Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,010,363 C→T 100% C146Y (TGT→TAT)  USA300HOU_RS10125 ← Putative multidrug export ATP‑binding/permease protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,010,3630CT97.4% 112.6 / ‑4.8 38C146Y (TGT→TAT) USA300HOU_RS10125Putative multidrug export ATP‑binding/permease protein
Reads supporting (aligned to +/- strand):  ref base C (0/1);  major base T (20/16);  minor base G (1/0);  total (21/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTA‑ACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGT  >  USA300TCH1516_ALE/2010231‑2010488
                                                                                                                                    |                                                                                                                              
cGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTA‑Ac                                                                                                                       <  1:281898/141‑1 (MQ=255)
    tCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTA‑ACCaaa                                                                                                                   >  2:268614/1‑141 (MQ=255)
             ttAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTA‑ACCAAATATTCATTa                                                                                                          >  1:285551/1‑141 (MQ=255)
               aaTCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTA‑ACCAAATATTCATTAAc                                                                                                        >  1:302834/1‑141 (MQ=255)
                aTCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTA‑ACCAAATATTCATTAAcc                                                                                                       <  1:322034/141‑1 (MQ=255)
                    tCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTA‑ACCAAATATTCATTAACCCGGt                                                                                                   <  1:26021/141‑1 (MQ=255)
                     ccAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTA‑ACCAAATATTCATTAACCCGGtt                                                                                                  >  1:381432/1‑141 (MQ=255)
                     acAAAGAAAACGTACAACGTTAAAATGTAAAATGGGAAGATAAACATTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTA‑ACCAAATATTCATTAACCCGGtt                                                                                                  <  2:231048/140‑1 (MQ=255)
                           aaaaCGTACACCGTTAGAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTA‑ACCAAATATTCATTAACCCGGTTAAAATg                                                                                            >  2:123445/1‑141 (MQ=255)
                           aaaaCGTACACCGTTAGAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTA‑ACCAAATATTCATTAACCCGGTTAAAATg                                                                                            >  2:123474/1‑141 (MQ=255)
                           aaaaCGTACAACGTTAAAATGTAAAATGAGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTA‑ACCAAATATTCATTAACCCGGTTAAAATg                                                                                            <  2:349328/141‑1 (MQ=255)
                              aCGTACACAGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTA‑ACCAAATATTCATTAACCCGGTTAAAATGaaa                                                                                         <  2:244213/141‑1 (MQ=255)
                                            aatgtaaaaggGGAAGATAAACAGTGCTGCTAAAGTCAATTTCAAATATAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTA‑ACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTc                                                                           <  2:19450/141‑1 (MQ=255)
                                             atgtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTA‑ACCAAATATCCATTAACCCAGTTAAAATGAAATCTTTTCTTTGTTCa                                                                          >  2:355339/1‑141 (MQ=255)
                                               gtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGTAATAATAATTATTATATAATCTA‑ACCAAATATTCATTAACCCAGTTAAAATAAAATCTTTTGTTTGTTCaaa                                                                        >  1:411912/1‑140 (MQ=255)
                                                taaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTA‑ACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAAca                                                                       >  2:21313/1‑141 (MQ=255)
                                                 aaaataGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATTGATAGTGCAATAATAATTGTTATATAATCTA‑ACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAAcat                                                                      <  2:348258/141‑1 (MQ=255)
                                                    atgGGAAGAAAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAATAACATTATGGATAGTGCAATAATAATTGTTATATAATCTA‑ACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAAcatcat                                                                   <  2:119968/141‑1 (MQ=255)
                                                       ggAAGATAAGCAGTGCTGCTAAAGGCAACTTCACATCCAAAAAAAAAATGATGGATAGTGCGCTCTTTCTTGTTATATAATCTA‑ACCAAATATTCATTAACCCTTTCAAAATGAAATCTTTTGTTTGTTCAACATCATTaa                                                                <  1:58893/141‑1 (MQ=255)
                                                       ggAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTA‑ACCAAATATTCATTAACCCGGTTAAAATGAAATATTTTGTTTGTTCAAAATCATTaa                                                                >  1:88897/1‑141 (MQ=255)
                                                             tAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTA‑ACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCActc                                                          <  1:123445/141‑1 (MQ=255)
                                                             tAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTA‑ACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCActc                                                          <  1:123474/141‑1 (MQ=255)
                                                                aCAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTA‑ACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAg                                                       <  2:85969/141‑1 (MQ=255)
                                                                          tAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTAT‑CAATGAATGCCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTg                                             <  1:418614/141‑1 (MQ=255)
                                                                                cAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTA‑ACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTTACCTAc                                       >  2:422592/1‑141 (MQ=255)
                                                                                cAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTA‑ACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTAc                                       >  1:162244/1‑141 (MQ=255)
                                                                                      cacaTCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTA‑ACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTACTCACTCTAGATATTACTTGACTTACTTGatt                                 >  1:86550/1‑141 (MQ=255)
                                                                                       acaGCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTA‑ACCAAATAGTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGatta                                <  1:170030/141‑1 (MQ=255)
                                                                                        caTCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATGTAATACA‑ACCAAATATTCAGTAACCTGGTTAAAATGAAATCTTTTCTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGattat                               >  2:411375/1‑141 (MQ=255)
                                                                                          tCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTA‑ACCAAATACTCATTAAACCGGTTAAAACGAAATCTTTTCTTTCTTCAACATCATTAATTACTATAGATATTACTTGCGCTACTTGCttacta                             >  2:125787/1‑141 (MQ=255)
                                                                                                 aGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTA‑ACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATaaa                      >  1:211747/1‑141 (MQ=255)
                                                                                                      aTTATGGATAGTGCAATAATAATTGTTATATAATCTA‑ACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAAtctc                 >  1:325183/1‑141 (MQ=255)
                                                                                                       ttATGGATAGTGCAATAATAATTGTTATATAATCTA‑ACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCg                <  2:167904/141‑1 (MQ=255)
                                                                                                       ttATGGATAGTGCAATAATAATTGTTATATAATCTA‑ACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCg                >  1:105127/1‑141 (MQ=255)
                                                                                                              tAGTGCAATAATAATTGTTATATAATCTA‑ACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTaa         >  1:408572/1‑141 (MQ=255)
                                                                                                                     atactaatCGCTATTGAATATA‑ACCAAATATTCATAAACCCGGTTAAAATGAAATCATTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACTTACTTGATTATTAGCATAAAATCTTCCACTTAACGCtttt  >  2:282346/1‑139 (MQ=255)
                                                                                                                     ataataatTGTTATATAATCTA‑ACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTATATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGt  <  1:268614/141‑1 (MQ=255)
                                                                                                                     ataataatTGTTATATAATCTA‑ACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGt  >  2:105180/1‑141 (MQ=255)
                                                                                                                                    |                                                                                                                              
CGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTA‑ACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGT  >  USA300TCH1516_ALE/2010231‑2010488

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: ‑