Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 37,589 G→T 8.0% intergenic (+613/‑224) USA300HOU_RS14915 → / → ugpQ_1 hypothetical protein/Glycerophosphodiester phosphodiesterase, cytoplasmic

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE37,5890GT 8.0% 165.9 / 2.1 46intergenic (+613/‑224)USA300HOU_RS14915/ugpQ_1hypothetical protein/Glycerophosphodiester phosphodiesterase, cytoplasmic
Reads supporting (aligned to +/- strand):  ref base G (18/24);  new base T (2/2);  total (20/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAGTTCTCAGTAAAATTGCAGATAAGAGGTACGTTAAAAGCAGTTCTAGGCAAAATTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCATAATCAATACGAATCTATCGACTTCTTTATTTATGATATTCATC  >  USA300TCH1516_ALE/37452‑37729
                                                                                                                                         |                                                                                                                                            
cAGTTCTCAGTAAAATTGCAGATAAGAGGTACGTTAAAAGCAGTTCTAGGCAAAATTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAg                                                                                                                                           <  1:405869/141‑1 (MQ=255)
  gTTCTCAGTAAAATTGCAGATAAGAGGTACGTTAAAAGCAGTTCTAGGCAAAATTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGAt                                                                                                                                         >  2:81229/1‑141 (MQ=255)
  gTTCTCAGTAAAATTGCAGATAAGAGGTACGTTAAAAGCAGTTCTAGGCAAAATTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGAt                                                                                                                                         >  1:398670/1‑141 (MQ=255)
  gTTCTCAGTAAAATTGCAGATAAGAGGTACGTTAAAAGCAGTTCTAGGCAAAATTGCAGATAAGAGGTGCGTTAAAAGCAGGTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGAt                                                                                                                                         >  1:354545/1‑141 (MQ=255)
     ctcAGTAAAATTGCAGATAAGAGGTACGTTAAAAGCAGTTCTAGGCAAAATTGCAGATAAGAGGTGCGTTAAGAGAAGTTCTCAGTCAAGAAGAAGAAATGGGATAAGTAAAAAGCAATCCTAAGTAAAATTTCAGATAAg                                                                                                                                      >  1:67238/1‑141 (MQ=18)
     ctcAGTAAAATTGCAGATAAGAGGTACGTTAAAAGCAGTTCTAGGCAAAATTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTTCAGATAAg                                                                                                                                      >  1:94324/1‑141 (MQ=255)
     ctcAGTAAAATTGCAGATAAGAGGTACGTTAAAAGCAGTTCTAGGCAAAATTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATACTAAGTAAAATTGCAGATAAg                                                                                                                                      >  2:245583/1‑141 (MQ=255)
        aGTAAAATTGCAGATAAGAGGTACGTTAAAAGCAGTTCTAGGCAAAATTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAgggg                                                                                                                                   >  1:242301/1‑141 (MQ=255)
                 gCAGATAAGAGGTACGTTAAAAGCAGTTCTAGGCAAAATTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGaaaa                                                                                                                          <  1:308525/141‑1 (MQ=255)
                 gCAGATAAGAGGTACGTTAAAAGCAGTTCTAGGCAAAATTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGaaaa                                                                                                                          <  2:4786/141‑1 (MQ=255)
                 gCAGATAAGAGGTACGTTAAAAGCAGTTCTAGGCAAAATTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGaaaa                                                                                                                          <  1:366972/141‑1 (MQ=255)
                 gCAGATAAGAGGTACGTTAAAAGCAGTTCTAGGCAAAATTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGaaaa                                                                                                                          <  1:361676/141‑1 (MQ=255)
                                 ttAAAAGCAGTTCTAGGCAAAATTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACa                                                                                                          >  2:154630/1‑141 (MQ=255)
                                  tAAAAGCAGTTCTAGGCAAAATTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACaa                                                                                                         <  2:456490/141‑1 (MQ=255)
                                   aaaaGCAGTTCTAGGCAAAATTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACaaa                                                                                                        >  1:82154/1‑141 (MQ=255)
                                       gCAGTTCTAGGCAAAATTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATgg                                                                                                    <  2:251879/141‑1 (MQ=255)
                                           ttCTAGGCAAAATTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCt                                                                                                >  1:448378/1‑141 (MQ=255)
                                                 gCAAAATTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGAc                                                                                          >  1:112196/1‑141 (MQ=255)
                                                 gCAAAATTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGAc                                                                                          >  1:237193/1‑141 (MQ=255)
                                                 gCAAAATTGCAGATAAGAGGTGAGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGAc                                                                                          >  1:431117/1‑141 (MQ=255)
                                                     aaTTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATaa                                                                                      <  1:99961/141‑1 (MQ=255)
                                                          cAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGAt                                                                                 >  2:33064/1‑141 (MQ=255)
                                                          cAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGAt                                                                                 >  2:1417/1‑141 (MQ=255)
                                                          cAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGAt                                                                                 >  2:66267/1‑141 (MQ=255)
                                                                    gTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTaaaaa                                                                       <  2:132676/141‑1 (MQ=255)
                                                                      gCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTAGAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAatg                                                                     <  1:244789/141‑1 (MQ=255)
                                                                      gCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAatg                                                                     <  1:97319/141‑1 (MQ=255)
                                                                      gCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAatg                                                                     <  1:293426/141‑1 (MQ=255)
                                                                          tAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAatgagat                                                                 <  2:106366/141‑1 (MQ=255)
                                                                               gCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGAc                                                            >  1:314004/1‑141 (MQ=255)
                                                                                   ttCTCAGTAAAATTGCTTATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTTCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAg                                                        <  2:67238/141‑1 (MQ=255)
                                                                                   ttCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTTCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAg                                                        <  2:94324/141‑1 (MQ=255)
                                                                                   ttCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAg                                                        >  2:322220/1‑141 (MQ=255)
                                                                                   ttCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAg                                                        <  2:52609/141‑1 (MQ=255)
                                                                                   ttCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAg                                                        <  1:4320/141‑1 (MQ=255)
                                                                                   ttCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAg                                                        <  2:100911/141‑1 (MQ=255)
                                                                                     ctcAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGAt                                                      <  2:398670/141‑1 (MQ=255)
                                                                                     ctcAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGAt                                                      <  1:81229/141‑1 (MQ=255)
                                                                                     ctcAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAAAAAAAAAAAAAAAATGAGATGAGACGTAGAt                                                      <  2:354545/141‑1 (MQ=37)
                                                                                                  cTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCATAATc                                         <  1:360471/141‑1 (MQ=255)
                                                                                                  cTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCATAATc                                         <  2:278315/141‑1 (MQ=255)
                                                                                                  cTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCATAATc                                         <  2:143704/141‑1 (MQ=255)
                                                                                                                gTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCATAATCAATACGAATCTATc                           <  2:242301/141‑1 (MQ=255)
                                                                                                                 ttAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCATAATCAATACGAATCTATCg                          <  1:277748/141‑1 (MQ=255)
                                                                                                                                 gTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCATAATCAATACGAATCTATCGACTTCTTTATTTATGa          >  1:35355/1‑141 (MQ=255)
                                                                                                                                 gTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCATAATCAATACGAATCTATCGACTTCTTTATTTATGa          >  2:186134/1‑141 (MQ=255)
                                                                                                                                         gCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCATAATCAATACGAATCTATCGACTTCTTTATTTATGATATTCAtc  >  1:407974/1‑141 (MQ=255)
                                                                                                                                         gCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCATAATCAATACGAATCTATCGACTTCTTTATTTATGATATTCAtc  <  1:322220/141‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                            
CAGTTCTCAGTAAAATTGCAGATAAGAGGTACGTTAAAAGCAGTTCTAGGCAAAATTGCAGATAAGAGGTGCGTTAAAAGCAGTTCTCAGTAAAATTGCTGATAAGGGGTAAGTTAAAAGCAATCCTAAGTAAAATTGCAGATAAGGGGTACAGAAAAACTAGACTTGATTACAAAATGGAGCTTGGGACATAAATGATTTTTTAAAAATGAGATGAGACGTAGATTAACTCCATAATCAATACGAATCTATCGACTTCTTTATTTATGATATTCATC  >  USA300TCH1516_ALE/37452‑37729

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