Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,324,247 C→A 12.8% P340Q (CCA→CAA)  mutL → DNA mismatch repair protein MutL

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,324,2470CA12.8% 122.4 / 2.1 52P340Q (CCA→CAA) mutLDNA mismatch repair protein MutL
Reads supporting (aligned to +/- strand):  ref base C (27/17);  new base A (2/6);  total (29/23)
Fisher's exact test for biased strand distribution p-value = 1.18e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

GTAGACGTAAATGTTCATCCAACAAAACTAGAAGTGCGTTTATCAAAAGAAGAGCAACTATACCAATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCCAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATCTGAAGAAAGTAACAGTAAGCCATTTATGGAAGAAAATCAA  >  USA300TCH1516_ALE/1324108‑1324383
                                                                                                                                           |                                                                                                                                        
gtagACGTAAATGTTCATCCAACAAAACTAGAAGTGCGTTTATCAAAAGAAGAGCAACTATACCAATTGATTGTGGGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATGATGTGcc                                                                                                                                          >  1:260478/1‑140 (MQ=255)
 tagACGTAAATGTTCATCCAACAAAACTAGAAGTGCGTTTATCAAAAGAAGAGCAACTATACCAATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCCa                                                                                                                                         >  1:382788/1‑140 (MQ=255)
 tagACGTAAATGTTCATCCAACAAAACTAGAAGTGCGTTTATAAAAAGTTGTGCAACGATACCCATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCCa                                                                                                                                         >  1:760823/1‑140 (MQ=255)
    aCGCAAATGTTCATCCAACAAAACTAGAAGTGCGTTTATCAAAAGAAGAGCAACTATACCAATTAATTGTGAGCAAACTATAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCCaaaa                                                                                                                                      <  2:698433/140‑1 (MQ=255)
        aaaaGTTCATCCAACAAAACTAGAAGTGCGATTAGCAAAAGAAGAGAAACTAAACAAATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTAAGTGaaaaaaaaaa                                                                                                                                  <  2:706826/140‑1 (MQ=255)
         aaTGTTCATCCAACAAAACTAGAAGTGCGTTTATCAAAAGAAGAGCAACTATACCAATTGATTGTGTTCGAAATAAAGAAAGCAATAAAACACCGTATATTCATTCATAAAACAACCTTGAATTAAGTGCCaaaaaaaaa                                                                                                                                 >  2:170321/1‑140 (MQ=255)
         aaTGTTCATCCAACAAAACTAGAAGTGCGTTTATCAAAAGAAGAGCAACTATACCAATTGATTATCAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTAGGCTTATGTGCCaaaaaaaaa                                                                                                                                 >  2:85765/1‑140 (MQ=255)
            gTTCAACAAACAAAGCTAGAACTGCGTATATAAACAGAAGAGCAACTATACCAATTTATTGTGAGCAAAATACAAGAAGCATTTAAAGACAGTATATTAATTCCTAAAAATAACTTGGATTATGTACCAAAAAAAAATaa                                                                                                                              <  2:60096/140‑1 (MQ=255)
              tgcaacaacaaAATTAGAAATGCGTTAATCAGAAGAAAAAGCACAATAACAAATGAAGATGAGCAAAATAAAAGATGCATTTAAAGACTGTATAATAATTCCTAAAAATAACTAAGATAATGAGCAAAAAAAAAATAAAg                                                                                                                            <  2:145941/135‑1 (MQ=255)
                 tCCAACAAAACTAGAAGTGCGTTTATCAAAAGAAGAGCAACTATACCAATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCCAAAAAAAAATAAAGAAt                                                                                                                         >  2:31872/1‑140 (MQ=255)
                      caaAACTAGAAGTGCGATTAAAAAAAAAAGAGCAACTATACCAATTGATTGTGAGCAAAATACAAGAAGCATTTGCGAACCGAAGATTAATTCCTAAAATTAACTTGGATTATGTGCCAAAAAAAAATAAAGTATTAcat                                                                                                                    <  2:96528/140‑1 (MQ=255)
                         aaCTAGAAGTGCGTTTATCAAAAGAAGAGCAACTATACCAATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCCAAAAAAAAATAAAGTATTAcattca                                                                                                                 >  1:192539/1‑140 (MQ=255)
                         aaCTAGAAGTGCGTTTATCAAAAGAAGAGCAACTATACCAATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCCAAAAAAAAATAAAGAATTAcattca                                                                                                                 >  2:694561/1‑140 (MQ=255)
                          aCTAGAAGTGCGTTTATCAAAAGAAGAGCAACTATACCAATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCCAAAAAAAAATAAAGTATTAcattcat                                                                                                                >  2:372945/1‑140 (MQ=255)
                             aGAAGTGCGTTTATCAAAAGAAGAGCAACTATACCAATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCCAAAAAAAAATAAAGTATTACATTCATTCg                                                                                                             >  1:469119/1‑140 (MQ=255)
                             aGAAGTGCGTTTATCAAAAGAAGAGCAACTATACCAATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAAATTGGATTATGTGCAAAAAAAAAATAAAGTATAACATACATTCg                                                                                                             >  2:294081/1‑140 (MQ=255)
                                aGTGCGTTTATCAAAAGAAGAGCAACTATACCAATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATATGTTGGAAAAAGCTCAAAAAAAAAATAAAGTATTACATTCATTCGaag                                                                                                          >  2:777551/1‑139 (MQ=255)
                                  tGCGTTTATCAAAAGAAGAGCAACTATACCAATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCCAAAAAAAAATAAAGTATTACATTCATTCGaacaa                                                                                                        <  1:708539/140‑1 (MQ=255)
                                       tcgacAAAAAAAAAGCAAATAGTCCAATTAATTGAGAGGAAAATACAAGAAGCAATTACAGACCGTATATTAAATCATAAAAATAACTTAAAATAAAT‑AAAAAAAAAAATAAAGTATTACATTCATTCGAACAACaaaaa                                                                                                  <  2:570012/136‑1 (MQ=255)
                                              aagaagAGCAACTATACCAAAAGAATTACAGCAAAATTGCAGTATAACGGAAAAGCCTGATATTAATTCCTAAAAATAACTTGGATTATGTGCCAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGaa                                                                                            <  1:371848/140‑1 (MQ=255)
                                                       aaCTATACCAATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCCAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACaa                                                                                   >  2:122755/1‑140 (MQ=255)
                                                         cTATACCAATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCCAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAg                                                                                 <  2:760823/140‑1 (MQ=255)
                                                                   tgattgTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCCAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAAcaca                                                                       >  1:179153/1‑140 (MQ=255)
                                                                     attgTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCCAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACaga                                                                     >  2:248600/1‑140 (MQ=255)
                                                                     aatttgAGCAAAATACAAGAAAGATTTAAAGACCGTAAAATAATGCGTAAAAAGAACTTGGATTATGTGCCAAAAAAAAATAAAGTATCACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACaga                                                                     <  2:324721/136‑1 (MQ=255)
                                                                       tgtgAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCCAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAgaga                                                                   <  2:64733/140‑1 (MQ=255)
                                                                       tgtgAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCCAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAgaga                                                                   >  1:116160/1‑140 (MQ=255)
                                                                       tgtgAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCCAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAgaga                                                                   <  1:529150/140‑1 (MQ=255)
                                                                           aGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCCAAAAAAAAATAAAGTAGTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATaa                                                               <  2:420374/140‑1 (MQ=255)
                                                                             cAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCCAAAAAAAAATACTGCAGGACAAACATTCTAACAACAAAAAATCGAATTTGAACAAAGACAAAACACATAGAATAAcc                                                             >  1:184168/1‑140 (MQ=255)
                                                                                       gaagCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATATGCAAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGAc                                                   <  2:214234/140‑1 (MQ=255)
                                                                                       gaagCATTTAAAGACCGTAAATTAATACCTAAAAATAACTTGGATTATGTGCCAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGAc                                                   <  2:599937/140‑1 (MQ=255)
                                                                                       aaaacATTTAAAGACCGAAAATTAATTCCTAAAAAAAACTTGGATTATGTAAAAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGAc                                                   <  2:589574/136‑1 (MQ=255)
                                                                                         agCATTTAAAGACAGTATACTGACTGCCAAAAATAACTTGGATTATGTGCCAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACgg                                                 >  2:250882/1‑139 (MQ=255)
                                                                                           cataaaaaGAACGAATAATAATTCATAACAATAACTTGGATAAAAAAAAAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGttt                                               <  2:681724/135‑1 (MQ=255)
                                                                                           cATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCCAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAAACGAATTTGAACAAAGACAAAACACAGAGAATAACCAAAAGAAAACGtat                                               >  2:149024/1‑138 (MQ=255)
                                                                                             tttAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCCAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTc                                             >  1:604471/1‑140 (MQ=255)
                                                                                              ttAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCCAAAAAAAAAAAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAAACAAGAGAAGAAGTTTTCa                                            >  1:506915/1‑140 (MQ=255)
                                                                                               tAAAGACCGTATATTAAATCCTAAAAATAACTTGGATTATGTGCCAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCAt                                           <  1:706094/140‑1 (MQ=255)
                                                                                                  aGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCCAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATCTg                                        <  1:686524/140‑1 (MQ=255)
                                                                                                   gACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCCAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATCTga                                       >  1:161885/1‑140 (MQ=255)
                                                                                                     ccGTATATTAATTCCTAAAAATAACTTGGATTATGTGCCAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATCTgaag                                     <  1:248600/140‑1 (MQ=255)
                                                                                                      cGTATATTAATTCCTAAAAATAACTTGGATTATGTGCCAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATCTgaaga                                    >  1:553624/1‑140 (MQ=255)
                                                                                                             tAATTCCTAAAAATAACTTGGATTATGTGCCAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATCTGAAGAAAGTAAc                             <  1:803828/140‑1 (MQ=255)
                                                                                                                     aaaaaTAACTTGGATTATGTGCCAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATCTGAAGAAAGTAACAGTAAGcc                     >  1:466667/1‑140 (MQ=255)
                                                                                                                        aaTAACTTGGATTATGTGCCAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAAACAAAACACAGAGAATAACCAAGAGAAGACGTATTCATCTGAACAAAATAACAGTAAGACact                  >  2:264269/1‑138 (MQ=255)
                                                                                                                           aaCTTGGATGATGTCCCAAAAAAAAATAAAGTATTACATTCATTCGACCATCCAAAAATCTAATCTGAACAAAGTCAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATCTGAAGAAAGTAACAGTAAGCCATTTAt               <  1:183944/140‑1 (MQ=255)
                                                                                                                             cTTGGATTATGTGCCAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATCTGAAGAAAGTAACAGTAAGCCATTTATgg             >  1:162466/1‑140 (MQ=255)
                                                                                                                             cTTGGATTATGGGCCAAAAAAAAATAAAGTAACACATTCATTCGAACAACAAAAAAGCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATCTGAAGAAAGTAACAGTAAGCCATTTATgg             <  1:717473/140‑1 (MQ=255)
                                                                                                                                    tATGTGCCAAAAAAAAATACAGAATTCCATGCATGCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATCTGAAGAAAGTAACAGTAAGCCATTTATGGAAGaaaa      >  1:764479/1‑140 (MQ=255)
                                                                                                                                      tgtgCAAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACATAAGACAGAGAATAACCAAGAGAAGACGTTTGCATCTGAAGAAAGTAACAGTAAGCCATTTATGGAAGAAAATc    <  2:745498/140‑1 (MQ=255)
                                                                                                                                       gtgCCAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACACAACACATAGAATAACCAAGAGAAGACGTTTTCATCTGAAGAAAGTAACAGTAAGCCATTTATGGAAGAAAATCa   >  1:798901/1‑140 (MQ=255)
                                                                                                                                       gtgCCAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACGGAGAATAACCAAGAGAAGACGTTTTCATCTGAAGAAAGTAACAGTAAGCCATTTATGGAAGAAAAACa   >  1:410101/1‑140 (MQ=255)
                                                                                                                                       gtgCC‑AAAAAAAATAAAGTATTACATTCATTCGAACAAAAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATCTGAAGAAAGTAACAGTAAGCCATTTATGGAAGAAAATCaa  >  1:768317/1‑140 (MQ=255)
                                                                                                                                           |                                                                                                                                        
GTAGACGTAAATGTTCATCCAACAAAACTAGAAGTGCGTTTATCAAAAGAAGAGCAACTATACCAATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCCAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATCTGAAGAAAGTAACAGTAAGCCATTTATGGAAGAAAATCAA  >  USA300TCH1516_ALE/1324108‑1324383

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑