Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913_3_vch_tpiA 2,106,741 A→T S162S (TCT→TCA)  wbbH ← O‑antigen polymerase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_vch_tpiA2,106,7410AT96.9% 99.0 / ‑2.5 32coding (486/1167 nt)wbbHO‑antigen polymerase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base T (18/13);  minor base . (0/1);  total (18/14)
Fisher's exact test for biased strand distribution p-value = 4.38e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.17e-01

TCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACT  >  NC_000913_3_vch_tpiA/2106597‑2106878
                                                                                                                                                |                                                                                                                                         
tctATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGAcc                                                                                                                                       >  1:378473/1‑149 (MQ=255)
 ctATTAAAACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTT‑GACCaa                                                                                                                                     <  2:275654/149‑1 (MQ=255)
    ttAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCaaat                                                                                                                                   >  1:575979/1‑149 (MQ=255)
         acCTACGATGAATGCATAAGAGATGATAACCATAAAGAAAATTTACTTACCAGTAATGAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAaataaata                                                                                                                              >  1:449951/1‑149 (MQ=255)
           cTACGATGAATGCATAAGAGATGATAACCATAAAGACCATTTTCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACATGTAATTTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAAtaaataaa                                                                                                                            <  1:548069/149‑1 (MQ=255)
                       cATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGtt                                                                                                                <  2:378473/149‑1 (MQ=255)
                            gagaTGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAAt                                                                                                           >  1:570654/1‑149 (MQ=255)
                            gagaTGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAAAAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAAt                                                                                                           >  1:198178/1‑149 (MQ=255)
                                        aTAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGcct                                                                                               >  1:516791/1‑147 (MQ=255)
                                          aaaGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCaaataa                                                                                                                                 >  1:227522/1‑113 (MQ=255)
                                          aaaGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCaaataa                                                                                                                                 <  2:227522/113‑1 (MQ=255)
                                           aaGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAATGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATAATTGGCTGCATGTa                                                                                            >  1:573542/1‑149 (MQ=255)
                                              aCAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAAtaaataaa                                                                                                                            <  2:213972/114‑1 (MQ=255)
                                              aCAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAAtaaataaa                                                                                                                            >  1:213972/1‑114 (MQ=255)
                                                       ttACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAAtt                                                                                >  1:182428/1‑149 (MQ=255)
                                                           cAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCtt                                                                            >  1:534436/1‑149 (MQ=255)
                                                                ttCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAATTTATTAATGTTATAGTAGTTATAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAtgt                                                                       <  1:143264/149‑1 (MQ=255)
                                                                         aTTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGTTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAAc                                                              <  1:322783/149‑1 (MQ=255)
                                                                             cAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCa                                                          >  1:239399/1‑149 (MQ=255)
                                                                               aaGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATTTTTGGTTGCATGCATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGc                                                        <  1:447856/149‑1 (MQ=255)
                                                                                               aaaCAAGTAAAGTAAATGTTTTACTTACCTTTGTCCACCTAGATTTTTTTTACCAAATAAATAAAACAAAATTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTTTTCAACATAAGCATCTCTTATCAAATTc                                        >  2:377410/1‑149 (MQ=255)
                                                                                                    agtaaagtaaATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCAtata                                   >  1:487058/1‑149 (MQ=255)
                                                                                                       aaagtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGGTTGGCTGCATGTATGCTGAGAAATTTCTTGATATGGTTTCAACATCAGCATCTCTTATCAAATTCATATAGCt                                <  2:252507/149‑1 (MQ=255)
                                                                                                         agtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATTATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaa                              <  2:353846/149‑1 (MQ=255)
                                                                                                         aagaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTTGATTCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaa                              <  2:68527/146‑1 (MQ=255)
                                                                                                               tGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAATAAGc                        >  1:54424/1‑149 (MQ=255)
                                                                                                                   ttaattagCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAATTAACGTAGGTCTTATCAAATTCATATAGCTAAGTAAGCTAGt                    <  2:533549/149‑1 (MQ=255)
                                                                                                                           cTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACt            >  1:445217/1‑149 (MQ=255)
                                                                                                                               gTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTa        <  1:537623/149‑1 (MQ=255)
                                                                                                                                  ttAGTAAATTTTTTTGACCAAATAAATAAAGCATAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAAc                                                              <  1:103543/92‑1 (MQ=255)
                                                                                                                                  ttAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAAc                                                              >  2:103543/1‑92 (MQ=255)
                                                                                                                                     gTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACt  >  1:579957/1‑149 (MQ=255)
                                                                                                                                                |                                                                                                                                         
TCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACT  >  NC_000913_3_vch_tpiA/2106597‑2106878

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑