Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,568,885 T→A 9.3% L245* (TTA→TAA)  pbpX_2 → Putative penicillin‑binding protein PbpX

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,568,8850TA 9.3% 137.8 / 6.0 43L245* (TTA→TAA) pbpX_2Putative penicillin‑binding protein PbpX
Reads supporting (aligned to +/- strand):  ref base T (15/24);  new base A (2/2);  total (17/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-01

AGGTTTAATTATCCAAAACGTTACGAAGCAATCCTATACAAAATATATTACAAATTCATGGCTCAAGCCTTTGCATATGACACATACATCATTCAAACAAACCAATTACAAATCAAAACATGATGCTATTGGCTATGAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTGGGATACACCATCAGCATATATGATGACATCAACTGAAGATTTGGAACATTGGATAAAATTCCAACTTAATCCACCTGATAAATACAAATCAT  >  USA300TCH1516_ALE/2568745‑2569022
                                                                                                                                            |                                                                                                                                         
aGGTTTAATTATCCAAAACGTTACGAAGCAATCCTATACAAAATATATTACAAATTCATGGCTCAAGCCTTTGCATATGACACATACATCATTCAAACAAACCAATTACAAATCAAAACATGATGCTATTGGCTATGAAtt                                                                                                                                           <  1:16999/141‑1 (MQ=255)
          aTCCAAAACGTTACGAAGCAATCCTATACAAAATATATTACAAATTCATGGCTCAAGCCTTTGCATATGACACATACCTCATTCAAACAAACCAATTACAAATCCAAACCTGATGCTATTGGCTATGAATTACAAGGTTCg                                                                                                                                 <  2:459218/141‑1 (MQ=255)
            ccAAAACGTTACGAAGCAATCCTATACAAAATATATTACAAATTCATGGCTCAAGCCTTTGCATATGACACATACATCATTCAAACAAACCAATTACAAATCAAAACATGATGCTATTGGCTATGAATTACAAGGTTCGac                                                                                                                               >  2:73475/1‑141 (MQ=255)
                    ttACGAAGCAATCCTATACAAAATATATTACAAATTCATGGCTCAAGCCTTTGCATATGACACATACATCATTCAAACAAACCAATTACAAATCAAAACATGATGCTATTGGCTATGAATTACAAGGTTCGACACCTgtcg                                                                                                                       >  1:337270/1‑141 (MQ=255)
                    ttACGAAGCAATCCTATACAAAATATATTACAAATTCATGGCTCAAGCCTTTGCATATGACACATACATCATTCAAACAAACCAATTACAAATCAAAACATGATGCTATTGGCTATGAATTACAAGGTTCGACACCTgtcg                                                                                                                       >  1:284787/1‑141 (MQ=255)
                               tCCTATACAAAATATATTACAAATTCATGGCTCAAGCCTTTGCATATGACACATACATCATTCAAACAAACCAATTACCAATCAAAACATGATGCTATTGGCTATGAATTACAAGGTTAGACCCCTGTCCTCTCTAAACCt                                                                                                            <  2:211151/141‑1 (MQ=255)
                                   ataAAAAATATATTACAAATTCATGGCTCAAGCCATTGCATATGACACATACATCATTCAAACAAACCAATTACAAATCAAAACATGATGCTATTGGCTATGAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAAt                                                                                                        <  2:425339/141‑1 (MQ=255)
                                    taCAAAATATATTACAAATTCATGGCTCAAGCCTTTGCATATGACACATACATCATTCAAACAAACCAATTACAAATCAAAACATGATGCTATTGGCTATGAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAAtt                                                                                                       <  1:93313/141‑1 (MQ=255)
                                    taCAAAATATATTACAAATTCATGGCTCAAGCCTTTGCATATGACACATACATCATTCAAACAAACCAATTACAAATCAAAACATGATGCTATTGGCTATGAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAAtt                                                                                                       <  1:457632/141‑1 (MQ=255)
                                      cAAAATATATTACAAATTCATGGCTCAAGCCTTTGCATATGACACATACATCATTCAAACAAACCAATTACAAATCAAAACATGATGCTATTGGCTATGAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTa                                                                                                     >  2:334442/1‑141 (MQ=255)
                                      cAAAATATATTACAAATTCATGGCTCAAGCCTTTGCATATGACACATACATCATTCAAACAAACCAATTACAAATCAAAACATGATGCTATTGGCTATGAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTa                                                                                                     >  2:424330/1‑141 (MQ=255)
                                             tatTACAAATTCATGGCTCAAGCCTTTGCATATGACACATACATCATTCAAACAAACCAATTACAAATCAAAACATGATGCTATTGGCTATGAATAACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTg                                                                                              >  1:288599/1‑141 (MQ=255)
                                             tatTACAAATTCATGGCTCAAGCCTTTGCATATGACACATACATCATTCAAACAAACCAATTACAAATCAAAACATGATGCTATTGGCTATGAATAACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTg                                                                                              >  1:226790/1‑141 (MQ=255)
                                                 atagaTTCATGGCTCAAGCATTTGCATATGACACATACATCATTCAAACAAACCAATTACAAATCAAAACATGATGCTATTGGCTATGAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTGGGAt                                                                                          <  2:147001/137‑1 (MQ=255)
                                                 aCAAATTCATGGCTCAAGCCTTTGCATATGACACATACATCATTCAAACAAACCAATTACAAATCAAAACATGATGCTATTGGCTATGAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTGGGAt                                                                                          <  2:341037/141‑1 (MQ=255)
                                                 aCAAATTCATGGCTCAAGCCTTTGCATATGACACATACATCATTCAAACAAACCAATTACAAATCAAAACATGATGCTATTGGCTATGAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTGGGAt                                                                                          <  2:238905/141‑1 (MQ=255)
                                                 aCAAATTCATGGCTCAAGCCTTTGCATATGACACATACATCATTCAAACAAACCAATTACAAATCAAAACATGATGCTATTGGCTATGAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTGGGAt                                                                                          <  2:340421/141‑1 (MQ=255)
                                                   aaaTTCATGGCTCAAGCCTTTGCATATGACACATACATCATTCAAACAAACCAATTACAAATCAAAACATGATGCTATTGGCTATGAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTGGGATac                                                                                        <  1:402035/141‑1 (MQ=255)
                                                     agtCATGGCTCAAGCCTTTGCATATTACACATACATCATTCAAACAAACCAATTACAAATCAAAACATGATTCTATTGGCTATGAATTACAATGTTCTACACCTGTCGTCTCTAAACCTGAATTTAACCTTTGGGATacac                                                                                      <  2:437540/139‑1 (MQ=255)
                                                     aTTCATGGCTCAAGCCTTTGCATATGACACATACATCATTCAAACAAACCAATTACAAATCAAAACATGATGCTATTGGCTATGAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTGGGATacac                                                                                      <  2:398975/141‑1 (MQ=255)
                                                     aTTCATGGCTCAAGCCTTTGCATATGACACATACATCATTCAAACAAACCAATTACAAATCAAAACATGATGCTATTGGCTATGAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTGGGATacac                                                                                      <  1:380878/141‑1 (MQ=255)
                                                     aTTCATGGCTCAAGCCTTTGCATATGACACATACATCATTCAAACAAACCAATTACAAATCAAAACATGATGCTATTGGCTATGAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTGGGATacac                                                                                      <  2:146012/141‑1 (MQ=255)
                                                     aTTCATGGCTCAAGCCTTTGCATATGACACATACATCATTCAAACAAACCAATTACAAATCAAAACATGATGCTATTGGCTATGAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTGGGATacac                                                                                      <  1:155934/141‑1 (MQ=255)
                                                                                        tcatTCAAACAAACCAATTACAAATCAAAACATGATGCTATTGGCTATGAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTGGGATACACCATCAGCATATATGATGACATCAACTGAAGATTTg                                                   >  1:321595/1‑141 (MQ=255)
                                                                                         catTCAAACAAACCAATTACAAATCAAAACATGATGCTATTGGCTATGAATAACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTGGGATACACCATCAGCATATATGATGACATCAACTGAAGATTTgg                                                  <  2:288599/141‑1 (MQ=255)
                                                                                         catTCAAACAAACCAATTACAAATCAAAACATGATGCTATTGGCTATGAATAACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTGGGATACACCATCAGCATATATGATGACATCAACTGAAGATTTgg                                                  <  2:226790/141‑1 (MQ=255)
                                                                                              aaacaaacCAATTACAAATCAAAACATGATGCTATTGGCTATGAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTGGGATACACCATCAGCATATATGATGACATCAACTGAAGATTTGGAACAt                                             >  1:296688/1‑141 (MQ=255)
                                                                                              aaacaaacCAATTACAAATCAAAACATGATGCTATTGGCTATGAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTGGGATACACCATCAGCATATATGATGACATCAACTGAAGATTTGGAACAt                                             >  1:411165/1‑141 (MQ=255)
                                                                                              aaacaaacCAATTACAAATCAAAACATGATGCTATTGGCTATGAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTGGGATACACCATCAGCATATATGATGACATCAACTGAAGATTTGGAACAt                                             >  1:445774/1‑141 (MQ=255)
                                                                                                 caaacCAATTACAAATCAAAACATGATGCTATTGGCTATGAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTGGGATACACCATCAGCATATATGATGACATCAACTGAAGATTTGGAACATTgg                                          <  1:390560/141‑1 (MQ=255)
                                                                                                 caaacCAATTACAAATCAAAACATGATGCTATTGGCTATGAATTACAAGGTTCGACACCTGTCGACTATAAACATGCATTTAACCTTTGGGATAAACAATCAGAATATATGATGACATCAACTGAAGATTTGGAACATTgg                                          <  1:67464/141‑1 (MQ=255)
                                                                                                     ccAATTACAAATCAAAACATGATGCTATTGGCTATGAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTGGGATACACCATCAGCATATATGATGACATCAACTGAAGATTTGGAACATTGGATaa                                      <  1:186952/141‑1 (MQ=255)
                                                                                                     ccAATTACAAATCAAAACATGATGCTATTGGCTATGAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTGGGATACACCATCAGCATATATGATGACATCAACTGAAGATTTGGAACATTGGATaa                                      <  1:440745/141‑1 (MQ=255)
                                                                                                      cAATTACAAATCAAAACATGATGCTATTGGCTATGAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTGGGATACACCATCAGCATATATGATGACATCAACTGAAGATTTGGAACATTGGATaaa                                     >  2:166601/1‑141 (MQ=255)
                                                                                                                tCAAAACATGATGCTATTGGCTATGAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTGGGATACACCATCAGCATATATGATGACATCAACTGAAGATTTGGAACATTGGATAAAATTCCAACtt                           <  1:166601/141‑1 (MQ=255)
                                                                                                                     aCATGATGCTATTGGCTATGAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTGGGATACACCATCAGCATATATGATGACATCAACTGAAGATTTGGAACATTGGATAAAATTCCAACTTAATcc                      <  2:321595/141‑1 (MQ=255)
                                                                                                                        tgatgCTATTGGCTATGAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTGGGATACACCATCAGCATATATGATGACATCAACTGAAGATTTGGAACATTGGATAAAATTCCAACTTAATCCAcc                   >  2:226175/1‑141 (MQ=255)
                                                                                                                        tgatgCTATTGGCTATGAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTGGGATACACCATCAGCATATATGATGACATCAACTGAAGATTTGGAACATTGGATAAAATTCCAACTTAATCCAcc                   <  2:219123/141‑1 (MQ=255)
                                                                                                                         gatgCTATTGGCTATGAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTGGGATACACCATCAGCATATATGATGACATCAACTGAAGATTTGGAACATTGGCCAGAATTCCAACTTAATCCACCt                  >  1:214971/1‑141 (MQ=255)
                                                                                                                         gatgCTATTGGCTATGAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTGGGATACACCATCAGCATATATGATGACATCAACTGAAGATTTGGAACATTGGATAAAATTCCAACTTAATCCACCt                  >  2:271668/1‑141 (MQ=255)
                                                                                                                         gatgCTATTGGCTATGAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTGGGATACACCATCAGCATATATGATGACATCAACTGAAGATTTGGAACATTGGATAAAATTCCAACTTAATCCACCt                  >  2:6225/1‑141 (MQ=255)
                                                                                                                                ttGGCTATGAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTGGGATACACCATCAGCATATATGATGACATCAACTGAAGATTTGGAACATTGGATAAAATTCCAACTTAATCCACCTGATAAAt           <  1:280166/141‑1 (MQ=255)
                                                                                                                                        gAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTGGGATACACCATCAGCATATATGATGACATCAACTGAAGATTTGGAACATTGGATAAAATTCCAACTTAATCCACCTGATAAATACAAATCa   <  1:106428/141‑1 (MQ=255)
                                                                                                                                         aaTTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTGGGATACACCATCAGCATATATGATGACATCAACTGAAGATTTGGAACATTGGATAAAATTCCAACTTAATCCACCTGATAAATACAAATCAt  >  1:85053/1‑141 (MQ=255)
                                                                                                                                            |                                                                                                                                         
AGGTTTAATTATCCAAAACGTTACGAAGCAATCCTATACAAAATATATTACAAATTCATGGCTCAAGCCTTTGCATATGACACATACATCATTCAAACAAACCAATTACAAATCAAAACATGATGCTATTGGCTATGAATTACAAGGTTCGACACCTGTCGTCTCTAAACCTGAATTTAACCTTTGGGATACACCATCAGCATATATGATGACATCAACTGAAGATTTGGAACATTGGATAAAATTCCAACTTAATCCACCTGATAAATACAAATCAT  >  USA300TCH1516_ALE/2568745‑2569022

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