Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,128,065 A→G 18.2% K273E (AAA→GAA)  xerC_2 → Tyrosine recombinase XerC

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,128,0650AG18.2% 95.5 / 18.6 44K273E (AAA→GAA) xerC_2Tyrosine recombinase XerC
Reads supporting (aligned to +/- strand):  ref base A (22/14);  new base G (4/4);  total (26/18)
Fisher's exact test for biased strand distribution p-value = 6.97e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.10e-01

CCCCTAGATATATCAGTATCGCTAAATCTGATATGAAACACATTATGGACGTCATAAGTACATTTGCAATTAGCTATGATGGTTACATTTTCAAAGAAGCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGCAAAAGGTGTATCTATACATTACATTTCTAAAAGATTAGGTCATAAAAATATAGCAATAACT  >  USA300TCH1516_ALE/2127925‑2128205
                                                                                                                                            |                                                                                                                                            
ccccTACATATATCAGTATCCCTAAATCTTATATAAAACACATTATGGACGTCATAAGTACATTTGCAATTAGCTATGATGGTTACATTTTCAAAGAAGCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGa                                                                                                                                              <  1:341003/141‑1 (MQ=255)
 cccTAGATATATCAGTATCGCTAAATCTGATATGAAACACATTATGGACGTCATAAGTACATTTGCAATTAGCTATGATGGTTACATTTTCAAAGAAGCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGaa                                                                                                                                             <  2:428118/141‑1 (MQ=255)
 cccTAGATATATCAGTATCGCTAAATCTGATATGAAACACATTATGGACGTCATAAGTACATTTGCAATTAGCTATGATGGTTACATTTTCAAAGAAGCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGaa                                                                                                                                             <  1:433422/141‑1 (MQ=255)
 cccTAGATATATCAGTATCGCTAAATCTGATATGAAACACATTATGGACGTCATAAGTACATTTGCAATTAGCTATGATGGTTACATTTTCAAAGAAGCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGaa                                                                                                                                             <  1:301795/141‑1 (MQ=255)
 cccTAGATATATCAGTATCGCTAAATCTGATATGAAACACATTATGGACGTCATAAGTACATTTGCAATTAGCTATGATGGTTACATTTTCAAAGAAGCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGaa                                                                                                                                             <  2:135996/141‑1 (MQ=255)
 cccTAGATATATCAGTATCGCTAAATCTGATATGAAACACATTATGGACGTCATAAGTACATTTGCAATTAGCTATGATGGTTACATTTTCAAAGAAGCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGaa                                                                                                                                             <  2:146937/141‑1 (MQ=255)
           atCAGTATCGCTAAATCTGATATGAAACACATTATGGACGTCATAAGTACATTTGCAATTAGCTATGATGGTTACATTTTCAAAGAAGCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGGAATCAGCCTGt                                                                                                                                   >  1:210424/1‑141 (MQ=255)
           atCAGTATCGCTAAATCTGATATGAAACACATTATGGACGTCATAAGTACATTTGCAATTAGCTATGATGGTTACATTTTCAAAGAAGCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGGAATCAGCCTGt                                                                                                                                   >  1:168420/1‑141 (MQ=255)
           atCAGTATCGCTAAATCTGATATGAAACACATTATGGACGTCATAAGTACATTTGCAATTAGCTATGATGGTTACATTTTCAAAGAAGCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGGAATCAGCCTGt                                                                                                                                   >  1:438751/1‑141 (MQ=255)
           atCAGTATCGCTAAATCTGATATGAAACACATTATGGACGTCATAAGTACATTTGCAATTAGCTATGATGGTTACATTTTCAAAGAAGCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGGAATCAGCCTGt                                                                                                                                   >  1:427487/1‑141 (MQ=255)
               gTATCGCTAAATCTGATATGAAACACATTATGGACGTCATAAGTACATTTGCAATTAGCTATGATGGTTACATTTTCAAAGAAGCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGAAATCAGCCTGTagag                                                                                                                               >  1:270551/1‑141 (MQ=255)
                           cTGATATGAAACACATTATGGACGTCATAAGTACATTTGCAATTAGCTATGATGGTTACATTTTCAAAGAAGCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAatatat                                                                                                                   >  1:173037/1‑141 (MQ=255)
                             gATATGAAACACATTATGGACGTCATAAGTACATTTGCAATTAGCTATGATGGTTACATTTTCAAAGAAGCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCa                                                                                                                 >  2:34093/1‑141 (MQ=255)
                                              ggACGTCATAAGTACATTTGCAATTAGCTATGATGGTTACATTTTCAAAGAAGCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATcgcacgc                                                                                                >  1:286254/1‑141 (MQ=255)
                                              ggACGTCATAAGTACATTTGCAATTAGCTATGATGGTTACATTTTCAAAGAAGCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATcgcacgc                                                                                                >  2:106076/1‑141 (MQ=255)
                                              ggACGTCATAAGTACATTTGCAATTAGCTATGATGGTTACATTTTCAAAGAAGCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATcgcacgc                                                                                                >  2:380804/1‑141 (MQ=255)
                                                                tGCAATTAGCTATGATGGTTACATTTTCAAAGAAGCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGAAATCGGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTg                                                                              >  2:344814/1‑141 (MQ=255)
                                                                  cAATTAGCTATGATGGTTACATTTTCAAAGAAGCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGtt                                                                            <  2:288682/141‑1 (MQ=255)
                                                                  cAATTAGCTATGATGGTTACATTTTCAAAGAAGCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGtt                                                                            <  2:86400/141‑1 (MQ=255)
                                                                               tgGTTACATTTTCAAAGAAGCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGGAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGc                                                               <  2:438751/141‑1 (MQ=255)
                                                                               tgGTTACATTTTCAAAGAAGCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGGAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGc                                                               <  2:427487/141‑1 (MQ=255)
                                                                               tgGTTACATTTTCAAAGAAGCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGGAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGc                                                               <  2:168420/141‑1 (MQ=255)
                                                                               tgGTTACATTTTCAAAGAAGCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGGAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGc                                                               <  2:210424/141‑1 (MQ=255)
                                                                                ggTTACATTTTCAAAGAAGCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGCa                                                              >  2:153269/1‑141 (MQ=255)
                                                                                  ttACATTTTCAAAGAAGCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGCaaa                                                            <  1:34093/141‑1 (MQ=255)
                                                                                      aTTTTCAAAGAAGCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGAAATCGGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGCAAAAGgt                                                        <  1:344814/141‑1 (MQ=255)
                                                                                       ttttCAAAGAAGCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGCAAAAGgtg                                                       >  2:154303/1‑141 (MQ=255)
                                                                                       ttttCAAAGAAGCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGCAAAAGgtg                                                       >  2:235174/1‑141 (MQ=255)
                                                                                         ttCAAAGAAGCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGCAAAAGGTGTa                                                     <  2:377634/141‑1 (MQ=255)
                                                                                           cAAAGAAGCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGCAAAAGGTGTATc                                                   >  1:63715/1‑141 (MQ=255)
                                                                                              agaagCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGCAAAAGGTGTATCtat                                                >  1:422398/1‑141 (MQ=255)
                                                                                              agaagCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGCAAAAGGTGTATCtat                                                >  2:423776/1‑141 (MQ=255)
                                                                                              agaagCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGCAAAAGGTGTATCtat                                                >  2:268091/1‑141 (MQ=255)
                                                                                              agaagCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGCAAAAGGTGTATCtat                                                >  1:292390/1‑141 (MQ=255)
                                                                                              agaagCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGAAAGCAGGTTTGAGAGGCAATATCTTACCATGCATGACAGCTCAGGGATGAGTTCACACTCTTTTTTGGGATGTACGAGCAAAGGGTGTATCtag                                                >  1:389287/1‑140 (MQ=255)
                                                                                               gaagCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGCAAAAGGTGTATCtata                                               >  2:51726/1‑141 (MQ=255)
                                                                                                    cGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGCAAAAGGTGTATCTAtacatta                                          >  1:235405/1‑141 (MQ=255)
                                                                                                       aTCTATAATTAACCTTCATGCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGCAAAAGGTGTATCTAtacattacat                                       >  1:318790/1‑141 (MQ=255)
                                                                                                         cTATAATTAACCTTCATGCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGCAAAAGGTGTATCTATACATTACAttt                                     <  2:368900/141‑1 (MQ=255)
                                                                                                          tataATTAACCTTCATGCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGCAAAAGGTGTATCTATACATTACATTTc                                    <  2:331838/141‑1 (MQ=255)
                                                                                                          tataATTAACCTTCATGCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGCAAAAGGTGTATCTATACATTACATTTc                                    <  2:420456/141‑1 (MQ=255)
                                                                                                             aaTTAACCTTCATGCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGCAAAAGGTGTATCTATACATTACATTTCTaa                                 <  1:118966/141‑1 (MQ=255)
                                                                                                                    cTTCATGCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGCAAAAGGTGTATCTATACATTACATTTCTAAAAGATTa                          >  1:235242/1‑141 (MQ=255)
                                                                                                                        aTGCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGCAAAAGGTGTATCTATACATTACATTTCTAAAAGATTAGGTc                      <  1:162497/141‑1 (MQ=255)
                                                                                                                         tGCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGCAAAAGGTGTATCTATACATTACATTTCTAAAAGATTAGGTCa                     >  2:173635/1‑141 (MQ=255)
                                                                                                                          gCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGCAAAAGGTGTATCTATACATTACATTTCTAAAAGATTAGGTCAt                    <  1:106076/141‑1 (MQ=255)
                                                                                                                          gCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGCAAAAGGTGTATCTATACATTACATTTCTAAAAGATTAGGTCAt                    >  1:107958/1‑141 (MQ=255)
                                                                                                                          gCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGCAAAAGGTGTATCTATACATTACATTTCTAAAAGATTAGGTCAt                    <  1:380804/141‑1 (MQ=255)
                                                                                                                          gCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGCAAAAGGTGTATCTATACATTACATTTCTAAAAGATTAGGTCAt                    <  2:286254/141‑1 (MQ=255)
                                                                                                                               cAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGCAAAAGGTGTATCTATACATTACATTTCTAAAAGATTAGGTCATaaaaa               <  1:153269/141‑1 (MQ=255)
                                                                                                                                            aaaTCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGCAAAAGGTGTATCTATACATTACATTTCTAAAAGATTAGGTCATAAAAATATAGCAATAACt  >  2:173610/1‑141 (MQ=255)
                                                                                                                                            |                                                                                                                                            
CCCCTAGATATATCAGTATCGCTAAATCTGATATGAAACACATTATGGACGTCATAAGTACATTTGCAATTAGCTATGATGGTTACATTTTCAAAGAAGCCGGATCTATAATTAACCTTCATGCTATCAATAATGCTTTGAAATCAGCCTGTAGAGTCAATAATATATCAATTATTACATCGCACGCATTAAGACACACTCATTGTTCTTATTTACTAGCAAAAGGTGTATCTATACATTACATTTCTAAAAGATTAGGTCATAAAAATATAGCAATAACT  >  USA300TCH1516_ALE/2127925‑2128205

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑