Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 2,785,994 C→A intergenic (‑207/+217) aur ← / ← isaB Zinc metalloproteinase aureolysin/Immunodominant staphylococcal antigen B

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,785,9940CA97.7% 130.1 / ‑3.0 43intergenic (‑207/+217)aur/isaBZinc metalloproteinase aureolysin/Immunodominant staphylococcal antigen B
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base A (26/16);  total (27/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.99e-01

ATGATTATTTCTATTTATTTCTATACTTTTTGTTCGTTGATTTTATTTATTGATTCTTTTCTTTTTTAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGCTTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTGAGATAACTATTTAAATAATCATAATCAAATAAACATTTTTATCAATTTCAAACAACTATG  >  USA300TCH1516_ALE/2785858‑2786125
                                                                                                                                        |                                                                                                                                   
aTGATTATTTCTATTTATTTCTATACTTTTTGTTCGTTGATTTTATTTATTGATTCTTTTCTTTTTTAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTa                                                                                                                                 >  1:124039/1‑141 (MQ=255)
    ttatttctatttatttctatACTTTTTGTTCGTTGATTTTATTTATTGATTCTTTTCTTTTTTAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTAtttt                                                                                                                             <  1:173182/141‑1 (MQ=255)
        ttctatttatttctatACTTTTTGTTCGTTGATTTTATTTATTGATTCTTTTCTTTTTTAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTtgtg                                                                                                                         >  2:696707/1‑141 (MQ=255)
            atttatttctatACTTTTTGTTCGTTGATTTTATTTATTGATTCTTTTCTTTTTTAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGaaaa                                                                                                                     <  2:380584/141‑1 (MQ=255)
               tatttctatACTTTTTGTTCGTTGATTTTATTTATTGATTCTTTTCTTTTTTTTTTTTTTTTTTTGTAGCTAAATAAAATTTTAAAAATTGAGTTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAatat                                                                                                                  >  2:516417/1‑141 (MQ=255)
                   tctatACTTTTTGTTTTTTTATTTTATTTATTGATTCTTTTCTTTTTTAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTTTTAAAATATTAAc                                                                                                              >  4:152512/1‑141 (MQ=255)
                       taCTTTTTGTTCGTTGATTTTATTTATTGATTCTTTTCTTTTTTTTTTTTTTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTTTCATGTATTTATTTTTGTGTAATTATTaatatat                                                                                                          >  2:534790/1‑136 (MQ=255)
                          tttttGTTCGTTGATTTTATTTATTGATTCTTTTCTTTTTTAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACa                                                                                                       >  1:431156/1‑141 (MQ=255)
                             ttGTTCGTTGATTTTATTTATTGATTCTTTTCTTTTTTAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACaaaa                                                                                                    >  3:223699/1‑141 (MQ=255)
                              tGTTCGTTGATTTTATTTATTGATTCTTCTCTTTTTTAAAAATGTTATCTGTAGCTAAATCAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAAt                                                                                                   >  1:457077/1‑141 (MQ=255)
                               gTTCGTTGATTTTATTTATTGATTCTTTTCTTTTTTAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGCTTTATTTTTGTGAAAATATTAACAAATACAAAATa                                                                                                  >  1:760953/1‑141 (MQ=255)
                                           tatttattGATACTTTTCTTTTTTAAAAATGTTTTCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACGAAATAGGGCTCtatata                                                                                      <  2:461884/141‑1 (MQ=255)
                                             tttattGATTCTTTTCTTTTTTAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGatttattt                                                                                                                              >  2:73291/1‑99 (MQ=255)
                                             tttattGATTCTTTTCTTTTTTAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACt                                                                                    <  2:124039/141‑1 (MQ=255)
                                             tttattGATTCTTGTCTTTTTTAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGatttattt                                                                                                                              <  1:73291/99‑1 (MQ=255)
                                                      tcttttctttTTTAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGGAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATg                                                                           >  1:533452/1‑141 (MQ=255)
                                                         tttcttttTTAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCtt                                                                        >  2:52782/1‑141 (MQ=255)
                                                         tttcttttTTAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCtt                                                                        >  1:742340/1‑141 (MQ=255)
                                                            cttttTTAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGaa                                                                     >  2:605095/1‑141 (MQ=255)
                                                              tttttAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAat                                                                   >  1:166889/1‑141 (MQ=255)
                                                                 ttAAAAATGTTATCTGTAGCTAAATAAAATTTTAATTATTTTTCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATAtg                                                                >  2:226891/1‑141 (MQ=255)
                                                                      aaTGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTgaga                                                           >  4:307146/1‑141 (MQ=255)
                                                                      aaTGTTACCTGTAGCTAAATAAAATTTTAAAAATCGATCATAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTgaga                                                           >  4:38062/1‑141 (MQ=255)
                                                                         gTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTGAGATaa                                                        <  1:34185/141‑1 (MQ=255)
                                                                           tATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTGAGATAACt                                                      <  1:19932/141‑1 (MQ=255)
                                                                              cTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCtt                                                                        >  2:422271/1‑120 (MQ=255)
                                                                              cTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCtt                                                                        <  1:422271/120‑1 (MQ=255)
                                                                                       aataaaATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTGAGATAACTATTTAAataatc                                          <  2:431156/141‑1 (MQ=255)
                                                                                         taaaATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACaa                                                                                                      >  4:202975/1‑79 (MQ=255)
                                                                                         taaaATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACaa                                                                                                      <  3:202975/79‑1 (MQ=255)
                                                                                          aaaaTTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTGAGATAACTATTTAAataatcata                                       >  1:423598/1‑141 (MQ=255)
                                                                                            aaTTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTGAGATAACTATTTAAataatcataat                                     <  1:469687/141‑1 (MQ=255)
                                                                                                ttAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTGAGATAACTATTTAAATAATCATAATCaaa                                 >  1:726491/1‑141 (MQ=255)
                                                                                                       ttGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTGAGATAACTATTTAAATAATCATAATCAAATaacaat                          >  2:642664/1‑137 (MQ=255)
                                                                                                          aGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACGAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTGAGATAACTATTTAAATAATCATAATCAAATAAACAtttt                       <  2:609086/141‑1 (MQ=255)
                                                                                                              tAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTGAGATAACTATTTAAATAATCATAATCAAATAAACATTTTTATc                   <  1:534790/141‑1 (MQ=255)
                                                                                                              tAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTGAGATAACTATTTAAATAATCATAATCAAATAAACATTTTTATc                   <  3:302480/141‑1 (MQ=255)
                                                                                                                   atatTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGctc                                                                                            <  1:328616/63‑1 (MQ=255)
                                                                                                                   atatTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGctc                                                                                            >  2:328616/1‑63 (MQ=255)
                                                                                                                   atatTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTTAGATAACTATTTAAATAATCATAATCAAATAAACATTTTTATCAAttt              <  1:516417/141‑1 (MQ=255)
                                                                                                                       tttAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTGAGATAACTATTTAAATAATCATAATCAAATAAACATTTTTATCAATTTCaaa          <  2:457077/141‑1 (MQ=255)
                                                                                                                        ttAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTGAGATAACTATTTAAATAATCATAATCAAATAAACATTTTTATCAATTTCAaac         >  1:607224/1‑141 (MQ=255)
                                                                                                                         tAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTGAGATAACTATTTAAATAATCATAATCAAATAAACATTTTTATCAATTTCAaaca        >  2:136319/1‑141 (MQ=255)
                                                                                                                          aaaaTTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTGAGATAACTATTTAAATAATCATAATCAAATAAACATTTTTATCAATTTCAaacaa       >  3:25773/1‑141 (MQ=255)
                                                                                                                               ttATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTGAGATAACTATTTAAATAATCATAATCAAATAAACATTTTTATCAATTTCAAACAACTATg  >  4:181719/1‑141 (MQ=255)
                                                                                                                                        |                                                                                                                                   
ATGATTATTTCTATTTATTTCTATACTTTTTGTTCGTTGATTTTATTTATTGATTCTTTTCTTTTTTAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGCTTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTGAGATAACTATTTAAATAATCATAATCAAATAAACATTTTTATCAATTTCAAACAACTATG  >  USA300TCH1516_ALE/2785858‑2786125

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: ‑