGTGTCAAACTAGGGCATACATGATTAAGGAAAGATAAGCTGTCATGTGTTTGAACTTCAGAGAGGATAATGTTATGAAAAAAATTATGGTTATTTTCGGt  <  2:306163/141‑1 (MQ=255)
                                                                                                                                           |                                                                                                                                            
GACGCATCGCTAGTATTGATTTTAAGTGACCACTCAGAATTTAAAAATTTATCGGACAGTCATTTTGATAAAATGAAGCATAAAGTGATTTTTGATACAAAAAATGTTGTGAAATCATCATTTGAAGATGTATCGTATTATAATTATGGCAATATATTTAATTTTATCGACAAATAAAATGTGTCAAACTAGGGCATACATGATTAAGGAAAGATAAGCTGTCATGTGTTTGAACTTCAGAGAGGATAATGTTATGAAAAAAATTATGGTTATTTTCGGT  >  CP000730/189226‑189505

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