Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,504,803 T→C 12.9% intergenic (+107/+297) USA300HOU_RS12890 → / ← gltT hypothetical protein/Proton/sodium‑glutamate symport protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,504,8030TC12.9% 79.7 / 5.4 31intergenic (+107/+297)USA300HOU_RS12890/gltThypothetical protein/Proton/sodium‑glutamate symport protein
Reads supporting (aligned to +/- strand):  ref base T (17/10);  new base C (2/2);  total (19/12)
Fisher's exact test for biased strand distribution p-value = 6.30e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.90e-01

ATGACATGGGCAAAATGCACATGAAACACTAATTGTAATTTAAATTACAAATTTTAGTTGCCATCAAGGTATATACGAGTAAAAGCAGCGGTAAGTTGATTTCCAATTTGGAATCATTTTACTGCTGCTTTTTATATTTGAAATACTTTCATATTGAATAGCTCCACTTGCCGTTCGCCTGCGCTTTGCGCATGCATAAAAGCCCCTAACAACCTGAGGTCACTGCGCTCCGGTTCGCCTGCGCTTTAGCGCATGCATAAAA  >  USA300TCH1516_ALE/2504665‑2504926
                                                                                                                                          |                                                                                                                           
aTGACATGGGCAAAATGCACATGAAACACTAATTGTAATTTAAATTACAAATTTTAGTTGCCATCAAGGTATATACGAGTAAAAGCAGCGGTAAGTTGATTTCCAATTTGGAATCATTTTACTGCTGCTTTTTATATTTGa                                                                                                                           <  1:45409/141‑1 (MQ=255)
  gACATGGGCAAAATGCACATGAAACACTAATTGTAATTTAAATTACAAATTTTAGTTGCCATCAAGGTATATACGAGTAAAAGCAGCGGTAAGTTGATTTCCAATTTGGAATCATTTTACTGCTGCTTTTTATATTCGaaa                                                                                                                         >  2:60002/1‑141 (MQ=255)
  gACATGGGCAAAATGCACATGAAACACTAATTGTAATTTAAATTACAAATTTTAGTTGCCATCAAGGTATATACGAGTAAAAGCAGCGGTAAGTTGATTTCCAATTTGGAATCATTTTACTGCTGCTTTTTATATTCGaaa                                                                                                                         >  2:60005/1‑141 (MQ=255)
  gACATGGGCAAAATGAACATGCAACACTAATTGTAATTTAAATTACAAATTTTAGTTGCCATCAAGGTATATACGAGTAAAAGCAGCGGTAAGTTGATTTCCAATTTGGAATCATTTTACTGCTGCTTTTTATATTTGaaa                                                                                                                         <  2:131482/141‑1 (MQ=255)
   aCATGGGCAAAATGCACATGAAACACTAATTGTAATTTAAATTACAAATTTTAGTTGCCATCAAGGTATATACGAGTAAAAGCAGCGGTAAGTTGATTTCCAATTTGGAATCATTTTACTGCTGCTTTTTATATTTGAAAt                                                                                                                        <  2:147840/141‑1 (MQ=255)
     aTGGGCAAAATGCACATGAAACACTAATTGTAATTTAAATTACAAATTTTAGTTGCCATCAAGGTATATACGAGTAAAAGCAGCGGTAAGTTGATTTCCAATTTGGAATCATTTTACTGCTGCTTTTTATATTTGAAATAc                                                                                                                      <  1:167362/141‑1 (MQ=255)
     aTGGGCAAAATGCACATGAAACACTAATTGTAATTTAAATTACAAATTTTAGTTGCCATCAAGGTATATACGAGTAAAAGCAGCGGTAAGTTGATTTCCAATTTGGAATCATTTTACTGCTGCTTTTTATATTTGAAATAc                                                                                                                      >  2:103251/1‑141 (MQ=255)
     aTGGGCAAAATGCACATGAAACACTAATTGTAATTTAAATTACAAATTTTAGTTGCCATCAAGGTATATACGAGTAAAAGCAGCGGTAAGTTGATTTCCAATTTGGAATCATTTTACTGCTGCTTTTTATATTTGAAATAc                                                                                                                      <  2:12087/141‑1 (MQ=255)
       gggCAAAATGCACATGAAACACTAATTGTAATTTAAATTACAAATTTTAGTTGCCATCAAGGTATATACGAGTAAAAGCAGCGGTAAGTTGATTTCCAATTTGGAATCATTTTACTGCTGCTTTTTATATTTGAAATACtt                                                                                                                    >  1:31591/1‑141 (MQ=255)
            aaaTGCACATGAAACACTAATTGTAATTTAAATTACAAATTTTAGTTGCCATCAAGGTATATACGAGTAAAAGCAGCGGTAAGTTGATTTCCAATTTGGAATCATTTTACTGCTGCTTTTTATATTTGAAATACTTTCata                                                                                                               >  2:83529/1‑141 (MQ=255)
                gCACATGAAACACTAATTGTAATTTAAATTACAAATTTTAGTTGCCATCAAGGTATATACGAGTAAAAGCAGCGGTAAGTTGATTTCCAATTTGGAATCATTTTACTGCTGCTTTTTATATTTGAAATACTTTCATATTGa                                                                                                           >  1:161171/1‑141 (MQ=255)
                gCACATGAAACACTAATTGTAATTTAAATTACAAATTTTAGTTGCCATCAAGGTATATACGAGTAAAAGCAGCGGTAAGTTGATTTCCAATTTGGAATCATTTTACTGCTGCTTTTTATATTTGAAATACTTTCATATTGa                                                                                                           >  1:1302/1‑141 (MQ=255)
                                ttGTAATTTAAATTACAAATTTTAGTTGCCATCAAGGTATATACGAGTAAAAGCAGCGGTAAGTTGATTTCCAATTTGGAATCATTTTACTGCTGCTTTTTATATTTGAAATACTTTCATATTGAATAGCTCCACTTGCCg                                                                                           >  2:23814/1‑141 (MQ=255)
                                   tAATTTAAATTACAAATTTTAGTTGCCATCAAGGTATATACGAGTAAAAGCAGCGGTAAGTTGATTTCCAATTTGGAATCATTTTACTGCTGCTTTTTATATTTGAAATACTTTCATATTGAATAGCTCCACTTGCCGTTc                                                                                        <  2:10191/141‑1 (MQ=255)
                                    aaTTTAAATTACAAATTTTAGTTGCCATCAAGGTATATACGAGTAAAAGCAGCGGTAAGTTGATTTCCAATTTGGAATCATTTTACTGCTGCTTTTTATATTTGAAATACTTTCATATTGAATAGCTCCACTTGCCGTTCg                                                                                       >  2:225949/1‑141 (MQ=255)
                                               cAAATTTTAGTTGCCATCAAGGTATATACGAGTAAAAGCAGCGGTAAGTTGATTTCCAATTTGGAATCATTTTACTGCTGCTTTTTATATTTGAAATACTTTCATATTGAATAGCTCCACTTGCCGTTCGCCTGCGCTTTg                                                                            >  2:23265/1‑141 (MQ=255)
                                                   ttttAGTTGCCATCAAGGTATATACGAGTAAAAGCAGCGGTAAGTTGATTTCCAATTTGGAATCATTTTACTGCTGCTTTTTATATTTGAAATACTTTCATATTGAATAGCTCCACTTGCCGTTCGCCTGCGCTTTGCgca                                                                        >  2:87829/1‑141 (MQ=255)
                                                   ttttAGTTGCCATCAAGGTATATACGAGTAAAAGCAGCGGTAAGTTGATTTCCAATTTGGAATCATTTTACTGCTGCTTTTTATATTTGAAATACTTTCATATTGAATAGCTCCACTTGCCGTTCGCCTGCGCTTTGCgca                                                                        >  1:173360/1‑141 (MQ=255)
                                                                    gTATATACGAGTAAAAGCAGCGGTAAGTTGATTTCCAATTTGGAATCATTTTACTGCTGCTTTTTATATTTGAAATACTTTCATATTGAATAGCTCCACTTGCCGTTCGCCTGCGCTTTGCGCATGCATAAAAGCCCCTaa                                                       <  2:1302/141‑1 (MQ=255)
                                                                    gTATATACGAGTAAAAGCAGCGGTAAGTTGATTTCCAATTTGGAATCATTTTACTGCTGCTTTTTATATTTGAAATACTTTCATATTGAATAGCTCCACTTGCCGTTCGCCTGCGCTTTGCGCATGCATAAAAGCCCCTaa                                                       <  2:161171/141‑1 (MQ=255)
                                                                                     cagcGGTAAGTTGATTTCCAATTTGGAATCATTTTACTGCTGCTTTTTATATTTGAAATACTTTCATATTGAATAGCTCCACTTGCCGTTCGCCTGCGCTTTGCGCATGCATAAAAGCCCCTAACAACCTGAGGTCACTgc                                      >  2:21293/1‑141 (MQ=255)
                                                                                        cGGTAAGTTGATTTCCAATTTGGAATCATTTTACTGCTGCTTTTTATATTTGAAATACTTTCATATTGAATAGCTCCACTTGCCGTTCGCCTGCGCTTTGCGCATGCATAAAAGCCCCTAACAACCTGAGGTCACTGCGCt                                   >  2:124002/1‑141 (MQ=255)
                                                                                        cGGTAAGTTGATTTCCAATTTGGAATCATTTTACTGCTGCTTTTTATATTTGAAATACTTTCATATTGAATAGCTCCACTTGCCGTTCGCCTGCGCTTTGCGCATGCATAAAAGCCCCTAACAACCTGAGGTCACTCCGCt                                   >  2:109534/1‑141 (MQ=255)
                                                                                         ggTAAGTTGATTTCCAATTTGGAATCATTTTACTGCTGCTTTTTATATTTGAAATACTTTCATATTGAATAGCTCCACTTGCCGTTCGCCTGCGCTTTGCGCATGCATAAAAGCCCCTAACAACCTGAGGTCACTGCGCTc                                  <  2:84770/141‑1 (MQ=255)
                                                                                                       cAATTTGGAATCATTTTACTGCTGCTTTTTATATTTGAAATACTTTCATATTGAATAGCTCCACTTGCCGTTCGCCTGCGCTTTGCGCATGCATAAAAGCCCCTAACAACCTGAGGTCACTGCGCTCCGGTTCGCCTgcgc                    >  1:11821/1‑141 (MQ=255)
                                                                                                           ttGGAATCATTTTACTGCTGCTTTTTATATTTGAAATACTTTCATATTGAATAGCTCCACTTGCCGTTCGCCTGCGCTTTGCGCATGCATAAAAGCCCCTAACAACCTGAGGTCACTGCGCTCCGGTTCGCCTGCGCTTTa                >  1:80948/1‑141 (MQ=255)
                                                                                                           ttGGAATCATTTTACTGCTGCTTTTTATATTTGAAATACTTTCATATTGAATAGCTCCACTTGCCGTTCGCCTGCGCTTTGCGCATGCATAAAAGCCCCTAACAACCTGAGGTCACTGCGCTCCGGTTAGCCTGCGCTTTa                >  2:199457/1‑141 (MQ=255)
                                                                                                               aaTCATTTTACTGCTGCTTTTTATATTTGAAATACTTTCATATTGAATAGCTCCACTTGCCGTTCGCCTGCGCTTTGCGCATGCATAAAAGCCCCTAACAACCTGAGGTCACTGCGCTCCGGTTCGCCTGCGCTTTAgcgc            >  2:61542/1‑141 (MQ=255)
                                                                                                               aaTCATTTTACTGCTGCTTTTTATATTCGAAATACTTTCATATTGAATAGCTCCACTTGCCGTTCGCCTGCGCTTTGCGCATGCATAAAAGCCCCTAACAACCTGAGGTCACTGCGCTCCGGTTCGCCTGCGCTTTAgcgc            <  1:60005/141‑1 (MQ=255)
                                                                                                               aaTCATTTTACTGCTGCTTTTTATATTCGAAATACTTTCATATTGAATAGCTCCACTTGCCGTTCGCCTGCGCTTTGCGCATGCATAAAAGCCCCTAACAACCTGAGGTCACTGCGCTCCGGTTCGCCTGCGCTTTAgcgc            <  1:60002/141‑1 (MQ=255)
                                                                                                                         ctgctgCTTTTTATATTTGAAATACTTTCATATTGAATCGCTCCACTTGCCGTTCGCCTGCGCTTTGCGCATGCATAAAATCCCCTAACAACCTGAGGTCACTGCGCTCCGGTTCGCCTGCGCTTTAGCGCATGCATaaaa  <  1:23814/141‑1 (MQ=255)
                                                                                                                                          |                                                                                                                           
ATGACATGGGCAAAATGCACATGAAACACTAATTGTAATTTAAATTACAAATTTTAGTTGCCATCAAGGTATATACGAGTAAAAGCAGCGGTAAGTTGATTTCCAATTTGGAATCATTTTACTGCTGCTTTTTATATTTGAAATACTTTCATATTGAATAGCTCCACTTGCCGTTCGCCTGCGCTTTGCGCATGCATAAAAGCCCCTAACAACCTGAGGTCACTGCGCTCCGGTTCGCCTGCGCTTTAGCGCATGCATAAAA  >  USA300TCH1516_ALE/2504665‑2504926

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