Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,465,100 A→G 9.6% N19N (AAT→AAC)  folA ← Dihydrofolate reductase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,465,1000AG 9.6% 121.6 / 3.0 47N19N (AAT→AAC) folADihydrofolate reductase
Reads supporting (aligned to +/- strand):  ref base A (19/23);  new base G (2/3);  total (21/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.49e-01

AAGTAAGTACAACATTTCGACGATTCGGTAGTGGTTTACCAATCGATTCAAATGTCTTACGACCCATTACTAAAGTATGACCTGTTGATAATTTTTTAACATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGATTTTCAAAACCAATTACTCGTTGCAAGTCATGTGCAACTAGAATGGATAAAGTCATAATTATCCTCCTTCTTCTATCATTTCATTTTTTATTACTAAGTTATCTTTAATTTAACACAATTTTTATCATAAAGTGTGA  >  USA300TCH1516_ALE/1464964‑1465237
                                                                                                                                        |                                                                                                                                         
aagtaagtACAACATTTCGACGATTGGGCTTTGTTTTACCAATCGATTCAAATGTCTTACGACCCATTACTAAAGTATGACCTGTTGATAATTTTTTAACATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGAtttt                                                                                                                                       >  1:805414/1‑141 (MQ=255)
aagtaagtACAACATTTCGACGATTCGGTAGTGGTTTACCAATCGATTCAAATGTCTTACGACCCATTACTAAAGTATGACCTGTTGATAATTTTTTAACATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGAtttt                                                                                                                                       >  1:108270/1‑141 (MQ=255)
       taCAACATTTCGACGATTCGGTAGTGGTTTACCAATCGATTTAAATGTCTTACGACCCATTACTAAAGTATGACCTGTTGATAATTTTTTAACATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGGTTTTGaaaatc                                                                                                                                <  1:758589/141‑3 (MQ=255)
       taCAACATTTCGACGATTCGGTAGTGGTTTACCAATCGATTCAAATGTCTTACGACCCATTACTAAAGTATGACCTGTTGATAATTTTTTAACATGCTTCAACTCATTTGGTAGGTGCCAAGGTAATTGGTTTTGaaaatc                                                                                                                                <  1:427955/141‑3 (MQ=255)
       gacaacaTTTCGACGATTCGGTAGTGGTTTACCAATCGATTCAAATGTCTTACGACCCATTACTAAAGTATGACCTGTTGATAATTTTTTAACATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGGTTTTGaaaatc                                                                                                                                <  1:741405/140‑3 (MQ=255)
                  gacgaTTCGGTAGTGGTTTACCAATCGATTCAAATGTCTTACGACCCATTACTAAAGTATGACCTGTTGATAATTTTTTAACATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGATTTTCAAAACCAATTACTCGtt                                                                                                                     <  1:155081/141‑1 (MQ=255)
                  gacgaTTCGGTAGTGGTTTACCAATCGATTCAAATGTCTTACGACCCATTACTAAAGTATGACCTGTTGATAATTTTTTAACATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGATTTTCAAAACCAATTACTCGtt                                                                                                                     <  1:155588/141‑1 (MQ=255)
                   acgaTTCGGTAGTGGTTTACCAATCGATTCCAATGCCTTATGACCCATTTCTAAAGTATGACCGGTTGATAATTTTTTAACATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGATTTTCAAAACCAATTACTCGTTg                                                                                                                    <  1:551363/141‑1 (MQ=255)
                   acgaTTCGGTAGTGGTTTACCAATCGATTCAAATGTCTTACGACCCATTACTAAAGTATGACCTGTTGATAATTTTTTAACATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGATTTTCAAAACCAATTACTCGTTg                                                                                                                    <  1:482295/141‑1 (MQ=255)
                      aTTCGGTAGTGGTTTACCAATCGATTCAAATGTCTTACGACCCATTACTAAAGTATGACCAGTTGATAATTTTTTAACATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGATTTTGAAAACCAATTACTCGTTGCaa                                                                                                                 <  1:422155/141‑1 (MQ=255)
                       ttCGGTAGTGGTTTACCAATCGATTCAAATGTCTTACGACCCATTACTAAAGTATGACCTGTTGATAATTTTTTAACATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGATTTTCAAAACCAATTACTCGTTGCAAg                                                                                                                <  1:926/141‑1 (MQ=255)
                           gTAGTGGTTTACCAATCGATTCAAATGTCTTACGACCCATTACTAAAGTATGACCTGTTGATAATTTTTTAACATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGATTTTCAAAACCAATTACTCGTTGCAAGTCAt                                                                                                            >  1:254432/1‑141 (MQ=255)
                           gTAGTGGTTTACCAATCGATTCAAATGTCTTACGACCCATTACTAAAGTATGACCTGTTGATAATTTTTTAACATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATAGAACTTCAAAACCAATTACTCGTTGCAAGTCAt                                                                                                            <  1:805062/141‑1 (MQ=255)
                              gTGGTTTACCAATCGATTCAAATGTCTTACGACCCATTACTAAAGTATGACCTGTTGATAATTTTTTAACATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGATTTTCAAAACCAATTACTCGTTGCAAGTCAtgtg                                                                                                         <  1:268021/141‑1 (MQ=255)
                                     aCCAATCGATTCAAATGTCTTACGACCCATTACTAAAGTATGACCTGTTGATAATTTTTTAACATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGATTTTCAAAACCAATTACTCGTTGCAAGTCATGTGCAACTAg                                                                                                  >  1:404535/1‑141 (MQ=255)
                                     aCCAATCGATTCAAATGTCTTACGACCCATTACTAAAGTATGACCTGTTGATAATTTTTTAACATGCTTCAAATACTTTGACAGCGGCCAAGGTAATTGGTTTTCAAAACCAATTACTCGTTGCACGTCAGGTGCagatag                                                                                                  >  1:389553/1‑136 (MQ=255)
                                         aTCGATTCAAATGTCTTACGACCCATTACTAAAGTATGACCTGTTGATAATTTTTTAACATGCTTCAAATCATTTGGTAGGTGCCAAGGGAAGTTAGTTTCAAAACCAATTACTCGTTGCAAGTCATGTGCAACTAGAATg                                                                                              >  1:153381/1‑141 (MQ=255)
                                           cGATTCAAATGTCTTACGACCCATTACTAAAGTATGACCTGTTGATAATTTTTTAACATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGATTTTCAAAACCAATTACTCGTTGCAAGTCATGTGCAACTAGAATGGa                                                                                            <  1:651468/141‑1 (MQ=255)
                                              ttCAAATGTCTTACGACCCATTACTAAAGTATGACCTGTTGATAATTTTTTAACATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGATTTTCAGAACCAATTACTCGTTGGAAGTCATGTGCAACTAGAATGGATaa                                                                                         >  1:650579/1‑141 (MQ=255)
                                                     ttCTTACGACCCATTACTAAAGTATGACCTGTTGATAATTTTTTAACATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGATTTGCAAAACCAATTACTCGTTGCAAGTCATGTGCAACTAGAATGGATAAAGTCATa                                                                                  <  1:24214/140‑1 (MQ=255)
                                                      tCTTACGACCCATTAGTAAAGTATGACCTGTTGATAATTTTTTAACATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGATTTTCAAAACCAATTACTCGTTGCAAGTCATGTGCAACTAGAATGGATAAAGTCATaa                                                                                 >  1:410239/1‑141 (MQ=255)
                                                      tCTTACGACCCATTACTAAAGTATGACCTGTTGATAATTTTTTCACCTGCTTCAAATCACTTGGTAGGTGCCAAGGGAAGTTATTTTCAAAACCAATTACTCGTTGCAAGTCATGTGCCACTAGAATGGATAAAGTCATaa                                                                                 >  1:769494/1‑141 (MQ=255)
                                                        ttACGACCCATTACTAAAGTATGACCTGTTGATAATTTTTTAACATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGATTTTCAAAACCAATTACTCGTTGCAAGTCATGTGCAACTAGAATGGATAAAGTCATAAtt                                                                               <  1:199683/141‑1 (MQ=255)
                                                           cGACCCATTACTAAAGTATGACCTGTTGATAATTTTTTAACATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGATTTTCAAAACCAATTACTCGTTGCAAGTCATGTGCAACTAGAATGGATAAAGTCATAATTAtc                                                                            <  1:393739/141‑1 (MQ=255)
                                                            taCCTATTACTAAAGTATGACCTGTTGATAATTTTTTAACATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGATTTTCAAAACCAATTACTCGTTGCAAGTCATGTGCAACTAGAATGGATAAAGTCATAATTAtcc                                                                           <  1:324373/140‑1 (MQ=255)
                                                                cATTACTAAAGTATGACCTGTTGATAATTTTTTAACATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGATTTTCAAAACTAATTTCGAACGTCATACCGGGTGCCACTAAAATTGTTATAGTCATAATTATcctcct                                                                       >  1:385390/1‑141 (MQ=255)
                                                                cATTACTAAAGTATGACCTGTTGATAATTTTTTAACATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGATTTTCAAAACCAATTACTCGTTGCAAGTCATGTGCAACTAGAATGGATAAAGTCATAATTATcctcct                                                                       >  1:273698/1‑141 (MQ=255)
                                                                cATTACTAAAGTATGACCTGTTGATAATTTTTTAAAATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGATTTTCAAAACCAATTACTCGTTGCAAGTCATGTGCAACTAGAATGGATAAAGTCATAATTATcctcct                                                                       >  1:233312/1‑141 (MQ=255)
                                                                   tACTAAAGTATGACCTGTTGATAATTTTTTAACATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGATTTTCAAAACCAATTACTCGTTGCAAGTCATGTGCAACTAGAATGGATAAAGTCATAATTATCCTCcttct                                                                    >  1:225388/1‑141 (MQ=255)
                                                                     cTAAAGTATGACCTGTTGATAATTTTTTAACATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGATTTTCAAAACCAATTACTCGTTGCAAGTCATGTGCAACTAGAATGGATAAAGTCATAATTATCCTCCttcttc                                                                  >  1:85265/1‑141 (MQ=255)
                                                                              gACCTGTTGATAATTTTTTAACATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGATTTTCAAAACCAATTACTCGTTGCAAGTCATGTGCAACTAGAATGGATAAAGTCATAATTATCCTCCTTCTTCTAtcatttc                                                         >  1:465282/1‑141 (MQ=255)
                                                                                 cTGTTGATAATTTTTTAACATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGATTTTCAAAACCAATTACTCGTTGCAAGTCATGTGCAACTAGAATGGATAAAGTCATAATTATCCTCCTTCTTCTAtcatttcatt                                                      <  1:199665/141‑1 (MQ=255)
                                                                                    ttGATAATTTTTTAACAGGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGATTTTCAAAACCAATTACTCGTTGCAAGTCATGTGCAACTAGAATGGATAAAGTCATAATTATCCTCCTTCTTCTATCATTTCAttttt                                                   <  1:292271/141‑1 (MQ=255)
                                                                                    ttGATAATCTTCTCACATGGTTCACATCATGTGGTAGGTGTCAAGGTAATTGATTTTCAAAACCAATTACTCGTTGCAAGTCATGTGCAACTAGAATGGATAAAGTCATATTTTTTCTCCTTCTTCTATCATTTCAttttt                                                   <  1:342404/141‑1 (MQ=255)
                                                                                        tAATTTTTTAACATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGATTTTCAAAACCAATTACTCGGTGCAATTCATGTGCAACTAGAATGGATAAAGTCATAATTATCCTCCTTCTTCTATCATTTCATTTTttatt                                               >  1:718062/1‑141 (MQ=255)
                                                                                                 aaCATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGGTTTTCAAAACCAATTACTCGTTGCAAGTCATGTGCAACTAGAATGGATAAAGTCATAATTATACTCCTTCTTCTATCATTTCCTTTTTTATTACTAAGttt                                      >  1:623588/1‑140 (MQ=255)
                                                                                                 aaCATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGATTTTCAAAACCAATTACTCGTTGCAAGTCATGTGCAACTAGAATGGATAAAGTCATAATTATCCTCCTTCTTCTATCATTTCATTTTTTATTACTAAGTTa                                      >  1:152537/1‑141 (MQ=255)
                                                                                                 aaCATGCTTCAAATCATTTGGAAGGTGACAAGGGAATTGATTTTCAAAACCAATTACTCGTTGCAAGTCATGTGCAACTAGAATGGATAAAGTCATAATTATCCTCCTTCTTCTATCATTTCATTTTTTATTACTAAGttt                                      >  1:805260/1‑140 (MQ=255)
                                                                                                    aTGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGATTTTCAAAACCAATTACTCGTTGCAAGTCATGTGCAACTAGAATGGATAAAGTCATAATTATCCTCCTTCTTCTATCATTTCATTTTTTATTACTAAGTTATCt                                   <  1:376156/141‑1 (MQ=255)
                                                                                                               cATTTGGTAGGTGCCAAGGTAATTGATTTTCAAAACCAATTACTCGTTGCAAGTCATGTGCAACTAGAATGGATAAAGTCATAATTATCCTCCTTCTTCTATCATTTCATTTTTTATTACTAAGTTATCTTTAATTTAaca                        <  1:703148/141‑1 (MQ=255)
                                                                                                                   tGGTAGGTGCCAAGGTAATTGATTTTCAAAACCAATTACTCGTTGCAAGTCATGTGCAACTAGAATGGATAAAGTCATAATTATCCTCCTTCTTCTATCATTTCATTTTTTATTACTAAGTTATCTTTAATTTAACACAAt                    <  1:35717/141‑1 (MQ=255)
                                                                                                                          tGCCAAGGTAATTGATTTTCAAAACCAATTACTCGTTGCAAGTCATGTGCAACTAGAATGGATAAAGTCATAATTATCCTCCTTCTTCTATCATTTCATTTTTTATTACTAAGTTATCTTTAATTTAACACAATTTTTATc             <  1:536749/141‑1 (MQ=255)
                                                                                                                          ggCCAAGGTAATTGATTTTCAAAACCAATTACTCGTTGCAAGTCATGTGCAACTAGAATGGATAAAGTCATAATTATCCTCCTTCTTCTATCATTTCATTTTTTATTACTAAGTTATCTTTAATTTAACACAATTTTTATc             <  1:707620/140‑1 (MQ=255)
                                                                                                                             cAAGGTAATTGATTTTCAAAACCAATTACTCGTTGCAAGTCATGTGCAACTAGAATGGATAAAGTCATAATTATCCTCCTTCTTCTATCATTTCATTTTTTATTACTAAGTTATCTTTAATTTAACACAATTTTTATCATa          >  1:584624/1‑141 (MQ=255)
                                                                                                                              aaGGTAATTGATTTTCAAAACCAATTACTCGTTGCAAGTCATGTGCAACTAGAATGGATAAAGTCATAATTATCCTCCTTCTTCTATCATTTCATTTTTTATTACTAAGTTATCTTTAATTTAACACAATTTTTATCATaa         >  1:717719/1‑141 (MQ=255)
                                                                                                                                 gTAATTGATTTTCAAAACCAATTACTCGTTGCAAGTCATGTGCAACTAGAATGGATAAAGTCATAATTATCCTCCTTCTTCTATCATTTCATTTTTTATTACTAAGTTATCTTTAATTTAACACAATTTTTATCATAAAgt      <  1:683139/141‑1 (MQ=255)
                                                                                                                                     ttGATTTTCAAAACCAATTACTCGTTGCAAGTCATGTGCAACTAGAATGGATAAAGTCATAATTATCCTCCTTCTTCTATCATTTCATTTTTTATTACTAAGTTATCTTTAATTTAACACAATTTTTATCATAAAGTGTGa  <  1:655331/141‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                         
AAGTAAGTACAACATTTCGACGATTCGGTAGTGGTTTACCAATCGATTCAAATGTCTTACGACCCATTACTAAAGTATGACCTGTTGATAATTTTTTAACATGCTTCAAATCATTTGGTAGGTGCCAAGGTAATTGATTTTCAAAACCAATTACTCGTTGCAAGTCATGTGCAACTAGAATGGATAAAGTCATAATTATCCTCCTTCTTCTATCATTTCATTTTTTATTACTAAGTTATCTTTAATTTAACACAATTTTTATCATAAAGTGTGA  >  USA300TCH1516_ALE/1464964‑1465237

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑