Predicted mutation
evidence seq id position mutation freq annotation gene description
RA KT2440 2,391,020 T→G 40.8% Q563P (CAG→CCG)  bvgS ← Virulence sensor protein BvgS

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*KT24402,391,0200TG40.8% 16.0 / 2.7 30Q563P (CAG→CCG) bvgSVirulence sensor protein BvgS
Reads supporting (aligned to +/- strand):  ref base T (7/8);  new base G (3/9);  total (13/17)
Fisher's exact test for biased strand distribution p-value = 4.24e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAAGGTAGCTGTAGTTGCAACTTTTCAGGCAACCCTCGCGGTCGCGCACATACATGGGGTGGGGCGTACCGTTGAGCAGGGCGCGCATGAATGCCAACTGGTCGTTCAGCGCGCGTTCGGCGCGCTGGCGCTGGCGAATCTGCAGGCGCAGGCGGGCATTCCAGAGCAGGGCCAGCAACAAAAGCACGGCCGTGGCCAGCACCACCTGCAGGGCCAGGCGGCTGTAGCCTTTGGAGTTGTCATCCTC  >  KT2440/2390895‑2391141
                                                                                                                             |                                                                                                                         
cAAGGTAGCTGTAGTTGCAACTTTTCAGGCAACCCTCGCGGTCGCGCACATACATGGGGTGGGGCGTACCGTTGAGCAGGGCGCGCATGAATGCCCACTGGTCGTTCCGCCCGCGTTCGGCgcgcaggcggagg                                                                                                                   >  4:170564/1‑130 (MQ=255)
cAAGGTAGCTGTAGTTGCAACTTTTCAGGCAACCCTCGCGGTCGCGCACATACATGGGGTGGGGCGTACCGTTGAGCAGGGCGCGCATGAATGCCAACTGGTCGTTGAGCCCGCGGTGGGCGCgctggccctggc                                                                                                                  >  4:170568/1‑135 (MQ=255)
cAAGGTAGCTGTAGTTGCAACTTTTCAGGCAACCCTCGCGGTCGCGCACATACATGGGGTGGGGCGTACCGTTGAGCAGGGCGCGCATGAATGCCAACTGGTCGTTCAGCGCGCGGTCGGCGCccaggcgcgggc                                                                                                                  >  4:156528/1‑135 (MQ=255)
cAAGGTAGCTGTAGTTGCAACTTTTCAGGCAACCCTCGCGGTCGCGCACATACATGGGGTGGGGCGTACCGTTGAGCAGGGCGCGCATGAATGCCAACTGGTCGTTCACCGCGCGGTCGGCGcgcttgcgctgggg                                                                                                                 >  8:360427/1‑134 (MQ=255)
        cTGTAGTTGCAACTTTTCAGGCAACCCTCGCGGTCGCGCACATACATGGGGTGGGGCGTACCGTTGAGCAGGGCGCGCATGAATGCCAACTGGTCGTTCAGCGCGCGTTCGGCGCGCTGGCGCTGGCGAATCTgc                                                                                                          <  5:447981/135‑1 (MQ=255)
          gTAGTTGCAACTTTTCAGGCAACCCTCGCGGTCGCGCACATACATGGGGTGGGGCGTACCGTTGAGCAGGGCGCGCATGAATGCCAACTGGTCGTTCAGCGCGCGTTAGGCGCGCTGGCGCGGGCGCATCTggcgg                                                                                                       >  8:284127/1‑132 (MQ=255)
              ttGCAACTTTTCAGGCAACCCTCGCGGGCGCGCACATACATGGGGGGGGGCGTACCGTTGAGCAGGGCGCGCATGAATGCCAACTGGGCGTTCAGCGCGCGTTCGGCGCGCTGGCGCTGGCGAATCTgcaggcg                                                                                                     <  2:46864/134‑1 (MQ=255)
              ttGCAACTTTTCAGGCAACCCGCGCGGTCGCGCACATACAGGGGGGGGGGCGTACCGTTGAGCAGGGCGCGCATGAATGCCAACTGGTCGTTCAGCGCGCGTTCGGCGCGCTGGCGCTGGCGAATCTgcaggcg                                                                                                     <  6:237325/134‑1 (MQ=255)
               tGCAACTTTTCCGCCACCCCGCGCGGCCGCGCACATCCAGGGGGGGGGGCGTCCCGTGGAGCCGGGCGCGCATGAATGCCACCGGGGCGTGCCGCGCGCGTGCGGCGCGCGGGCGCTGGCGAATCTgcaggcgca                                                                                                   <  2:438897/135‑1 (MQ=255)
               tGCAACTTTTCAGGCAACCCTCGCGGTCGCGCACATACATGGGGTGGGGCGTACCGTTGAGCAGGGCGCGCATGAATGCCAACTGGTCGTTCAGCGCGCGTTCGGCGCGCTGGCGCTGGCGAATCTgcaggcgca                                                                                                   <  2:67949/135‑1 (MQ=255)
                 cAACTTTTCAGGCAACCCTCGCGGTCGCGCACATACATGGGGTGGGGCGTACCGTTGAGCAGGGCGCGCATGAATGCCAACTGGTCGTTCAGCGCGCGGTCGGCGCGCTGGCGCTGGCGAATCTgcaggcgcaggc                                                                                                <  7:360427/136‑1 (MQ=255)
                  accTTTTCCGGCACCCCTCGCGGTCGCGCACATCCCGGGGGGGGGGCGTCCCGTTGAGCAGGGCGCGCATGAATGCCAACTGGGCGTTCAGCGCGCGTGCGGCGCGCGCGCGCTGGCGAATCTgcaggcgcaggc                                                                                                <  5:44759/133‑1 (MQ=255)
                  aaCTTTTCAGGCAACCCTCGCGGTCGCGCACAAACATGGGGTGGGGCGTACCGTTGAGCAGGGCGCGCATGAATGCCAACTGGTCGTTCAGCGCGCGTTCGGCGCGCTGGCGCTGGCGAATCTgcaggcgcaggc                                                                                                <  2:16162/135‑1 (MQ=255)
                  aaCTTTTCAGGCAACCATCGCGGACGCGCACATCCAGGGGGTGGGGCGGACCGTTGAGCAGGGCGCGCATGAATGCCAACTGGTCGTTCAGCGCGCGGTCGGCGCGCGGGCGCTGGCGAATCTgcaggcgcaggc                                                                                                <  5:162571/135‑1 (MQ=255)
                                     gcgGGCGCGCACATACATGGGGTGGGGCGTACCGTTGAGCAGGGCGCGCATGAATGCCAACTGGTCGTTCAGCGCGCGGTCGGCGCGCTGGCGCTGGCGAATCTGCAGGCGCAGGCGGGCATTCCAGAGCAggg                                                                              <  8:384081/134‑1 (MQ=255)
                                                          gtggggCGTACCGTTGAGCAGGGCGCGCATGAATGCCAACTGGTCGTTCAGCGCGCGTTCGGCGCGCTGGCGCTGGCGAATCTGCAGGCGCAGGCGGGCCTTACAGAGCAGGGCCAGCAACAAAAGCACGGCCGt                                                        >  6:209946/1‑135 (MQ=255)
                                                            ggggCGTACCGTTGAGCAGGGCGCGCATGAATGCCAACTGGTCGTTAAGACCGCGTTACGCGCCCCGGCGCGGTGCATTATGCAGTCGCCGGCCGGCATTACACAGCACCGCCAGACACAAAATCACCGCCCTgg                                                      >  6:420298/1‑135 (MQ=255)
                                                              ggCGTACCGTTGAGCAGGGCGCGCATGAATGCCAACTGGTCGTTCAGCGCGCGTTCGGCGCGCTGGCGCGGGCGCATCTGCAGGCGGCGGCGGGGGTTCCAGAGCCGGGGCCGCCACAAAATCCCCGCCCTgggcc                                                   >  7:123022/1‑133 (MQ=255)
                                                                cgcaCCGTGGCGCCGGGCGCGCATTAAGGCCACCTGGGCGTTCCGCGCGCGTGCGGCGCGGGGGCGCTGGCGAAGCTGCAGGCGCAGGCGGGCATCCCAGAGCAGGGCCAGCAACAAACGCACGGCCGTGGCCAg                                                  <  5:209946/132‑1 (MQ=255)
                                                                cGTACCGTTGAGCAGGGCGCGCATGAATGCCAACTGGTCGTTCAGCGCGCGGTCGGCGCGCTGGCGCTGGCGAATCTGCACGCGCCGGCGGGCCTTACAGAGCAGGGCCCGCCACAAAAGCACGGCCGTgggccc                                                  >  2:43852/1‑131 (MQ=255)
                                                                cGTACCGTTGAGCAGGGCGCGCATGAATGCCAACTGGTCGTTCAGCGCGCGGTCGGCGCGCGGGCGCTGGCGCATCTGCACGCGCAGGCGGGCCTTACAGAGCAGGGCCAGCAACAAAAGCACCGCCGTGGcccc                                                  >  3:290687/1‑133 (MQ=255)
                                                                cGTACCGTTGAGCAGGGCGCGCATGAATGCCAACTGGTCGTTCAGCGCGCGGTCGGCGCGCGGGCGCGGGGGAATCTGCACGCGCAGGCGGGCATTCCAGCGCAGGGCCCGCCACAAAAGCACGGCCGTGGcccc                                                  >  5:179586/1‑133 (MQ=255)
                                                                 gTACCGTTGAGCAGGGCGCGCATGAATGCCAACTGGTCGTTCAGCGCGCGGTAGGCGCGCTGGCGCTGGCGAATCTGCAGGCGCAGGCGGGCATTCCAGAGCAGGGCCCGCAACAAAAGCACGGCCCTGGCCAGc                                                 >  4:284581/1‑135 (MQ=255)
                                                                      gTTGCGCAGGGCGCGCATGAATGCCAACTGGTCGTGCCGCGCGCGTGCGGCGCGGTGGCGCTGGCGAATCTGCAGGCGCAGGCGGGCATTCCAGCGCCGGGCCAGCAACAAAAGCACGGCCGTGGCCAGcaccac                                            <  4:290687/135‑1 (MQ=255)
                                                                      gTTGAGCAGGGCGCGCATGAATGCCATCTGGTCGTTAACAGCGCGTTATGAGAGCAGGCGCTGGGGAAACTTGACGCGCCCGCGAGCAATCAATAAAACGGTCAGCAAACAAAGCACGGCCGGGGGAAGcacaaac                                           >  8:214916/1‑132 (MQ=255)
                                                                      gTTGAGCAGGGCGCGCATGAATGCCAACTGGTCGTTCACCGCCCCTTCCGCGCCCAGGCGCTGGGGAATGAGCAAGCGCAGGCGGGCAATACAGAGCACGGCCAGCAACAAAAGCACGGCCCGGGCCCGcaccac                                            >  4:226292/1‑135 (MQ=255)
                                                                            cAGGGCGCGCATGAATGCCAACTGGTCGTTCAGCCCGCGTTCCGCGCGCTGGCGCTGGCGAAACTGGAGGCCCAGGCGGGCAATCCCCAGCAGGGGCAGCAACAAAAGCACCGCCGCGGCCAGCCCCACCGGCac                                      >  2:46842/1‑134 (MQ=255)
                                                                             aGGGCGCGCATCAAGGCCAACTGGGCGGGCAGCGCGCGTGCGGCGCGCGGGCGCTGGCGAAGCTGCAGGCGCAGGCGGGCATTCCAGAGCAGGGCCAGCAACAAACGCACGGCCGTGGCCAGCACCACCTGCAggg                                    <  7:281676/136‑1 (MQ=255)
                                                                                gcgcgcATGACGCCCAACGGGCCGTCCCGCGCGCGGGCGGCGCGCGGGCGCGGGCGAATCTGCCGGCGCAGGCGGGCATTCCAGAGCCGGGCCAGCAACAAAAGCACGGCCGTGGCCAGCACCACCTGCAGGGcc                                  <  1:43852/135‑1 (MQ=255)
                                                                                ccgcgcTTGAAGCCCACGTGGGGGTGCAGCGGGCGTGCGGCGCGCGGGCGCTGGCGAATCTGCAGGCGCAGGCGGGCATTCCAGAGCAGGGCCAGCAACAAAAGCACGGCCGTGGCCAGCACCACCTGCAGGGcc                                  <  1:260216/134‑1 (MQ=255)
                                                                                  gcgcATGAATGCCAACTGGTCGTTGAGCGCGCGTTCGGCGCGCGGGCGCGGGCGAATATTCAGGCGCCGGCGGGCAGTCCAGCGCAGGGCCAGCAAAAAAATCAACGCCGTGGGCCCCCCCCCCAGCAGGGCCAg                                >  2:13749/1‑135 (MQ=255)
                                                                                      aTGAAGGCCAACTGGCCGGTCAGCGCGCGTGCGGCGCGCGGGCGCTGGCGACTCTGCAGGCGCAGGCGGGCATTCCAGACCCGGGCCAGCAACAAAAGCACGGCCGTGGCCAGCACCACCTGCAGGGCCAggcggc                           <  7:378957/136‑1 (MQ=255)
                                                                                       tGAAGGCCACCTGGGCGTGCCGCGCGGGGGCGGCGCGCGGGCGCTGGCGAATCTGCCGGCGCAGGCGGGCATTCCCGAGCAGGGCCAGCAACAAACGCACGGCCGTGGCCAGCACCACCTGCAGGGCCAggcggc                           <  6:100291/135‑1 (MQ=255)
                                                                                                                gcgTTAGGCGCGCTGGCGCTGGCGAATCTGCAGGCGCAGGCGGGCATTCCAGAGCAGGGCCAGCAACAAAACCACGGCCGTGGCCACCACCCCCTGCCGGGCCAGGCCGCAGTAGCCGTTTGAGTTGTGATccac  >  8:333895/1‑133 (MQ=255)
                                                                                                                             tggcgctggcgAATCTGCAGGCGCAGGCGGGCATTCCAGAGCAGGGCCAGCAACAAAAGCACGGCCGTGGCCAGCACCACCTGCAGGGCCAggcg                             >  7:331356/1‑95 (MQ=255)
                                                                                                                             tggcgctggcgAATCTGCAGGCGCAGGCGGGCATTCCAGAGCAGGGCCAGCAACAAAAGCACGGCCGTGGCCAGCACCACCTGCAGGGCCAggcg                             <  8:331356/95‑1 (MQ=255)
                                                                                                                             |                                                                                                                         
CAAGGTAGCTGTAGTTGCAACTTTTCAGGCAACCCTCGCGGTCGCGCACATACATGGGGTGGGGCGTACCGTTGAGCAGGGCGCGCATGAATGCCAACTGGTCGTTCAGCGCGCGTTCGGCGCGCTGGCGCTGGCGAATCTGCAGGCGCAGGCGGGCATTCCAGAGCAGGGCCAGCAACAAAAGCACGGCCGTGGCCAGCACCACCTGCAGGGCCAGGCGGCTGTAGCCTTTGGAGTTGTCATCCTC  >  KT2440/2390895‑2391141

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑