Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 618,567 T→C 18.0% D1223D (GAT→GAC)  sdrD → Serine‑aspartate repeat‑containing protein D

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE618,5670TC18.0% 70.3 / 2.9 37D1223D (GAT→GAC) sdrDSerine‑aspartate repeat‑containing protein D
Reads supporting (aligned to +/- strand):  ref base T (16/14);  new base C (5/2);  total (21/16)
Fisher's exact test for biased strand distribution p-value = 6.74e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GATAGCGACTCAGATTCAGACAGCGACTCAGATTCAGACAGCGACTCAGACTCAGATAGTGATTCAGACTCAGATAGCGACTCAGATTCAGACAGCGACTCAGACTCAGACAGCGACTCAGACTCAGATAGTGACTCAGATTCAGATAGCGACTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGACTCAGATTCAGATAGTGATTCAGACTCAGATAGCGACTCAGATTCAGACAGCGACT  >  USA300TCH1516_ALE/618427‑618706
                                                                                                                                            |                                                                                                                                           
gATAGCGACTCAGATTCAGACAGCGACTCAGATTCAGACAGCGACTCAGACTCAGATAGTGATTCAGACTCAGATAGCGACTCAGATTCAGACAGCGACTCAGACTCAGACAGCGACTCAGACTCAGATAGTGACtcagat                                                                                                                                             >  1:127351/1‑141 (MQ=255)
  tAGCGACTCAGATTCAGACAGCGACTCAGATTCAGACAGCGACTCAGACTCAGATAGTGATTCGGACTCAGATAGCGACTCAGATTCAGACAGCGACTCAGACTCAGACAGCGACTCAGACTCAGATAGTGACtcagattc                                                                                                                                           <  1:266514/141‑1 (MQ=255)
    gcgactcagattcagacagcgactcagattcagacaGCGACTCAGACTCAGATAGTGACTCAGACTCAGATAGCGACTCAGATTCAGACAGCGACTCAGACCCAGACAGCGACTCAGACTCAGATAGCGACtcagatcccg                                                                                                                                         >  2:282267/1‑137 (MQ=255)
              ttcagacagcgactcagattcagacagcgactcagaCTCAGATAGTGATTCAGACTCAGATAGCGACTCAGATTCAGACAGCGACTCAGAGTCAGATGTCGACTCAGACCCAGATAGTGACTCAGATTCAGATAGCGACTc                                                                                                                               >  1:170655/1‑141 (MQ=17)
                 acagcgtgactcagattcagacacccactcagaTTCGGACTGTTATTCAGACTCAGACGGCCACTCAGATTCAGACCGCGCCTCAGACTCAGACACCGACTCAGACTCAGATAGTGATTCAGACTCAGATAGCGACTCAGa                                                                                                                            <  2:127351/134‑1 (MQ=2)
                      gcgactcagattcagacagcgactcagaCTCAGATAGCGATTCAGACTCAGATAGCGACTCAGATTCAGACAGCGACTCAGACTCAGACAGCGACTCAGACTCAGATAGCGACTCAGGTTCAGATAGCGACTCAGAATCgg                                                                                                                       >  2:186301/1‑141 (MQ=255)
                         actcagattcagacagcgactcagaCTCAGATAGTGATTCAGACTCAGATAGCGACTCAGATTCAGACAGCGACTCAGACTCAGACAGCGACTCAGACTCAGATAGTGACTCAGACTCAGATAGCGACTCAGAATCGGACa                                                                                                                    >  2:103811/1‑141 (MQ=255)
                         actcagattcagacagcgactcagaCTCAGATAGTGACTCAGACTCAGATAGCGACTCAGATTCGGACAGCGACTCAGACTCAGACAGCGACTCAGACTCAGATAGTGACTCAGATTCAGATAGCGACGCAGATTCGGAcg                                                                                                                    >  2:272344/1‑140 (MQ=255)
                             agattcagacagcgactcagaCTCAGATAGTGATTCAGACTCAGATAGCGACTCAGATTCAGACAGCGACTCAGACTCAGACAGCGACTCAGACTCAGATAGTGACTCAGATTCAGATAGCGACTCAGATTCGGACAGCGa                                                                                                                <  1:61699/141‑1 (MQ=255)
                                   tccacacgacacagaCTCCGAACGAGAATTAGAATCAGAAAGACACTCAGAATCAGACAGCGACTCAGACTCAGACAGCGACTCAGACTCAGATAGTGACTCAGATTCAGATAGCGACTCAGATTCGGACAGCGATTCAGa                                                                                                          <  2:127790/135‑1 (MQ=14)
                                    gacagcgactcagaCTCAGATAGTGATTCAGACTCAGATAGCGCCTCAGATTCAGACAGCGACTCAGACTCAGACAGCGACTCAGACTCAGATAGTGACTCAGATTCAGATAGCGACTCAGATTCGGACAGCGATTCAGAc                                                                                                         <  1:27182/141‑1 (MQ=255)
                                                  ctcagaTAGTGATTCAGACTCAGATAGCGACTCAGATTCAGACAGCGACTCAGACTCTGTCATCGACTCAGACTCAGATAGTGACTCAGATTCAGATAGCGACTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACtc                                                                                           <  1:287361/141‑1 (MQ=255)
                                                  ctcagaTAGTGATTCAGACTCAGATAGCGACTCAGATTCAGACAGCGACTCAGACTCAGACAGCGACTCAGACTCAGATAGTGACTCAGATTCAGATAGCGACTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACtc                                                                                           <  1:4637/141‑1 (MQ=255)
                                                  ctcagaTAGAGAATCAGACTCAGATAGCGACTCAGATTCAGACAGCGACTCAGACTCAGACAGCGACTCAGACTCAGATAGTGACTCAGATTCAGATAGCGACTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACtc                                                                                           <  1:383549/141‑1 (MQ=255)
                                                    cagaTAGTGATTCAGACTCAGATAGCGACTCAGATTCAGACAGCGACTCAGACTCAGACAGCGACTCAGACTCAGATAGTGACTCAGATTCAGATAGCGACTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACtcag                                                                                         <  1:57312/141‑1 (MQ=255)
                                                     agaTAGTGATTCAGACTCAGATAGCGACTCAGATTCAGACAGCGACTCAGACTCAGACAGCGACTCAGACTCAGATAGTGACTCAGATTCAGATAGCGACTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACtcaga                                                                                        >  1:114495/1‑141 (MQ=255)
                                                     agaTAGTGATTCAGACTCAGATAGCGACTCAGATTCAGACAGCGACTCAGACTCAGACAGCGACTCAGACTCAGATAGTGACTCAGACTCAGATAGCGACTCAGATTCGGACACCGACTCAGACTCAGATGGCGACccaga                                                                                        >  2:185956/1‑141 (MQ=11)
                                                                cAGACTCAGATAGCGACTCAGATTCAGACAGCGACTCAGACTCAGACAGCGACTCAGACTCAGATAGCGACTCAGATTCAGATAGCGACTAAGACTCGGCTAGCGATTCAGAATCAGATAGCGACTCAGATTCAGAGAGCg                                                                             >  2:25286/1‑141 (MQ=14)
                                                                   aCTCAGATAGCGACTCAGATTCAGACAGCGACTCAGACTCAGATAGCGACTCAGAGTCAGATAGTGACTCAGACTCAGGTAGGGAGTCAGATTCTGAAAGCGAATCAGACTCAGAGAGCGAGACAGAGTCAGATGGCggag                                                                          >  2:87398/1‑138 (MQ=11)
                                                                   aCTCAGATAGCGACTCAGATTCAGACAGCGACTCAGACTCAGACGGCGACTCAGACTCTGATAGTGACTCAGATTCGGAGAGCGCCTCAGATTCGGACAGAGATTAAGACTGAGGTAGCGACTCAGGGTAAGGTAGCGaga                                                                          >  2:150555/1‑139 (MQ=14)
                                                                    cTCAGATAGCGACTCACATTCAGACAGCGACTCAGACTCAGACACCGACTCAGACTCAGATAGTGACTCAGATTCAGATAGCGACTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACTCAGATTCAGATAGCGATTc                                                                         <  2:206469/141‑1 (MQ=255)
                                                                        gATAGCGACTCAGATTCAGACAGCGACTCAGACTCAGACAGCGAATCAGACTCAGATAGTGACTCAGATTCAGATAGCGACTCAGAGTCGGACAGCGATTCAGACTCAGATATCGACTCAGATTCAGATAGCGATTCGGAc                                                                     >  1:224374/1‑141 (MQ=255)
                                                                              gACTCAGATTCAGACAGCGACTCAGACTCAGACAGCGACTCAGACTCAGATAGCGACTCAGATTCAGATAGCGACTCAGACTCAGACAGCCACTCAGAATCAGATAGCGACTCACAAACAGACAGCGAGTCGGAccccaaa                                                               >  2:5856/1‑135 (MQ=11)
                                                                                   aGATTCAGACAGCGACTCAGACTCAGACTGCGACTCAGACTCAGATAGTGACTCAGATTCAGATAGCGACTCAGATTCGGACAGCGATTCAGACTCTGATAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGa                                                          <  1:224030/141‑1 (MQ=255)
                                                                                   aGATTCAGACAGCGACTCAGACTCAGACAGCGACTCAGACTCAGATAGTGACTCAGATTCAGATAGCGACTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGa                                                          <  1:92273/141‑1 (MQ=255)
                                                                                     aTTCAGACAGCGACTCAGACTCAGACAGCGACTCAGACTCAGATAGTGACTCAGATTCAGATAGCGACTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGACt                                                        >  1:325081/1‑141 (MQ=255)
                                                                                     aTTCAGACAGCGACTCAGACTCAGACAGCGACTCAGACTCAGATAGTGACTCAGATTCAGATAGCGACTCAGACTCGGACACCGATTCAGACTCACATAGCGACGCAGATTCAGATAGCGATACGGACTCAGATAGCGAcc                                                        >  2:154317/1‑140 (MQ=17)
                                                                                     aTTCAGACAGCGACTCAGACTCAGACAGCGACTCAGACTCAGATAGTGACTCAGACTCAGATAGCGACCCAGATTCAGATAGCGATTCAGACTCAGATAACGACTCAGACTCAGATAGCGATGCAGACTCAGAGAACGAcc                                                        >  2:193451/1‑140 (MQ=11)
                                                                                            caaggactcagactcagacagggactcagactcagaTAGTGACTCAGATTCAGATAGCGACTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGACtcagattc                                                 <  2:8610/137‑1 (MQ=255)
                                                                                                  ctcagactcagacagcgacccagactcggaTAGTGACGCAGATTCAGATAGCGACTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGACTCAGATTCAGATAg                                           <  1:263227/141‑1 (MQ=255)
                                                                                                    cagactcagacagcgactcagactcagaTAGTGACTCAGACTCAGATAGCGACCCAGATTCGGCCAGCGAATCAGACTCAAATAGCGACTCAGATTCAGATAACGATTCGGACTCAGATAGCGCCTCACATTCAGAAAgcg                                         >  2:7618/1‑139 (MQ=14)
                                                                                                          cagacagcgactcagactcagaTAGTGACTCAGATTCAGATAGCGACTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGACTCAGATTCAGATAGTGATTCAg                                   >  1:325184/1‑141 (MQ=255)
                                                                                                            gacagcgactcagactcagaTAGTGACTCAGATTCAGATAGCGACTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGACTCAGATTCAGATAGTGATTCAGAc                                 >  1:176831/1‑141 (MQ=255)
                                                                                                                 cgactcagactcagaTAGTGACTCAGATTCAGATAGCGACTCAGATTCGGACAGCGATTCAGACTCAGATAGCGCCTCAGATTCAGATAGCGATTCGGACTCAGATAGCGACTCAGATTCAGATAGTGATTCAGACTCAGa                            <  2:114495/141‑1 (MQ=255)
                                                                                                                    ctcagactcagaTAGTGACTCAGATTCAGATAGCGACTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGACTCAGATTCAGATAGTGATTCAGACTCAGATAg                         >  1:384027/1‑141 (MQ=255)
                                                                                                                     tcagactcagaTAGTGACTCAGATTCAGATAGCGACTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGACTCAGATTCAGATAGTGATTCAGACTCAGATAGc                        >  1:136000/1‑141 (MQ=255)
                                                                                                                     tcagactcagaTAGTGACTCAGATTCAGATAGCGACTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACTCAGATTCAGATAACGATTCGGACTCCGATAGCGACTCAAACTCAGAAAGCGATTCCGACGCAGACAGc                        >  2:17994/1‑141 (MQ=14)
                                                                                                                     tcagactcagaTAGTGACTCAGATTCAGATAGCGACTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACTCAGATGCAGATAGCGATTCAGACGCAGATAGCGACCCAGATTCCGCTAGTGATTCAGACACAGATAGc                        >  2:90882/1‑141 (MQ=14)
                                                                                                                         actcagaTTGTGACTCAGATTCAGATAGCGACTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGACTCAGATTCAGATAGTGATTCAGACTCAGATAGCGACt                    <  1:231854/141‑1 (MQ=255)
                                                                                                                             cgatccggACGCAGACTCAGACAGCGACTCAGATTCTGACAGCGACTCAGACTCAGATAGCGACTCAGATTCAGACAGCGATTCGGACTCAGATAGCGACTCAGATTCAGATAGTGATTCAGACTCAGATAGCGACTCAGa                <  2:256933/134‑1 (MQ=11)
                                                                                                                                          gattcagatAGCGACTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGAGTCAGATTCAGATAGTGATTCAGACTCAGATAGCGAATCAGATTCAGACAGCGAc   >  1:187066/1‑141 (MQ=255)
                                                                                                                                           attcagatAGCGACTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGACTCAGATTCAGATAGTGATTCAGACTCAGATCGCGACTCAGAACCAGCCAGCGAcc  >  2:16859/1‑140 (MQ=255)
                                                                                                                                           attcagatAGCGACTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGACTCAGATTCAGATAGTGATTCAGACTCAGATAGCGACTCAGATTCAGACAGCGGCt  >  1:300874/1‑141 (MQ=255)
                                                                                                                                            |                                                                                                                                           
GATAGCGACTCAGATTCAGACAGCGACTCAGATTCAGACAGCGACTCAGACTCAGATAGTGATTCAGACTCAGATAGCGACTCAGATTCAGACAGCGACTCAGACTCAGACAGCGACTCAGACTCAGATAGTGACTCAGATTCAGATAGCGACTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACTCAGATTCAGATAGCGATTCGGACTCAGATAGCGACTCAGATTCAGATAGTGATTCAGACTCAGATAGCGACTCAGATTCAGACAGCGACT  >  USA300TCH1516_ALE/618427‑618706

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑