Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,532,665 G→T 10.3% G138C (GGT→TGT)  femA_3 → Aminoacyltransferase FemA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,532,6650GT10.3% 138.3 / 5.6 39G138C (GGT→TGT) femA_3Aminoacyltransferase FemA
Reads supporting (aligned to +/- strand):  ref base G (16/19);  new base T (2/2);  total (18/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.10e-01

TCATATTTAAAGAAACACAATTGTTTATATGTCCTTGTAGATCCATATTTAATTGAAAATTTACGCAATGCAGACGGTGAAATTGTTAAATCTTATGATAACCGAGCATTTGTTAGAACAATGGATAAATTAGGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCAAATCCGTTGGCTGTCAGTGTTAGATTTAAAAGATAAGACTGAAGACCAACTTTTAAAAGAAATGGATTATCAAACGAGACGTAATATTAAAAA  >  USA300TCH1516_ALE/2532533‑2532804
                                                                                                                                    |                                                                                                                                           
tCATATTTAAAGAAACACAATTGTTTATATGTCCTTGTAGATCCATATTTAATTGAAAATTTACGCAATGCAGACGGTGAAATTGTTAAATCTTATGATAACCGAGCATTTGTTAGAACAATGGATAAATTAGGTTATaaa                                                                                                                                     >  1:108038/1‑141 (MQ=255)
         aaGAAACACAATTGATTATATGTCCTTGTAGATCCAGATTTAATTGAAAATTTACGCAATGCAGACGGTGAAATTGTTAAATCTTATGATAACCGAGCATTTGTTAGAACAATGGATAAATTAGGTTATAAACACCAAGGt                                                                                                                            <  1:410463/141‑1 (MQ=255)
             aaCACAATTGTTTATATGTCCTTGTAGATCCATATTTAATTGAAAATTTACGCAATGCAGACGGTGAAATTGTTAAATCTTATGATAACCGAGCATTTGTTAGAACAATGGATAAATTAGGTTATAAACACCAAGGTTTcc                                                                                                                        <  1:417161/141‑1 (MQ=255)
                 caATTGTTTATATGTCCTTGTAGATCCATATTTAATTGAAAATTTGCGCCATGCAGGCGGTGAAATTGTTAAATCTTATGATAACCGAGCATTTGTTAGAACAATGGATAAATTAGGTTATAAACACCAAGGTTTCCCTGt                                                                                                                    <  1:321252/141‑1 (MQ=255)
                         tataTGTCCTTGTAGATCCATATTTAATTGAAAATTTACGCAATGCAGACGGTGAAATTGTTAAATCTTATGATAACCGAGCATTTGTTAGAACAATGGATAAATTAGGTTATAAACACCAAGGTTTCCCTGTAGGTTATg                                                                                                            >  2:9474/1‑141 (MQ=255)
                         tataTGTCCTTGTAGATCCATATTTAATTGAAAATTTACGCAATGCAGACGGTGAAATTGTTAAATCTTATGATAACCGAGCATTTGTTAGAACAATGGATAAATTAGGTTATAAACACCAAGGTTTCCCTGTAGGTTATg                                                                                                            >  1:173974/1‑141 (MQ=255)
                                       gATCCATATTTAATTGAAAATTTACGCAATGCAGACGGTGAAATTGTTAAATCTTATGATAACCGAGCATTTGTTAGAACAATGGATAAATTAGGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCaa                                                                                              <  2:288628/141‑1 (MQ=255)
                                       gATCCATATTTAATTGAAAATTTACGCAATGCAGACGGTGAAATTGTTAAATCTTATGATAACCGAGCATTTGTTAGAACAATGGATAAATTAGGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCaa                                                                                              <  2:283920/141‑1 (MQ=255)
                                       gATCCATATTTAATTGAAAATTTACGCAATGCAGACGGTGAAATTGTTAAATCTTATGATAACCGAGCATTTGTTAGAACAATGGATAAATTAGGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCaa                                                                                              >  2:86374/1‑141 (MQ=255)
                                           cATATTTAATTGAAAATTTACGCAATGCAGACGGTGAAATTGTTAAATCTTATGATAACCGAGCATTTGTTAGAACAATGGATAAATTAGGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCAAATcc                                                                                          <  1:78716/141‑1 (MQ=255)
                                           cATATNTAATTGAAAATTTACGCAATGCAGACGGTGAAATTGTTAAATCTTATGATAACCGAGCATTTGTTAGAACAATGGATAAATTAGGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCAAATcc                                                                                          <  1:118514/141‑1 (MQ=255)
                                                ttAATTGAAAATTTACGCAATGCAGACGGTGAAATTGTTAAATCTTATGATAACCGAGCATTTGTTAGAACAATGGATAAATTAGGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCAAATCCGTTgg                                                                                     >  2:14234/1‑141 (MQ=255)
                                                ttAATTGAAAATTTACGCAATGCAGACGGTGAAATTGTTAAATCTTATGATAACCGAGCATTTGTTAGAACAATGGATAAATTAGGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCAAATCCGTTgg                                                                                     >  2:262043/1‑141 (MQ=255)
                                                ttAATTGAAAATTTACGCAATGCAGACGGTGAAATTGTTAAATCTTATGATAACCGAGCATTTGTTAGAACAATGGATAAATTAGGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCAAATCCGTTgg                                                                                     >  2:180262/1‑141 (MQ=255)
                                                ttAATTGAAAATTTACGCAATGCAGACGGTGAAATTGTTAAATCTTATGATAACCGAGCATTTGTTAGAACAATGGATAAATTAGGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCAAATCCGTTgg                                                                                     >  2:107736/1‑141 (MQ=255)
                                                 tAATTGAAAATTTACGCAATGCAGACGGTGAAATTGTTAAATCTTATGATAACCGAGCATTTGTTAGAACAATGGATAAATTAGGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCAAATCCGTTGGc                                                                                    <  1:409262/141‑1 (MQ=255)
                                                  aaTTGAAAATTTACGCAATGCAGACGGTGAAATTGTTAAATCTTATGATAACCGAGCATTTGTTAGAACAATGGATAAATTAGGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCAAATCCGTTGGCt                                                                                   <  2:108038/141‑1 (MQ=255)
                                                        aaaTTTACGCAATGCAGACGGTGAAATTGTTAAATCTTATGATAACCGAGCATTTGTTAGAACAATGGATAAATTATGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCAAATCCGTTGGCTGTCAgt                                                                             >  1:339438/1‑141 (MQ=255)
                                                        aaaTTTACGCAATGCAGACGGTGAAATTGTTAAATCTTATGATAACCGAGCATTTGTTAGAACAATGGATAAATTATGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCAAATCCGTTGGCTGTCAgt                                                                             >  1:309450/1‑141 (MQ=255)
                                                        aaaTTTACGCAATGCAGACGGTGAAATTGTTAAATCTTATGATAACCGAGCATTTGTTAGAACAATGGATAAATTAGGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCAAATCCGTTGGCTGTCAgt                                                                             <  2:144819/141‑1 (MQ=255)
                                                                    tGCAGACGGTGAAATTGTTAAATCTTATGATAACCGAGCATTTGTTAGAACAATGGATAAATTAGGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCAAATCCGTTGGCTGTCAGTGTTAGATTTaaa                                                                 >  2:180287/1‑141 (MQ=255)
                                                                    tGCAGACGGTGAAATTGTTAAATCTTATGATAACCGAGCATTTGTTAGAACAATGGATAAATTAGGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCAAATCCGTTGGCTGTCAGTGTTAGATTTaaa                                                                 >  2:243316/1‑141 (MQ=255)
                                                                        gACGGTGAAATTGTTAAATCTTATGATAACCGAGCATTTGTTAGAACAATGGATAAATTAGGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCAAATCCGTTGGCTGTCAGTGTTAGATTTAAAAGAt                                                             <  2:65912/141‑1 (MQ=255)
                                                                                        aaTCTTATGATAACCGAGCATTTGTTAGAACAATGGATAAATTAGGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCAAATCCGTTGGCTGTCAGTGTTAGATTTAAAAGATAAGACTGAAGACCAAc                                             <  2:312447/141‑1 (MQ=255)
                                                                                        aaTCTTATGATAACCGAGCATTTGTTAGAACAATGGATAAATTAGGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCAAATCCGTTGGCTGTCAGTGTTAGATTTAAAAGATAAGACTGAAGACCAAc                                             <  2:296606/141‑1 (MQ=255)
                                                                                             tATGATAACCGAGCATTTGTTAGAACAATGGATAAATTAGGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCAAATCCGTTGGCTGTCAGTGTTAGATTTAAAAGATAAGACTGAAGACCAACTTTTa                                        <  1:86374/141‑1 (MQ=255)
                                                                                                         gCATTTGTTAGAACAATGGATAAATTAGGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCAAATCCGTTGGCTGTCAGTGTTAGATTTAAAAGATAAGACTGAAGACCAACTTTTAAAAGAAATGGAt                            >  2:93303/1‑141 (MQ=255)
                                                                                                         gCATTTGTTAGAACAATGGATAAATTAGGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCAAATCCGTTGGCTGTCAGTGTTAGATTTAAAAGATAAGACTGAAGACCAACTTTTAAAAGAAATGGAt                            >  1:132364/1‑141 (MQ=255)
                                                                                                            tttGTTAGAACAATGGATAAATTAGGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCAAATCCGTTGGCTGTCAGTGTTAGATTTAAAAGATAAGACTGAAGACCAACTTTTAAAAGAAATGGATTAt                         <  2:138890/141‑1 (MQ=255)
                                                                                                                ttAGAACAATGGATAAATTATGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCAAATCCGTTGGCTGTCAGTGTTAGATTTAAAAGATAAGACTGAAGACCAACTTTTAAAAGAAATGGATTATCaaa                     <  2:309450/141‑1 (MQ=255)
                                                                                                                ttAGAACAATGGATAAATTATGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCAAATCCGTTGGCTGTCAGTGTTAGATTTAAAAGATAAGACTGAAGACCAACTTTTAAAAGAAATGGATTATCaaa                     <  2:339438/141‑1 (MQ=255)
                                                                                                                           gATAAATTAGGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCAAATCCGTTGGCTGTCAGTGTTAGATTTAAAAGATAAGACTGAAGACCAACTTTTAAAAGAAATGGATTATCAAACGAGACGTAat          >  1:187470/1‑141 (MQ=255)
                                                                                                                               aaTTAGGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCAAATCCGTTGGCTGTCAGTGTTAGATTTAAAAGATAAGACTGAAGACCAACTTTTAAAAGAAATGGATTATCAAACGAGACGTAATATTa      >  2:335030/1‑141 (MQ=255)
                                                                                                                               aaTTAGGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCAAATCCGTTGGCTGTCAGTGTTAGATTTAAAAGATAAGACTGAAGACCAACTTTTAAAAGAAATGGATTATCAAACGAGACGTAATATTa      >  2:453174/1‑141 (MQ=255)
                                                                                                                                 ttAGGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCAAATCCGTTGGCTGTCAGTGTTAGATTTAAAAGATAAGACTGAAGACCAACTTTTAAAAGAAATGGATTATCAAACGAGACGTAATATTaaa    <  1:180262/141‑1 (MQ=255)
                                                                                                                                 ttAGGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCAAATCCGTTGGCTGTCAGTGTTAGATTTAAAAGATAAGACTGAAGACCAACTTTTAAAAGAAATGGATTATCAAACGAGACGTAATATTaaa    <  1:14234/141‑1 (MQ=255)
                                                                                                                                 ttAGGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCAAATCCGTTGGCTGTCAGTGTTAGATTTAAAAGATAAGACTGAAGACCAACTTTTAAAAGAAATGGATTATCAAACGAGACGTAATATTaaa    <  1:262043/141‑1 (MQ=255)
                                                                                                                                 ttAGGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCAAATCCGTTGGCTGTCAGTGTTAGATTTAAAAGATAAGACTGAAGACCAACTTTTAAAAGAAATGGATAATCAAACGAGACGTAATATTaaa    <  1:107736/141‑1 (MQ=255)
                                                                                                                                   aGGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCAAATCCGTTGGCTGTCAGTGTTAGATTTAAAAGATAAGACTGAAGACCAACTTTTAAAAGAAATGGATTATCAAACGAGACGTAATATTaaaaa  >  2:378454/1‑141 (MQ=255)
                                                                                                                                    |                                                                                                                                           
TCATATTTAAAGAAACACAATTGTTTATATGTCCTTGTAGATCCATATTTAATTGAAAATTTACGCAATGCAGACGGTGAAATTGTTAAATCTTATGATAACCGAGCATTTGTTAGAACAATGGATAAATTAGGTTATAAACACCAAGGTTTCCCTGTAGGTTATGATTCAATGAGCCAAATCCGTTGGCTGTCAGTGTTAGATTTAAAAGATAAGACTGAAGACCAACTTTTAAAAGAAATGGATTATCAAACGAGACGTAATATTAAAAA  >  USA300TCH1516_ALE/2532533‑2532804

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: ‑