Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,505,018 C→G 13.1% intergenic (+322/+82) 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_ALE2,505,0180CG13.1% 137.1 / 9.3 45intergenic (+322/+82)USA300HOU_RS12890/gltThypothetical protein/Proton/sodium‑glutamate symport protein
Reads supporting (aligned to +/- strand):  ref base C (16/22);  new base G (2/4);  total (19/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTCACTGCGCTCCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCTGAGGTCACTACGCTTCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCAAAGGTTGTAAGGGGCTTTAAATGTCAGATAGTATTTTTTAAATTGATTTTAAATATTCTTGACCTTTTGCTTTGTCATATACGTTTTCCCATTTAG  >  USA300TCH1516_ALE/2504883‑2505158
                                                                                                                                       |                                                                                                                                            
gtgaCTGCGCCCCCGTTCGCCTTCGCTTTAGCGCATGCATAAAAGCCCCTCACAACCTGAGGTCACTACGCTTCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACTTGAGGTCACTACGCTTCCGTTCg                                                                                                                                         <  2:26162/138‑1 (MQ=17)
gTCACTACGCTTCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCTGAGGTCACTACGCTTCGGTTCg                                                                                                                                         <  1:98179/141‑1 (MQ=11)
  cACTACGCTTCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCTGAGGTCACTACGCTTCGGTTCGcc                                                                                                                                       <  1:78130/141‑1 (MQ=11)
     tGCGCTCCGCTTCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCTGAGGTCACTGCGCTTCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTgc                                                                                                                                    <  2:81623/141‑1 (MQ=255)
            ccgTTCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCTGAGGTCACTACGCTTCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAg                                                                                                                             <  2:40670/139‑1 (MQ=255)
             ggTTCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCTGAGGTCACTACGCTTCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAgc                                                                                                                            <  1:19629/141‑1 (MQ=255)
              gTTCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTATCAACCTGAGGTCACTACGCTTCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCATGCGCtaaagcg                                                                                                                           <  1:4977/141‑7 (MQ=255)
                tCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCTGAGGTCACTACGCTTCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCgca                                                                                                                         >  1:23741/1‑141 (MQ=255)
                   ccTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCTGAGGTCACTACGCTTCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCgcatgc                                                                                                                      >  1:61565/1‑141 (MQ=255)
                   ccTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCTGAGGTCACTACGCTTCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCgcatgc                                                                                                                      >  1:30202/1‑141 (MQ=255)
                   ccTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCTGAGGTCACTACGCTTCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCgcatgc                                                                                                                      >  1:30168/1‑141 (MQ=255)
                   ccTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCTGAGGTCACTACGCTTCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTAAGGTCACTACGCTTCAGTACGCCTGCGCATTAACgcataa                                                                                                                      >  2:44208/1‑139 (MQ=14)
                    cTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCTGAGGTCACTACGCTTCGGTTCGCCTGCGCTTTAGCgcatgca                                                                                                                     <  2:37509/141‑1 (MQ=255)
                     tGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCTGAGGTCACTACGCTTCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCgcatgcat                                                                                                                    <  1:67703/141‑1 (MQ=255)
                     tGCGCTTGAGCGCATGCAGAAAAGCCTCTAACAACCTGAGGTCACTACGCTTCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCgcatgcat                                                                                                                    <  2:85352/141‑1 (MQ=255)
                       cgcTTTAGCGCATGCATAAAAGACCCTAACAACCTGAGGTCACTACGCTTCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCGCATGCATaa                                                                                                                  <  2:135024/141‑1 (MQ=255)
                         cTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCAGAGGTCACTACGCTTCGGTACGCCTGCGCAGTAGCGCATGCATaaaa                                                                                                                >  2:102418/1‑141 (MQ=11)
                         cTTTAGCGCATGCATAAAAGCCCCTAACAACCTGAGGTCACTACGCTTCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCGCATGCATaaaa                                                                                                                >  1:107586/1‑141 (MQ=255)
                         cTTTAGCGCATGCATAAAAGCCCCTAACAACCTGAGGTCACTACGCTTCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTAAGGTCGCTACGCTCCCGATCGCCTCCACATTAGCGCATACATagaa                                                                                                                >  2:32616/1‑141 (MQ=14)
                            tAGCGTATGCATAATAGCCCACAACTACCTGAGGTCACTACGCTTCGGTTTGACTGCGCTTTAGCGCATGCATAAAAGACCCTAGCAACCTGATGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCGCATGCATAAATGcc                                                                                                             <  2:42165/141‑1 (MQ=14)
                              gcgcATGCATAAAAGCCCCTAACAACCTGAGGTCACTACGCTTCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCGCATGCATAAAAGcccc                                                                                                           <  1:2041/141‑1 (MQ=255)
                                       tAAAAGCCCCTAACAACCTGAGGTCACTACGCTTCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCGGTTCGCCTGCGCTTTAg                                                                                                                             <  2:36696/114‑1 (MQ=37)
                                       tAAAAGCCCCTAACAACCTGAGGTCACTACGCTTCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAg                                                                                                                             >  1:36696/1‑114 (MQ=255)
                                       tAAAAGCCCCTAACAACCTGAGGTCACTACGCTTCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCa                                                                                                  >  1:37582/1‑141 (MQ=255)
                                          aaGCCCCTAACAACCTGAGGTCACTACGCTTCGGTTCGCCTGCGCTTTATCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCAAAg                                                                                               <  1:92812/141‑1 (MQ=255)
                                             ccccTAACAACCTGAGGTCACTACGCTTCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAAcctgaggtc                                                                                            <  1:100126/141‑8 (MQ=255)
                                             ccccTAACAACCTGAGGTCACTACGCTTCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCAAAGGtt                                                                                            <  2:37582/141‑1 (MQ=255)
                                                        cTGAGGTCACTACGCTTCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCAAAGGTTGTAAGGGGCtt                                                                                 <  1:123546/141‑1 (MQ=255)
                                                            ggTCACTACGCTTCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCAAAGGTTGTAAGGGGCTTTaaa                                                                             >  1:115293/1‑141 (MQ=255)
                                                            ggTCACTACGCTTCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTCCCGATCGCCCGCGCATTAGCGCATGCATAAAAGCCCCTAACACCCAAAGGTTGTAAGGGGCTTTaaa                                                                             >  2:68349/1‑141 (MQ=18)
                                                               cACTACGCTTCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCAAAGGTTGTAAGGGGCTTTAAATGt                                                                          >  1:106804/1‑141 (MQ=255)
                                                                   ccGCTTCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCAAAGGTTGTAAGGGGCTTTAAATGTCAGa                                                                      <  1:59255/140‑1 (MQ=255)
                                                                   aCGCTTCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCAAAGGTTGTAAGGGGCTTTAAATGTCAGa                                                                      >  1:123183/1‑141 (MQ=255)
                                                                   aCGCTTCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCAAAGGTTGTAAGGGGCTTTAAATGTCAGa                                                                      <  2:30202/141‑1 (MQ=255)
                                                                           gTTCGACTGCGCTTTAGCGCATGCCTACGAGTCCCTAACAGCCAGAGGTCACTAGGCTTCGCCGCGCCTGCGCATGAGCGCAGGCATAAGAGCCCCTAACAACCAAAGGTTGTAAGGGGCTTTAAATGTCAGATAGTAttt                                                              >  2:82619/1‑141 (MQ=25)
                                                                              cGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCAAAGGTTGTAAGGGGCTTTAAATGTCAGATAGTAtttttt                                                           >  1:59853/1‑141 (MQ=255)
                                                                              cGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCAAAGGTTGTAAGGGGCTTTAAATGTCAGATAGTAtttttt                                                           <  1:40344/141‑1 (MQ=255)
                                                                                 cTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCAAAGGTTGTAAGGGGCTTTAAATGTCAGATAGTATTTTTTaaa                                                        >  2:99076/1‑141 (MQ=255)
                                                                                      cTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCAAAGGTTGTAAGGGGCTTTAAATGTCAGATAGTATTTTTTAAATTGAt                                                   <  1:79167/141‑1 (MQ=255)
                                                                                         tAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTaacaa                                                                                                     <  1:56938/88‑1 (MQ=255)
                                                                                                   atAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGCTCGCCTGCGCTTTCGCGCATGCATAAAAGCCCCTAACAACCAAAGGTTGTAAGGGGCTTTAAATGTCAGATAGTATTTTTTAAATTGCTTTTAAATATTCtt                                      >  2:12669/1‑141 (MQ=255)
                                                                                                          tCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCAAAGGTTGTAAGGGGCTTTAAATGTCAGATAGTATTTTTTAAATTGATTTTAAATATTCTTGACCttt                               <  1:117659/141‑1 (MQ=255)
                                                                                                           cccTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCAAAGGTTGTAAGGGGCTTTAAATGTCAGATACTATTTTTTAAATTGATTTTAAATATTCTTGACCtttt                              <  1:100577/141‑1 (MQ=255)
                                                                                                            ccTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCAAAGGTTGTAAGGGGCTTTAAATGTCAGATAGTATTTTTTAAATTGATTTTAAATATTCTTGACCTTTTg                             >  1:81820/1‑141 (MQ=255)
                                                                                                                               tACGCTTCCGTTCGCCTGCGCTTTAGCGCATGCATAACCGACCCTAACAACCAAAGGTTGTAAGGGGCTTTAAATGTCAGATAGTATTTTTTAAATTGATTTTAAATATTCTTGACCTTTTGCTTTGTCATATACGTTTTc          <  2:90255/141‑1 (MQ=255)
                                                                                                                                       cGTTCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCAAAGGTTGTAAGGGGCTTTAAATGTCAGATAGTATTTTTTAAATTGATTTTAAATATTCTTGACCTTTTGCTTTGTCATATACGTTTTCCCATTTAg  <  2:115293/141‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                            
GTCACTGCGCTCCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCTGAGGTCACTACGCTTCGGTTCGCCTGCGCTTTAGCGCATGCATAAAAGTCCCTAACAACCTGAGGTCACTACGCTTCCGTTCGCCTGCGCTTTAGCGCATGCATAAAAGCCCCTAACAACCAAAGGTTGTAAGGGGCTTTAAATGTCAGATAGTATTTTTTAAATTGATTTTAAATATTCTTGACCTTTTGCTTTGTCATATACGTTTTCCCATTTAG  >  USA300TCH1516_ALE/2504883‑2505158

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: ‑