Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,633,188 A→G 10.5% T920T (ACT→ACC)  fnbA_2 ← Fibronectin‑binding protein A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,633,1880AG10.5% 93.4 / 2.0 43T920T (ACT→ACC) fnbA_2Fibronectin‑binding protein A
Reads supporting (aligned to +/- strand):  ref base A (26/11);  new base G (2/2);  total (28/15)
Fisher's exact test for biased strand distribution p-value = 5.79e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.99e-01

TCATTGATTTCAATAACAGGTGTTACTACTTTACCTTGTTCCACTGGTTTAGAAGGCTTTTTAGGTTCTTCTTTGGCAGGTGGTACTGGTTTACCAGGTTCAGCTGGTACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGCTCACTCGGCACTTCTGGTGTCGGTGGTGTTGGTGTTTCCGGCTCACTTGGTACTTCTGGTGTTGGTGGCGTTGGTGTTTCCGGCTCACTTGGTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTG  >  USA300TCH1516_ALE/2633057‑2633324
                                                                                                                                   |                                                                                                                                        
tCATTGATTTCAATAACAGGTGTTACTACTTTACCTTGTTCCACTGGTTTAGAAGGCTTTTTAGGTTCTTCTTTGGCAGGTGGTACTGGTTTACCAGGTTCAGCTGGTACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGc                                                                                                                                 <  2:78098/141‑1 (MQ=255)
       tttCAATAACAGGTGTTACTACTTTACCTTGTTCCACTGGTTTAGAAGGCTTTTTAGGTTCTTCTTTGGCAGGTGGTACTGGTTTACCAGGTTCAGCTGGTACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGCTCACTCg                                                                                                                          <  1:167527/141‑1 (MQ=255)
             tAACAGGTGTTTCTACTTTTCCTTGTTCAACTGGTTTAGAAGGCTTTTTAGGTTCTTCTTTGGCAGGTGGTACTGGTTTACCAGGTTCAGCTGGTACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGCTCACTCGGCACtt                                                                                                                    <  1:121529/141‑1 (MQ=255)
              aaCAGGTGTTACTACTTTACCTTGTTCCACTGGTTTAGAAGGCTTTTTAGGTTCTTCTTTGGCAGGTGGTACTGGTTTACCAGGTTCAGCTGGTACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGCTCACTCGGCACTTc                                                                                                                   >  1:20310/1‑141 (MQ=255)
              aaCAGGTGTTACTACTTTACCTTGTTCCACTGGTTTAGAAGGCTTTTTAGGTTCTTCTTTGGCAGGTGGTACTGGTTTACCAGGTTCAGCTGGTACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGCTCACTCGGCACTTc                                                                                                                   >  1:223481/1‑141 (MQ=255)
               aCAGGTGTTACTACTTTACCTTGTTCCACTGGTTTAGAAGGCTTTTTAGGTTCTTCTTTGGCAGGTGGTACTGGTTTACCAGGTTCAGCTGGTACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGCTCACTCGGCACTTCt                                                                                                                  >  1:120150/1‑141 (MQ=255)
                  ggTGTTACTACTTTACCTTGTTCCACTGGTTTAGAAGGCTTTTTAGGTTCTTCTTTGGCAGGTGGTACTGGTTTACCAGGTTCAGCTGCTACCTCTGGTGTTGGCGCTGTTGGAGTTTCTGGCTCCCTCGGCACTTCTGgt                                                                                                               >  2:66242/1‑141 (MQ=255)
                    tgtTACTACTTTACCTTGCTCCACTGGCTTTGATGGCTTTTTGACTGGAGTTCAGTCGTGTGGTACTGGTTTCCCCAGTTGATCTGGTACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGCTCACTCGGCACTTCTGgtgt                                                                                                             <  1:248930/141‑1 (MQ=255)
                       tactacTTTACCTTGTTCCACTGGTTTAGAAGGCTTTTTAGGTTCTTCTTTGGCAGGTGGTACTGGTTTACCAGGTTCAGCTGGTACCTCTGGTGTTGGCGGTGTTGGAGCTTCTGGCTCACTCGGCACTTCTGGTGTCgg                                                                                                          >  2:170077/1‑141 (MQ=255)
                        actactTTCCCTTGTTCCACTGGTTTAGAAGGCTTTTTAGGTTCTTCTTTGGCAGGTGGTACTGGTTTACCAGGTTCAGCTGGTACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGCTCACTCGGCACTTCTGGTGTCggt                                                                                                         <  1:234291/141‑1 (MQ=255)
                         ctactTTACCTTGTTCCACTGGTTTAGAAGGCTTTTTAGGTTCTTCTTTGGCAGGTGGTACTGGTTTACCAGGTTCAGCTGGTACCTCTGGTGTTGGCGGTGTTGGAGATTCTGGCTCACTGGGCACTTCTGGGGTggggg                                                                                                        >  1:102681/1‑139 (MQ=255)
                           actTTACCTTGTTCCACTGGTTTAGAAGGCTTTTTAGGTTCTTCTTTGGCAGGTGGTACTGGTTTACCAGGTTCAGGTGGTACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGCTCACTCGGCACTTCTGGTGTCggtggt                                                                                                      >  1:25826/1‑141 (MQ=255)
                             tttACCTTGTTCCACTGGTTTAGAAGGCTTTTTAGGTTCTTCTTTGGCAGGTGGTACTGGTTTACCAGGTTCAGCTGGTACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGCTCACTCGGCACTTCTGGTGTCGGtggggt                                                                                                    >  2:269683/1‑141 (MQ=255)
                               tACCTTGTTCCACTGGTTTAGAAGGCTTTTTCGGTTCTTCTTTGGAAGGTGGTACTGGTTTACCAGGTTCAGCTGGTACCTCTGGTGCTGGCGGGGTTGGAGTTTCTGGCTCCCTCGGCACTTCTGGTGCCggggggggtg                                                                                                  >  1:59617/1‑136 (MQ=17)
                               tACCTTGTTCCACTGGTTTAGAAGGCTTTTTAGGTTCTTCTTTGGCAGGTGGTACTGGTTTACCAGGTTCAGCTGGTACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGCTCACTCGGCACTTCTGGTGTCGGtggtgttg                                                                                                  >  1:151043/1‑141 (MQ=255)
                                 ccTTGTTCCACTGGTTTAGAAGGCTTTTTAGGTTCTTCTTTGGCAGGTGGTACTGGTTTACCAGGTTCAGCTGGTACCTCTGGTGCTGGCGGTGTTGGGGTTTCTGGCTCACTCGGCACTTCTGGTGTCGGtggtgttggt                                                                                                >  2:82177/1‑141 (MQ=255)
                                    tGTTCCACTGGTTTAGAAGGCTTTTTAGGTTCTTCTTTGGCAGGTGGTACTGGTTTACCAGGTTCAGCTGGTACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGCTCACTCGGCACTTCTGGTGTCGGTggtgttggtgtt                                                                                             >  1:270812/1‑141 (MQ=255)
                                     gTTCCACTGGTTTAGAAGGCTTTTTAGGTTCTTCTTTGGCAGGTGGTACTGGTTTACCAGGTTCAGCTGGTACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGCTCACTCGGCCCTTCTGGTGTCGGCGGTGTTGGTGttt                                                                                            >  2:214497/1‑141 (MQ=255)
                                      ttCCACTGGTTTAGAAGGCTTTTTAGGTTCTTCTTTGGCAGGTGGTACTGGTTTACCAGGTTCAGCTGGTACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGCTCACTCGGCACTTCTGGTGTCGGTGGTGTTGGTGTTTc                                                                                           >  1:89088/1‑141 (MQ=255)
                                         cACTGGTTTAGAAGGCTTTTTAGGTTCTTCTTTGGCAGGTGGTACTGGTTTACCAGGTTCAGCTGGTACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGCTCACTCGGCACTTCTGGTGTCGGTGACGTTGGTGTTTCCgg                                                                                        >  2:303654/1‑141 (MQ=255)
                                          aCTGGTTTAGAAGGCTTTTTAGGTTCTTCTTTGGCAGGTGGTACTGGTTTACCAGGTTCAGCTGGTACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGCTCACTCGGCACTTCTGGTGTCGGTGGTGTTGGTGTTTCCGGc                                                                                       <  1:74517/141‑1 (MQ=255)
                                           cTGGTTTAGAAGGCTTTTTAGGTTCTTCTTTGGCAGGTGGTACTGGTTTACCAGGTTCAGCTGGTACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGCTCACTCGGCACTTCTGGTGTCGGTGGTGTTGGTGTTTCCGGCt                                                                                      >  1:216869/1‑141 (MQ=255)
                                              gTTTAGAAGGCTTTTTACGTTCTTCTTTGGCAGGTGGTACTGGTTTACCAGGTTCAGCTGGTACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGCTCACTCGGCACTTCTGGTGTCGGTGGTGTTGGTGTTTCCGGCTCAc                                                                                   >  1:288787/1‑141 (MQ=255)
                                               tttAGAAGGCTTTTTAGGTTCTTCTTTGGCAGGTGGTACTGGTTTACCAAGTTCAGCTGGTACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGTTCACTCGGCAATTCTGGTGTCGGTAGTGTTGCTTTTTCCGCctctct                                                                                  >  2:136336/1‑141 (MQ=255)
                                                 tAGATGGCTTTGTAGGTTCGGTTTTGGCAGGTGTTATTGGTTTACGGGGTTCGGATGGTTTCTGTGTTGTTGGTGGTGGGGGGGTTTTGGTCTCCCTGGGCACTTCTGGTGTCGGTGGTGTTGGTGTTTCCGGCTCACTTg                                                                                <  2:35685/141‑1 (MQ=9)
                                                   gAAGGCTTTTTAGGTTCTTCTTTGGCAGGTGGTACTGGTTTACCAGGTTCAGCTGGTACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGCTCACTCGGCACTTCTGGTGTCGGTGGTGTTGGTGGTTCCGGCTGCCTTGGt                                                                              >  2:269399/1‑141 (MQ=255)
                                                            ttcggatcttctTTGGCAGGTGGTACTGGTTTACTATGTTCAGCTGGTTCGCATGGGGTTGGCGGTGTTGGGGTTTCTGGCTCACTCGGCCCTTCTGGTGGCGGCGGGGTGGGTGTTTCCTGATCACTTGGTACTTCTGgt                                                                     >  2:182465/7‑141 (MQ=255)
                                                            ttAGGTTCTTCTTTGGCAGGTGGTACTGGTTTACCAGGTTCAGCTGGTACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGCTCACTCGGCACTTCTGGTGTCGGTGGTGTTGGTGTTTCCGGCTCACTTGGTACTTCTGgt                                                                     >  1:281755/1‑141 (MQ=255)
                                                             tAGGTTCTTCTTTGGCAGGTGGTACTGGTTTACCAGGTTCAGCTGGTACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGCTCACTCGGCACTTCTGGTGTCGGTGGTGNTGGTGTTTCCGGCTCACTTGGTACTTCTGgtg                                                                    >  1:74155/1‑141 (MQ=255)
                                                                 ttctttTTTGGCTGTTTGTGGTGGTTTTTCTGTTTCAGGTGGTACTGCTGGTGTTGGCGGTGTTGGTGTTTCTGGCGCACTCGGCACTTCTGGTGTCGGTGGTGTTGGTGTTTCCGGCTCACTTGGTACTTGTGGTGTtgg                                                                <  2:281589/141‑1 (MQ=14)
                                                                          ggCAGGTGGTACTGGTTTACCAGGTTCAGCTGGTACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGCTCACTCGGCACTTCTGGTGTCGGTGGTGTTGGTGTTTCCGGCTCACTTGGTACTTCTGGTGTTGGTGGCGTTgg                                                       <  1:276433/141‑1 (MQ=255)
                                                                          ggCAGGTGGTACTGGTTTACCAGGTTCAGCTGGTACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGCTCACTCGGCACTTCTGGTGTCGGTGGTGTTGGTGTTTCCGGCTCACTTGGTACTTCTGGTGTTGGTGGCGTTgg                                                       >  2:133934/1‑141 (MQ=255)
                                                                           gCAGGTGGTACTGGTTTACCAGGTTCAGCTGGTACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGCTCACTCGGCACTTCTGGTGTCGGTGGTGTTGGTGTTTCCGGCTCACTTGGTACTTCTGGTGTTGGTGGCGTTGgt                                                      >  1:54414/1‑141 (MQ=255)
                                                                               gtggtACTGGTTTACCAGGTTCAGCTGGTACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGCTCACTCGGCACTTCTGGTGTCGGTGGTGTTGGTGTTTCCGGCTCACTTGGTACTTCTGGTGTTGGTGGCGTTGGTGttt                                                  <  1:174666/141‑1 (MQ=255)
                                                                                    aCTGGTTTACCAGGTTCAGCTGGTACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGCTCACTCGGCACTTCTGGTGTCGGTGGTGTTGGTGTTTCCGGCTCACTTGGTACTTCTGGTGTTGGTGGCGTTGGTGTTTCCGGc                                             >  2:14257/1‑141 (MQ=255)
                                                                                           tACCAGGTGCAGCTGGTACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGCTCACTCGGCACTTCTGGTGTCGGTGGTGTTGGTGTTTCCGGCTCACTTGGTACTTCTGGTGTTGGTGGCGTTGGTGTTTCCGGCTCACTTg                                      <  1:313746/141‑1 (MQ=255)
                                                                                            aCCAGGTTCAGCTGGTACCTCTGGTGGTGGCGGTGTTGGGGTTTCTGGCTCACTCGGCACTTCTGGTGTCGGTGGTGTTGGTGTTTCCGGCTCACTTGGTACTTCTGGTGTTGGTGGCGTTGGTGTTTCCGGCTCACTTgg                                     <  1:82177/141‑1 (MQ=255)
                                                                                             ccAGGTTCAGCTGGTACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGCTCACTCGGCACTTCTGGTGTCGGTGGTGTTGGTGTTTCCGGCTCACTTGGTACTTCTGGTGTTGCTGGGGTTGGTGTTTCCGGCTCACTTgtt                                    >  2:112977/1‑139 (MQ=255)
                                                                                                   gaaccTGGTACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGCTCACTCGGCACTTCTGGTGTCGGTGGTGTTGGTGTTTCCGGCTCACTTGGTACTTCTGGTGTTGGTGGCGTTGGTGTTTCCGGCTCACTTGGTACTTCt                              >  2:172962/5‑141 (MQ=255)
                                                                                                           tACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGCTCACTCGGCACTTCTGGTGTCGGTGGTGTTGGTGTTTCCGGCTCACTTGGTACTTCTGGTGTTGGTGGCGTTGGTGTTTCCGGCTCACTTGGTACTTCTGGTGTCgg                      <  1:223677/141‑1 (MQ=255)
                                                                                                                          cGGTGTTGGAGTTTCTGGCTCACTCGGCACTTCTGGTGTCGGTGGTGTTGGTGTTTCCGGCTCACTTGGTACTTCTGGTGTTGGTGGCGTTGGTGTCTCCGGCTCCCTTGGTACTTCTGGTGTCGGAGGCGTTGGTGGCAc       >  2:2361/1‑141 (MQ=255)
                                                                                                                              gtTGGAGTTTCTGGCTCACTCGGCACTTCTGGTGTCGGTGGTGTTGGTGTTTCCGGCTCACTTGGTACTTCTGGTGTTGGTGGCGTTGGTGTTTCCGGCTCACTTGGTACTTCTGGTGTCGGTGGCGTTGGTGGCACGAtt   <  1:139202/141‑1 (MQ=255)
                                                                                                                               ttGGTGTTTCGGGTTCATTCGTTACTGCTGGTGTCGGTGGTGTTGGTGTTTCCGGCTCACTTGGTACTTCTGGTGTGGGTGGCGTTGGTGTTTCCGGCTCACTTGGGGCTTCTGGTGTCGGTGGCGTTGGTGGCACGATTg  <  2:54414/141‑1 (MQ=17)
                                                                                                                                   |                                                                                                                                        
TCATTGATTTCAATAACAGGTGTTACTACTTTACCTTGTTCCACTGGTTTAGAAGGCTTTTTAGGTTCTTCTTTGGCAGGTGGTACTGGTTTACCAGGTTCAGCTGGTACCTCTGGTGTTGGCGGTGTTGGAGTTTCTGGCTCACTCGGCACTTCTGGTGTCGGTGGTGTTGGTGTTTCCGGCTCACTTGGTACTTCTGGTGTTGGTGGCGTTGGTGTTTCCGGCTCACTTGGTACTTCTGGTGTCGGTGGCGTTGGTGGCACGATTG  >  USA300TCH1516_ALE/2633057‑2633324

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑