Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 890,260 T→C V39A (GTT→GCT)  gcvH → Glycine cleavage system H protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE890,2600TC97.6% 158.3 / NA 42V39A (GTT→GCT) gcvHGlycine cleavage system H protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base C (19/22);  minor base A (1/0);  total (20/22)
Fisher's exact test for biased strand distribution p-value = 4.76e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TAATTAGGAGGGGATTCTCTTGGCAGTACCAAATGAATTGAAATATTCAAAAGAGCATGAATGGGTTAAAGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGTTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTAAAGTAGTTGAAGTCAACGAAGAACTAGAAGATAGTC  >  USA300TCH1516_ALE/890126‑890403
                                                                                                                                      |                                                                                                                                               
taattaGGAGGGGATTCTCTTGGCAGTACCAAATGAATTGAAATATTCAAAAGAGCATGAATGGGTTAAAGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTa                                                                                                                                    >  4:283071/1‑148 (MQ=255)
taattaGGAGGGGATTCTCTTGGCAGTACCAAATGAATTGAAATATTCAAAAGAGCATGAATGGGTTAAAGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTa                                                                                                                                    <  3:29889/148‑1 (MQ=255)
taattaGGAGGGGATTCTCTTGGCAGTACCAAATGAATTGAAATATTCAAAAGAGCATGAATGGGTTAAAGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTa                                                                                                                                    <  3:28123/148‑1 (MQ=255)
taattaGGAGGGGATTCTCTTGGCAGTACCAAATGAATTGAAATATTCAAAAGAGCATGAATGGGTTAAAGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTa                                                                                                                                    <  3:28120/148‑1 (MQ=255)
 aattaGGAGGGGATTCTCTTGGCAGTACCAAATGAATTGAAATATTCAAAAGAGCATGAATGGGTTAAAGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTAc                                                                                                                                   <  3:158398/148‑1 (MQ=255)
     aggaggGGATTCTCTTGGCAGTACCAAATGAATTGAAATATTCAAAAGAGCATGAATGGGTTAAAGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGa                                                                                                                               >  4:49075/1‑148 (MQ=255)
        aggGGATTCTCTTGGCAGTACCAAATGAATTGAAATATTCAAAAGAGCATGAATGGGTTAAAGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAAc                                                                                                                            >  3:27082/1‑148 (MQ=255)
        aggGGATTCTCTTGGCAGTACCAAATGAATCGAAATATTCAAAAGAGCATGACTGGGTAAAAGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAAc                                                                                                                            >  4:154644/1‑148 (MQ=255)
            gATTCTCTTGGCAGTACCAAATGAATTGAAATATTCAAAAGAGCATGAATGGGTTACAGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAgat                                                                                                                        <  3:235723/148‑1 (MQ=255)
               tctcTTGGCAGTACCAAATGAATTGAAATATTCAAAAGAGCATGAATGGGTTAAAGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAAc                                                                                                                            >  1:63035/1‑141 (MQ=255)
                    tGGCAGTACCAAATGAATTGAAATATTCAAAAGAGCATGAATGGGTTAAAGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAAt                                                                                                                <  3:252825/148‑1 (MQ=255)
                                          atatTCAAAAGAGCATGAATGGGTTAAAGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGt                                                                                          <  4:133506/148‑1 (MQ=255)
                                              tCAAAAGAGCATGAATGGGTTAAAGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCg                                                                                      >  3:118605/1‑148 (MQ=255)
                                                      gCATGAATGGGTTAAAGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGt                                                                                     <  1:57077/141‑1 (MQ=255)
                                                                   aaaGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTAt                                                                 >  3:336676/1‑148 (MQ=255)
                                                                                      cAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAAt                                              <  3:336697/148‑1 (MQ=255)
                                                                                      cAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAAt                                              <  3:362733/148‑1 (MQ=255)
                                                                                        ataatTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAAtct                                            <  4:367253/148‑1 (MQ=255)
                                                                                        ataatTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAAtct                                            <  4:2261/148‑1 (MQ=255)
                                                                                        ataatTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAAtct                                            <  3:325112/148‑1 (MQ=255)
                                                                                        ataatTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAAtct                                            <  4:6080/148‑1 (MQ=255)
                                                                                          acttGGAACCACAGAATACGCACAAAGCGAGTTAGGGGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGCAGGAGATACTGTTGGTAGCGTAGAACCAGTTAAAACTGTATCAGAATTATATGCAcc                                                 <  1:61256/139‑1 (MQ=255)
                                                                                          aatTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATctct                                          <  3:24141/148‑1 (MQ=255)
                                                                                              ggAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTa                                      >  4:206359/1‑148 (MQ=255)
                                                                                                aaTCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTaaa                                    >  4:337801/1‑148 (MQ=255)
                                                                                                aaTCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTaaa                                    >  3:70798/1‑148 (MQ=255)
                                                                                                aaTCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTaaa                                    >  3:69267/1‑148 (MQ=255)
                                                                                                aaTCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTaaa                                    >  3:168270/1‑148 (MQ=255)
                                                                                                aaTCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTaaa                                    >  3:229584/1‑148 (MQ=255)
                                                                                                     caGAATACGCACAAAGCGAGTTAGGTGATATTGATTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTa                                      >  2:28370/1‑141 (MQ=255)
                                                                                                       gAATACGCACAAAGCGCGAAAGTTAACTTTGCTTTCGTTGAATTACCAGAATCAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTaaa                                    >  2:48921/1‑141 (MQ=255)
                                                                                                       gAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTAAAGTAGTTg                             <  4:175229/148‑1 (MQ=255)
                                                                                                       gAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTAAAGTAGTTg                             <  4:317312/148‑1 (MQ=255)
                                                                                                             gCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTAAAGTAGTTGAAGTCa                       <  4:108271/148‑1 (MQ=255)
                                                                                                                 aaaGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTAAAGTAGTTGAAGTCAACga                   >  3:43146/1‑148 (MQ=255)
                                                                                                                    gCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTAAAGTAGTTGAAGTCAACgaaga                <  4:140416/148‑1 (MQ=255)
                                                                                                                    gCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTAAAGTAGTTGAAGTCAACgaaga                <  3:49075/148‑1 (MQ=255)
                                                                                                                     cGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTAAAGTAGTTGAAGTCAACgaagaa               >  4:119333/1‑148 (MQ=255)
                                                                                                                     cGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTAAAGTAGTTGAAGTCAACgaagaa               >  4:119327/1‑148 (MQ=255)
                                                                                                                      gAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTAAAGTAGTTGAAGTCAACGAAGAAc              <  3:283071/148‑1 (MQ=255)
                                                                                                                                  atTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTAAAGTAGTTGAAGTCAACGAAGAACTagaa         >  1:58947/1‑141 (MQ=255)
                                                                                                                                  atTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTAAAGTAGTTGAAGTAACAGAAGAACTAGAAGATAGTc  >  3:3408/1‑148 (MQ=255)
                                                                                                                                      |                                                                                                                                               
TAATTAGGAGGGGATTCTCTTGGCAGTACCAAATGAATTGAAATATTCAAAAGAGCATGAATGGGTTAAAGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGTTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTAAAGTAGTTGAAGTCAACGAAGAACTAGAAGATAGTC  >  USA300TCH1516_ALE/890126‑890403

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: ‑