Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_007793 1,631,629 A→G Y112H (TAT→CAT)  SAUSA300_RS08065 ← integrase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0077931,631,6290AG98.7% 189.9 / ‑4.9 74Y112H (TAT→CAT) SAUSA300_RS08065integrase
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base G (3/70);  total (3/71)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.20e-01

ATATTTCTTGCCTGCTTGTCTCATATCACGCTTAACATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATACCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAGGAGACCATTTTAATGAAAGTTTTTCTTCAATATATGCTTTTGTTTCATCATTCA  >  NC_007793/1631534‑1631721
                                                                                               |                                                                                            
atatTTTTTGCCTGCTTGTCTCATATCACGCTTAACATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGccac                                                                                          <  1:2439795/100‑3 (MQ=255)
atatTTTTTGCCTGCTTGTCTCATATCACGCTTAACATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCt                                                                                          <  1:2072346/100‑1 (MQ=255)
  cttccgatcttGCTTGTCTCATATCACGCTTAACATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGt                                                                                        <  1:1308956/90‑1 (MQ=255)
  ccgatctGCCTGCTTGTCTCATATCACGCTTAACATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGt                                                                                        <  1:608184/94‑1 (MQ=255)
  atTTTTTGCCTGCTTGTCTCATATCACGCTTAACATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGt                                                                                        <  1:4072528/100‑1 (MQ=255)
  atTTTTTGCCTGCTTGTCTCATATCACGCTTAACATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGt                                                                                        <  1:3750953/100‑1 (MQ=255)
  atTTTTTGCCTGCTTGTCTCATATCACGCTTAACATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGt                                                                                        <  1:318541/100‑1 (MQ=255)
   tcttcgatcTGTTTGTCTCATATCACGCTTAACATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGtg                                                                                       <  1:2592969/92‑2 (MQ=255)
   cttccgatcTGCTTGTCTCATATCACGCTTAACATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTa                                                                                       <  1:1171378/92‑1 (MQ=255)
   cgatctGCCTGCTTGTCGCATATCACGCTTATCATCAACTTTTTCCAATCCATTGCAAGTATATCTATATATTGTAGGATAACTTATATAATGCCCTGTa                                                                                       <  1:415431/95‑1 (MQ=255)
    atCTTGCCTGCTTGTCTCATATCACGCTTAACATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTag                                                                                      <  1:5206481/99‑2 (MQ=255)
     ttttGCCTGCTTGTCTCATATCACGCTTAGCATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATc                                                                                     <  1:3202926/98‑1 (MQ=255)
     ttttGCCTGCTTGTCTCATATCACGCTTAACATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATc                                                                                     <  1:4825654/98‑1 (MQ=255)
       ttccgatcTTGTCTCATATCACGCTTAACATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCtg                                                                                   <  1:2589948/93‑2 (MQ=255)
       ttGCCTGCTTGTCTCATATCACGCTTAACATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCtt                                                                                   <  1:5181082/100‑1 (MQ=255)
       cttccgatctGTCTCATATCACGCTTAACATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCtt                                                                                   <  1:4241122/91‑1 (MQ=255)
       cgatcTGCTTGCCTCATATCACGCTTAACATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTacggt                                                                                   <  1:2286582/96‑5 (MQ=255)
        ggCCTGCTCGTCTCATATCACGCTTAACATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCttt                                                                                  >  1:1651356/2‑100 (MQ=255)
         gCCTGCTTGTCTCATATCACGCTTAACATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCtttt                                                                                 <  1:2689152/100‑1 (MQ=255)
         gCCTGCTTGTCTCATATCACGCTTAACATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCttgc                                                                                 <  1:4185296/100‑3 (MQ=255)
            tGCTTGTCTCATATCACGCTTAACATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCa                                                                              <  1:5485338/100‑1 (MQ=255)
                         acACGCTTAACATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTa                                                                 <  1:1756279/99‑1 (MQ=255)
                           aCGCTTAACATCATCTCTTACCAATCCATTGCGAATATATATATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATc                                                               <  1:3784522/100‑1 (MQ=255)
                            cGCTTAACATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTAttg                                                              <  1:2580342/100‑3 (MQ=255)
                              cTTAACATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTgg                                                            <  1:5184130/100‑2 (MQ=255)
                                tAACATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCt                                                          <  1:3099728/100‑1 (MQ=255)
                                tAACATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCt                                                          <  1:3659344/100‑1 (MQ=255)
                                tAACATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCt                                                          <  1:5038726/100‑1 (MQ=255)
                                tAACATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCt                                                          <  1:4141865/100‑1 (MQ=255)
                                tAACATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCt                                                          <  1:5587003/100‑1 (MQ=255)
                                tAACATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCt                                                          <  1:1785151/100‑1 (MQ=255)
                                tAACATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCt                                                          <  1:1873275/100‑1 (MQ=255)
                                 aaCATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAGTTTGACTTGCTATCTGTCTa                                                         <  1:4260688/100‑1 (MQ=255)
                                 aaCATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTa                                                         <  1:4030443/100‑1 (MQ=255)
                                  aCATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAg                                                        <  1:1247714/100‑1 (MQ=255)
                                   tccgatcTTTTACTAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAgg                                                       <  1:1752330/94‑1 (MQ=255)
                                   cATCAACTTTTACTAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAgg                                                       <  1:2000590/100‑1 (MQ=255)
                                   cATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTTTAgg                                                       <  1:250833/100‑1 (MQ=255)
                                   cATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAgg                                                       <  1:4322290/100‑1 (MQ=255)
                                   cATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAgg                                                       <  1:5405139/100‑1 (MQ=255)
                                   cATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAgg                                                       <  1:4535327/100‑1 (MQ=255)
                                   cATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAgg                                                       <  1:5573242/100‑1 (MQ=255)
                                   cATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAgg                                                       <  1:4537740/100‑1 (MQ=255)
                                   cATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAgg                                                       <  1:5340243/100‑1 (MQ=255)
                                   cATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAgg                                                       <  1:786309/100‑1 (MQ=255)
                                   cATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAgg                                                       <  1:5168542/100‑1 (MQ=255)
                                   cATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAgg                                                       <  1:970690/100‑1 (MQ=255)
                                   cATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAgg                                                       <  1:3223105/100‑1 (MQ=255)
                                   cATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAgg                                                       <  1:3892289/100‑1 (MQ=255)
                                   cATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAgg                                                       <  1:1123364/100‑1 (MQ=255)
                                   cATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAgg                                                       <  1:1241470/100‑1 (MQ=255)
                                   cATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAgg                                                       <  1:1332630/100‑1 (MQ=255)
                                   cATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAgg                                                       <  1:1510157/100‑1 (MQ=255)
                                   cATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAgg                                                       <  1:1585490/100‑1 (MQ=255)
                                   cATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAgg                                                       <  1:2047227/100‑1 (MQ=255)
                                   cATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAgg                                                       <  1:2158436/100‑1 (MQ=255)
                                   cATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAgg                                                       <  1:2864158/100‑1 (MQ=255)
                                   cATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAgg                                                       <  1:3721898/100‑1 (MQ=255)
                                   cATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAgg                                                       <  1:3095526/100‑1 (MQ=255)
                                   cATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAgg                                                       <  1:3488440/100‑1 (MQ=255)
                                   cATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAgg                                                       <  1:3379058/100‑1 (MQ=255)
                                   cATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAgg                                                       <  1:1046621/100‑1 (MQ=255)
                                   cATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTACCTGTCTAgg                                                       <  1:2816914/100‑1 (MQ=255)
                                   cATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATACCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAgg                                                       <  1:3087018/100‑1 (MQ=255)
                                   cATCAACATTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAgg                                                       <  1:5405256/100‑1 (MQ=255)
                                     tCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAGgag                                                     <  1:4101703/100‑1 (MQ=255)
                                        aCTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAGGAGAcc                                                  <  1:2889115/100‑1 (MQ=255)
                                        aCTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAGGAGAcc                                                  <  1:2922899/100‑1 (MQ=255)
                                                                   cTATATATAGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAGGAGACCATTTTAATGAAAGTTTTTCTTCAatat                       >  1:587909/1‑100 (MQ=255)
                                                                       atataGTAGGATAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAGGAGACCATTTTAATGAAAGTTTTTCTTCAATATATGc                   <  1:4314889/100‑1 (MQ=255)
                                                                                  tAACTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAGGAGACCATTTTAATGAAAGTTTTTCTTCAATATATGCTTTTGTTtcat        <  1:4388759/100‑1 (MQ=255)
                                                                                    ccTTATATAATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAGGAGACCATTTTAATGAAAGTTTTTCTTCAATATATGCTTTTGTTtcatca      >  1:2093157/2‑100 (MQ=255)
                                                                                        atataATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAGGAGACCATTTTAATGAAAGTTTTTCTTCAATATATGCTTTTGTTTCATCATTCa  <  1:1714003/100‑1 (MQ=255)
                                                                                        atataATGCCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAGGAGACCATTTTAATGAAAGTTTTTCTTCAATATATGCTTTTGTTTCATCATTCa  <  1:2398686/100‑1 (MQ=255)
                                                                                               |                                                                                            
ATATTTCTTGCCTGCTTGTCTCATATCACGCTTAACATCAACTTTTACCAATCCATTGCGAATATATCTATATATAGTAGGATAACTTATATAATACCCTGTATCTTTTTCAATTTGACTTGCTATCTGTCTAGGAGACCATTTTAATGAAAGTTTTTCTTCAATATATGCTTTTGTTTCATCATTCA  >  NC_007793/1631534‑1631721

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑