Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 526,744 C→T 8.9% R355C (CGT→TGT)  metG → Methionine‑‑tRNA ligase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE526,7440CT 8.9% 113.3 / 3.8 45R355C (CGT→TGT) metGMethionine‑‑tRNA ligase
Reads supporting (aligned to +/- strand):  ref base C (19/22);  new base T (2/2);  total (21/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.81e-01

ATGAGTAAATCTAAAGGTAATGTCGTAGACCCTAATATTTTAATTGATCGCTATGGTTTAGATGCTACACGTTATTATCTAATGCGTGAATTACCATTTGGTTCAGATGGCGTATTTACACCTGAAGCATTTGTTGAGCGTACAAATTTCGATCTAGCAAATGACTTAGGTAACTTAGTAAACCGTACGATTTCTATGGTTAATAAGTACTTTGATGGCGAATTACCAGCGTATCAAGGTCCACTTCATGAATTAGATGAAGAAATGGAAGCTATGG  >  USA300TCH1516_ALE/526606‑526882
                                                                                                                                          |                                                                                                                                          
aTGAGTAAATCTAAAGGTAATGTCGTAGACCCTAATATTTTAATTGATCGCTATGGTTTAGATGCTACACGTTATTATCTAATGCGTGAATTACCATTTGGTTCAGATGGCGTATTTACACCTGAAGCATTTGTTGAGCGt                                                                                                                                          >  1:233803/1‑141 (MQ=255)
     tAAATCTAAAGGTAATGTCGTAGACCCTAATATTTTAATTGATCGCTATGGTTTAGATGCTACACGTTATTATCTAATGCGTGAATTACCATTTGGTTCAGATGGCGTATTTACACCTGAAGCATTTGTTGAGCGTACaaa                                                                                                                                     <  1:10111/141‑1 (MQ=255)
              aGGTAATGTCGTAGCCCCTAATATGTTAATTGATCGCTATGGTTTAGATGCTACACGTTATTATCTAATGCGTGAATTACCATTTGGTTCAGATGGCGTATTTACACCTGAAGCATTTGTTGAGCGTACAAATTTCGATCt                                                                                                                            <  1:327347/141‑1 (MQ=255)
                    tGTCGTAGACCCTAAGATTTTAATTGATCGCTATGGTTTAGATGCTACACGTTATTATCTAATGCGTGAATTACCATTTGGTTCAGATGGCGTATTTACACCTGAAGCATTTGTTGAGCGTACAAATTTCGATCTAGCaaa                                                                                                                      >  1:180168/1‑141 (MQ=255)
                    tGTCGTAGACCCTAAGATTTTAATTCATCGCTATGGTTTAGATGCTACACGTTATTATCTAATGCGTGAATTACCATTTGGTTCAGATGGCGTATTTACACCTGAAGCATTTGTTGAGCGTACAAATTTCGATCTAGCaaa                                                                                                                      >  1:180087/1‑141 (MQ=255)
                      tCGTAGACCCTAATATTTTAATTGATCGCTATGGTTTAGATGCTACACGTTATTATCTAATGCGTGAATTACCATTTGGTTCAGATGGCGTATTTACACCTGAAGCATTTGTTGAGCGTACAAATTTCGATCTAGCAAATg                                                                                                                    >  1:72705/1‑141 (MQ=255)
                      tCGTAGACCCTAATATTTTAATTGATCGCTATGGTTTAGATGCTACACGTTATTATCTAATGCGTGAATTACCATTTGGTTCAGATGGCGTATTTACACCTGAAGCATTTGTTGAGCGTACAAATTTCGATCTAGCAAATg                                                                                                                    >  1:267828/1‑141 (MQ=255)
                      tCGTAGACCCTAATATTTTAATTGATCGCGATGGTTTAGATGCTACACGTTATTATCTAATGCGTGAATTACCATTTGGTTCAGATGGGGTATTTACACCTGAAGCATTTGTTGAGCGTACAAATTTCGATCTAGCAAGTg                                                                                                                    >  2:177459/1‑141 (MQ=255)
                       cGTAGACCCTAATATTTTAATTGATCGCTATGGTTTAGATGCTACACGTTATTATCTAATGCGTGAATTACCATTTGGTTCAGATGGCATATTTACACCTGAAGCATTTGTTGAGCGTACAAATTTCGATCTAGCAAATGa                                                                                                                   <  2:103435/141‑1 (MQ=255)
                           gACCCTAATATTTTAATTGATCGCTATGGTTTAGATGCTACACGTTATTATCTAATGCGTGAATTACCATTTGGTTCAGATGGCGTATTTACACCTGAAGCATTTGTTGAGCGTACAAATTTCGATCTAGCAAATGACTTa                                                                                                               >  1:328281/1‑141 (MQ=255)
                            aCCCTAATATTTTAATTGATCGCTATGGTTTAGATGCTACACGTTATTATCTAATGCGTGAATTACCATTTGGTTCAGATGGCGTATTTACACCTGAAGCATTTGTTGAGCGTACAAATTTCGATCTAGCAAATGACTTAg                                                                                                              >  2:304611/1‑141 (MQ=255)
                              ccTAATATTTTAATTGATCGCTATGGTTTGGATGCTACACGTTATTATCGAATGCGTGAAGTACCATTTGGTTCAGATGGCGTATTTGCAAGTGAGGCATTTGTTGAGCGTACAAATTCCGACCTAGCAAATGACTTGGGt                                                                                                            >  2:134551/1‑141 (MQ=255)
                                               tCGTTATGGTTTAGATGCTAAACGTAATTATCTAATGCGTGAGTTGCACTTGGGTTCAGCTGGCGCATTTTCACCTTAGGCTTTTTTTGGTCGTAGAAATTTCGCTCTAGCAAATGACTTAGGTAACTTAGTAAACCGtcc                                                                                           >  2:151400/1‑139 (MQ=255)
                                                ggCTATTGTTGAGATTCTCCACGTTATTATCTAATGCGTGAATTACCATTTGGTGCAGATGGCGTATTTACCCCTGAAGCATTTGTTGAGCGTACAAATTTCGATCTAGCAAATGACTTAGGTAACTTAGTAAACCGTACg                                                                                          <  2:247139/140‑1 (MQ=255)
                                                cGCTATGGTTTAGATGCTACACGTTATTATCTAATGCGTGAATTACCATTTGGTTCAGATGGCGTATTTACACCTGAAGCATTTGTTGAGCGTACAAATTTTGATCTAGCAAATGACTTAGGTAACTTAGTAAACCGTACg                                                                                          <  1:267848/141‑1 (MQ=255)
                                                 gCTAGGGGTTAGATGCCACACGATATTATCTAATGCGTGAATTACCACATGGTTCAGAAGGCGCATTTACACCTGCAGCATATGTTGAGCGTACAAATCTCGCTCTAGCAAAGGAACTAGGTAGCTTAGTAGACCGTACGa                                                                                         >  2:116647/1‑141 (MQ=255)
                                                     tGGTTTAGATGCTACACGTTATTATCTAATGCGTGAATTACCATTTGGTTCAGATGGCGTATTTACACCTGAAGCATTTGTTGAGCGTACAAATTTCGATCTAGCAAATGACTTAGGTAACTTAGTAAACCGTACGATTTc                                                                                     >  1:342171/1‑141 (MQ=255)
                                                      ggTTTAGATGCTACACGTTATTATCTAATGCGTGAATTACCATTTGGTTCGGATGGCGTATTTACACCTGAAGCATTTGTTGAGCGTACAAATTTCGATCTAGCAAATGACTTAGGTAACTTAGTAAACCGTACGATTTCt                                                                                    <  2:244231/141‑1 (MQ=255)
                                                           aGATGCTACACGTTATTATCTAATGCGTGAATTACCATTTGGTTCAGATGGCGTATTTACACCTGAAGCATTTGTTGAGCGTACAAATTTCGATCTAGCAAATGACTTAGGTAACTTAGTAAACCGTACGATTTCTATGGt                                                                               >  1:195891/1‑141 (MQ=255)
                                                                   cacGTTATTATCTAATGCGTGAATTACCATTTGGTTCAGATGGCGTATTTACACCTGAAGCATTTGTTGAGCGTACAAATTTCGATCTAGCAAATGACTTAGGTAACTTAGTAAACCGTACGATTTCTATGGTTAATAAGt                                                                       <  2:149708/141‑1 (MQ=255)
                                                                        tattatCTAATGCGTGAATTACCATTTGGTTCAGATGGCGTATTTACACCTGAAGCATTTGTTGAGCGTACAAATTTCGATCTAGCAAATGACTTAGGTAACTTAGTAAACCGTACGATTTCTATGGTTAATAAGTACttt                                                                  <  1:134957/141‑1 (MQ=255)
                                                                            atCTAATGCGTGAATTACCATTTGGTTCAGATGGCGTATTTACACCTGAAGCATTTGTTGAGCGTACAAATTTCGATCTAGCAAATGACTTAGGTAACTTAGTAAACCGTACGATTTCTATGGTTAATAAGTACTTTGATg                                                              <  1:182014/141‑1 (MQ=255)
                                                                              cTAATGGGTGAATTATCTTTTGGTTCCGTTGTGGTATTTACTCCTGTAGCATTTGTTGAGCGTACAAATTTCGGTCTAGCGAATGACTTTGTTAATTTTGTAAACCGTACTATTTCGATGGTTATTAAGTACTTTGATGGc                                                            <  2:335340/141‑1 (MQ=255)
                                                                                aaTGCGTGAATTACCATTTGGTTCAGATGGCGTATTTACACCTGAAGCATTTGTTGAGCGTACAAATTTCGATCTAGCAAATGACTTAGGTAACTTAGTAAACCGTACGATTTCTATGGTTAATAAGTACTTTGATGGCGa                                                          <  1:188546/141‑1 (MQ=255)
                                                                                  ggctggAATGACCATGTGGGTCAGATGGCGGATTGACACCTGGAGCATTCGTTGAGCGTACAAAGTTCGATCTAGCAAAGGCCTTAGGTAACTTAGTAGTCCGGACGATTTCTATGGTTAATAAGTACTTTGATGGCGAAt                                                        <  2:29608/136‑1 (MQ=255)
                                                                                        aaTTACCTTTTGGTTCAGATGGCGTATTTACACCTGAAGCATTTGTTGAGCGTACAAATTTCGATCTAGCAAATGACTTAGGTAACTTAGTAAACCGTACGATTTCTATGGTTAATAAGTACTTTGATGGCGAATTACCAg                                                  <  1:284775/141‑1 (MQ=255)
                                                                                             ccATTTGGTTCAGATGGCGTATTTACACCTGAAGCATTTGTTGAGCGTACAAATTTCGATCTAGCAAATGACTTAGGTAACTTAGTAAACCGTACGATTTCTATGGTTAATAAGTACTTTGATGGCGAATTACCAGCGTAt                                             <  2:114708/141‑1 (MQ=255)
                                                                                             ccATTTGGTTCAGATGGCGTATTTACACCTGAAGCATTTGTTGAGCGTACAAATTTCGATCTAGCAAATGACTTAGGTAACTTAGTAAACCGTACGATTTCTATGGTTAATAAGTACTTTGATGGCGAATTACCAGCGTAt                                             <  2:318554/141‑1 (MQ=255)
                                                                                              cATTTGGTTCAGATGGCGTATTTACACCTGAAGCATTTGTTGAGCGTCCAACCTTCGACCTAGCAACCGCCACAGTTAACTTAGTAAACCGTACGATGTCGATGGTTAATAAGTACTTTGATGGCGAATTACCAGCGTATc                                            >  1:171699/1‑141 (MQ=255)
                                                                                              cATTTGGTTCAGATGGCGTATTTACACCTGAAGCATTTGTTGAGCGTACAAATTTCGATCTAGCAAATGACTTAGGTAACTTAGTAAACCGTACGATTTCTATGGTTAATAAGTACTTTTATGGCGAATTACCAGCGTATc                                            >  1:12116/1‑141 (MQ=255)
                                                                                              cATTTGGTTCAGATGGCGTATTTACACCTGAAGCATTTGTTGAGCGTACAAATTTCGATCTAGCAAATGACTTAGGTAACTTAGTAAACCGTACGATTTCTATGGTTAATAAGTACTTTGATGGCGAATTACCAGCGTAta                                            >  2:189745/1‑140 (MQ=255)
                                                                                               aTTTGGTTCAGATGGCGTATTTACACCTGAAGCATTTGTTGAGTGTACAAATTTCGATCTAGCAAATGACTTAGGTAACTTAGTAAACCGTACGATTTCTATGGTTAATAAGTACTTTGATGGCGAATTACCAGCGTATCa                                           >  1:318707/1‑141 (MQ=255)
                                                                                               aTTTGGTTCAGATGGCGTATTTACACCTGAAGAATTTGTTGAGTGTACAAATTTCGATCTAGCAAATGACTTAGGTAACTTAGTAAACCGTACGATTTCTATGGTTAATAAGTACTTTGATGGCGAATTACCAGCGTATCa                                           >  1:318696/1‑141 (MQ=255)
                                                                                                  tGGTTCAGATGGCGTATTTACACCTGAAGCATTTGTTGAGCGTACAAATTTCGATCTAGCAAATGACTTAGGTAACTTAGTAAACCGTACGATTTCTATGGTTAATAAGTACTTTGATGGCGAATTACCAGCGTATCAAgg                                        >  2:106753/1‑141 (MQ=255)
                                                                                                             gCGTATTTACACATGAAGCATTTGTTGAGCGTACAAATTTCGATCTAGCAAATGACTTAGGTAACTTAGTAAACCGTACGATTCCTATGGTTAATAAGTACTTTGATGACGACTTACCAACGTATCAATGCCCCCttactc                             >  2:68886/1‑137 (MQ=255)
                                                                                                                     acacCTGAAGCATTTGTTGAGCGTACAAATTTCGATCTAGCAAATGACTTAGGTAACTTAGTAAACCGTACGATTTCTATGGTTAATAAGTACTTTGATGGCGAATTACCAGCGTATCAAGGTCCACTTCATGAATTAGAt                     <  1:228830/141‑1 (MQ=255)
                                                                                                                        ccTGAAGCATTTGTTGAGCGTACAAATTTCGATCTAGCAAATGACTTAGGTAACTTAGTAATCCGTACGATTTCTATGGTTAATAAGTACTTTGATGGCGAATTACCAGCGTATCAAGGTCCACTTCATGAATTAGATgaa                  <  1:351199/141‑1 (MQ=255)
                                                                                                                        ccTGAAGCATTTGTTGAGCGGACAAATGTCGATCTAGCAAATGACTTAGGTAACTTAGGAAACCGTACTATTTCTATGGTTAATAAGTACTTTGATGGCGAATTACCAGCGTATCAAGGTCCACTTCATGAATTAGATgaa                  <  1:250028/141‑1 (MQ=255)
                                                                                                                          tGAAGCATTTGTTGAGCGTACAAATTTCGATCTAGCAAATGACTTAGGTAACTTAGTAAACCGTACGATTTCTATGGTTAATAAGTACTTTGATGGCGAATTACCAGCGTATCAAGGTCCACTTCATGAATTAGATgaaga                <  2:342171/141‑1 (MQ=255)
                                                                                                                               cATTTGTTGAGTGTACAAATTTCGATCTAGCAAATGACTTAGGTAACTTAGTAAACCGTACGATTTCTATGGTTAATAAGTACTTTGATGGCGAATTACCAGCGTATCAAGGTCCACTTCATGAATTAGATGAAGAAATgg           <  2:318696/141‑1 (MQ=255)
                                                                                                                               cATTTGTTGAGTGTACAAATTTCGATCTAGCAAATGACTTAGGTAACTTAGTAAACCGTACGATTTCTATGGTTAATAAGTACTTTGATGGCGAATTACCAGCGTATCAAGGTCCACTTCATGAATTAGATGAAGAAATgg           <  2:318707/141‑1 (MQ=255)
                                                                                                                                aTTTGTTGAGCGTACAAATTTCGATCTAGCAAATGACTTAGGTAACGTAGTAAACCGTACGATTTCTATGGTTAATAAGTACTTTGATGGCGAATTACCAGCGTATCAAGGTCCACTTCATGAATTAGATGAAGAAATGGa          <  2:17596/141‑1 (MQ=255)
                                                                                                                                  ttgttgAGCGTACAAATTTCGATCTAGCAAATGACTTAGGTAACTTAGTAAACCGTACGATTTCTATGGTTAATAAGTACTTTGATGGCGAATTACCAGCGTATCAAGGTCCACTTCATGAATTAGATGAAGAAATGGAAg        >  2:5561/1‑141 (MQ=255)
                                                                                                                                  ttgttgAGCGGACAAATTTCCATCTAGCAAATGACTTAGGTAACTTAGTAAACCGTACGATTTCTAGGGTTAATAAGTACTTTGATGGCGAATTACCAGCGTATCAAGGTCCACGTCATGAATTAGATGAAGAAATGGAAg        <  1:77780/141‑1 (MQ=255)
                                                                                                                                        aGCGTACAAAGTTCGATCTAGCAAATGACTTAGGTAACTTAGTAAACCGTACGATTTCTATGGTTAATAAGTACTTTGATGGCGAATTACCAGCGTATCAAGGTCCACTTCATGAATTAGATGAAGAAATGGAAGCTATgg  <  1:304611/141‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                          
ATGAGTAAATCTAAAGGTAATGTCGTAGACCCTAATATTTTAATTGATCGCTATGGTTTAGATGCTACACGTTATTATCTAATGCGTGAATTACCATTTGGTTCAGATGGCGTATTTACACCTGAAGCATTTGTTGAGCGTACAAATTTCGATCTAGCAAATGACTTAGGTAACTTAGTAAACCGTACGATTTCTATGGTTAATAAGTACTTTGATGGCGAATTACCAGCGTATCAAGGTCCACTTCATGAATTAGATGAAGAAATGGAAGCTATGG  >  USA300TCH1516_ALE/526606‑526882

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑