Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,854,250 T→C 13.8% S145S (TCA→TCG)  ccpA ← Catabolite control protein A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,854,2500TC13.8% 66.2 / 5.3 29S145S (TCA→TCG) ccpACatabolite control protein A
Reads supporting (aligned to +/- strand):  ref base T (13/12);  new base C (2/2);  total (15/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.04e-01

TTTTAGAATGTTCTCCACCTACTAAAGCAAATGATTTAGCGCCTTTTTCAATTAATTCTCCCGTAATTTCTTTCGCAGCTTCAGTAAAATCAATATTAACTGATGCTATATGTGCATCCTTACCATTTGTTCCTGATACTACTACAGGTACAGATGATTGATTTATCAATTCTTTCATTTCTTCAGTAATTGTACCACCAAGGAAAATAATACCATCAACCTGTTTACTTAATAAGTTATTAAAAATTTCTTTTTCCTTTTCAGGAT  >  USA300TCH1516_ALE/1854117‑1854383
                                                                                                                                     |                                                                                                                                     
ttttAGAATGTTCTCCACCTACTAAAGCAAATGATTTAGCGCCTTTTTCAATTAATTCTCCCGTAATTTCTTTCGCAGCTTCAGTAAAATCAATATTAACTGATGCTATATGTGCATCCTTACCATTTGTTCCTGAtacta                                                                                                                                >  1:161759/1‑141 (MQ=255)
ttttAGAATGTTCTCCACCTACTAAAGCAAATGATTTAGCGCCTTTTTCAATTAATTCTCCCGTAATTTCTTTCGCAGCTTCAGTAAAATCAATATTAACTGATGCTATATGTGCATCATTACCATTTGTTCCTGAtccta                                                                                                                                >  2:202013/1‑141 (MQ=255)
        tGTTCTCCACCTACTAAAGCAAATGATTTAGCGCCTTTTTCAATTAATTCTCCCGTAATTTCTTTCGCAGCTTCAGTAAAATCAATATTAACTGATGCTATATGTGCATCCTTACCATTTGTTCCTGATACTACTACAGGt                                                                                                                        <  2:287438/141‑1 (MQ=255)
              ccACCTACTAAAGCAAATGACATAGCGCCTTTTTCAATTAATTCTCCCGTAATTTATTTCGCAGCTTCAGTAAAATCAATATTAACTGATGATATATGAGCATCCTTACCATTAGTGCCTGGTCCTACGACAGGTAcgcat                                                                                                                  >  2:271819/1‑137 (MQ=255)
                  ctactaAAGCAAATGATTTAGCGCCTTTTTCAATTAATTCTCCCGTAATTTCTTTCGCAGCTTCAGTAAAATCAATATTAACTGATGCTATATGTGCATCCTTACCATTTGTTCCTGATACTACTACAGGTTCAGAtgctt                                                                                                              >  2:274588/1‑141 (MQ=255)
                    actaAAGCAAATGATTTAGCGCCTTTTTCAATTAATTCTCCCGTAATTTCTTTCGCAGCTTCAGTAAAATCAATATTAACTGATGCTATATGTGCATCCTTACCATTTGTTCCTGATACTACTACAGGTACAGAtgattga                                                                                                            <  1:216982/141‑1 (MQ=255)
                        aaGCAAATGATTTAGCGCCTTTTTCAATTAATTCTCCCGTAATTTCTTTCGCAGCTTCAGTAAAATCAATATTAACTGATGCTATATGTGCATCCTTACCATTTGTTCCTGATACTACTACAGGTACAGATGATTGATTTa                                                                                                        >  1:168565/1‑141 (MQ=255)
                                gATTTAGCGCCTTTTTCAATTAATTCTCCCGTAATTTCTTTCGCAGCTTCAGTAAAATCAATATTAACTGATGCTATATGTGCATCCTTACCATTTGTTCCTGATACTACTACAGGTACAGATGATTGATTTATCAATTCt                                                                                                <  1:324698/141‑1 (MQ=255)
                                  tttAGCGCCTTTTTCAATTAATTCTCCCGTAATTTCTTTCGCAGCTTCAGTAAAATCAATATTAACTGATGCTATATGTGCATCCTTACCATTTGTTCCTGATACTACTACAGGTACAGATGATTGATTTATCAATTCttt                                                                                              <  2:33069/141‑1 (MQ=255)
                                   ttAGCGCCTTTTTCAATTAATTCTCCCGTAATTTCTTTCGCAGCTTCAGTGAAACCAATATTAACTGATGCTATATGTGCATCCTTACCATTTGTTCCTGATACTACTACAGGTACAGATGATTGATTTATCAATTCTTTc                                                                                             >  1:262707/1‑141 (MQ=255)
                                           tttttCAATTAATTCTCCCGTAATTTCTTTCGCAGCTTCAGTAAAATCAATATTAACTGATGCTATATGTGCATCCTTACCATTTGTTCCTGATACTACTACAGGTACAGATGATTGATTTATCAATTCTTTCATttattc                                                                                     <  2:47132/141‑1 (MQ=255)
                                              ttCAATTAATTCTCCCGTAATTTCTTTCGCAGCTTCAGTAAAATCAATATTAACTGATGCTATATGTGCATCCTTACCATTTGTTCCCGATACTACTACAGGTACAGATGATTGATTTATCAATTCTTTCATTTCTTCAGt                                                                                  >  2:144656/1‑141 (MQ=255)
                                              ttCAATTAATTCTCCCGTAATTTCTTTCGCAGCTTCAGTAAAATCAATATTAACTGATGCTATATGTGCATCCTTACCATTTGTTCCCGATACTACTACAGGTACAGATGATTGATTTATCAATTCTTTCATTTCTTCAGt                                                                                  >  2:144724/1‑141 (MQ=255)
                                                cAATTAATTCTCCCGTAATTTCTTTCGCAGCTTCAGTAAAATCAATATTAACTGATGCTATATGTGCATCCTTACTATTTGTTCCTGATACTACTACAGGTACAGATGATTGATTTATCACTTCTTTCATTTCTTCAGTaa                                                                                <  1:274588/141‑1 (MQ=255)
                                                 aattatttCTCCCGTACTTTCTTTCTCTGATTCAGTAAATCCAATATTAACTGATTCTATATGTGCATCCTTACCATTTGTTCCTTATTCTACTACAGGTACAGATGATTGATTTATCAATTCTTTCATTTCTTCAGTAAt                                                                               <  2:112663/141‑1 (MQ=255)
                                                 aattaattCTCCCGTAATTTCTTTCGCAGCTTCAGTAAAATCAATATTAACTGATGCTATATGTGCATCCTTACCATTTGTTCCTGATACTACTACAGGTACAGATGATTGATTTATCAATTCTTTCATTTCTTCAGTAAt                                                                               <  2:381684/141‑1 (MQ=255)
                                                  attaattCTCCCGTAATTTCTTTCGCAGCTTCAGTAAAATCAATATTAACTGATGCTATATGTGCATCCTTACCATTTGTTCCTGATACTACTACAGGTACAGATGATTGATTTATCAATTCTTTCATTTCTTCAGTAAtt                                                                              >  1:348844/1‑141 (MQ=255)
                                                              gTAATTTCTTTCGCAGCTTCAGTAAAATCAATATTAACTGATGCTATATGTGCATCCTTACCATTTGTTCCTGATACTACTGCAGGTACAGATGATTGATTTATCAATTCTTTCATTTTTTCAGTAATTGTAGCACCCAgg                                                                  >  1:227628/1‑141 (MQ=255)
                                                              gTAATTTCTTTCGCAGCTTCAGTAAAATCAATATTAACTGATGCTATATGTGCATCCTTACCATTTGTTCCTGATACTACTACAGGTACAGCTGATTGATTTATCAATTCTTTCATTTCTTCAGTAATTGTACCACCAAgg                                                                  <  2:259674/141‑1 (MQ=255)
                                                                           cAGCTTCAGTAAAATCAATATTAACTGATGCTATATGTGCATCCTTACCATTTGTTCCTGATACTACTACAGGTACAGATGATTGATTTATCAATTCTTTCATTTCTTCAGTAATTGTACCACCAAGGAAAATAATACCAt                                                     <  2:168565/141‑1 (MQ=255)
                                                                               ttCAGTAAAATCAATATTAACTGATGCTATATGTGCATCCTTACCATTTGTTCCTGATACTACTACAGGTACAGATGCTTGATTTATCAATTCTTTCATTTCTTCAGTAATTGTACCACCAAGGAAAATAATACCATCAAc                                                 >  1:266515/1‑141 (MQ=255)
                                                                               tcatttAAAAACAATATTAACTGATGCTATATGTGCATCCTTACCATTTGTTCCTGATACTACTACAGGTACAGATGATTGATTTATCAATTCTTTCATTTCTTCAGTAATTGTACCACCAAGGAAAATAATACCATCAAc                                                 <  1:88106/136‑1 (MQ=255)
                                                                                       aaTCAATATTAACTGATGCTATATGTGCATCCTTACCATTTGTTCCCGATACTACTACAGGTACAGATGATTGATTTATCAATTCTTTCATTTCTTCAGTAATTGTACCACCAAGGAAAATAATACCATCAACCTGTTTAc                                         <  1:144724/141‑1 (MQ=255)
                                                                                       aaTCAATATTAACTGATGCTATATGTGCATCCTTACCATTTGTTCCCGATACTACTACAGGTACAGATGATTGATTTATCAATTCTTTCATTTCTTCAGTAATTGTACCACCAAGGAAAATAATACCATCAACCTGTTTAc                                         <  1:144656/141‑1 (MQ=255)
                                                                                             tatTAAGTGATGCTATATGTGCATCCTTACCATTTGTTCCTGATACTACTACAGGTACAGATGATTGATTTATCAATTCTTTCATTTCTTCAGTAATTGTACCACCAAGGAAAATAATACCATCAACCTGTTTACTtaata                                   >  2:219204/1‑141 (MQ=255)
                                                                                                              tgtgCATCCTTACCATTTGTTCCTGATACTACTACAGGTACAGATGATTGATTTATCAATTCTTTCATTTCTTCAGTAATTGTACCACCAAGGAAAATAATACCATAAACCTGTTTACTTAATAAGTTATTAAAAATTTCt                  >  2:30029/1‑141 (MQ=255)
                                                                                                                       ttACCATTTGTTCCTGATACTACTACAGGTACAGATGATTGATTTATCAATTCTTTCATTTCTTCAGTAATTGTACCACCAAGGAAAATAATACCATCAACCTGTTTACTTAATAAGTTATTAAAAATTTCTTTTTCCttt         >  1:322020/1‑141 (MQ=255)
                                                                                                                             tttGTTCCTGATACTACTACAGGTACAGATGATTGATTTATCAATTCTTTCATTTCTTCAGTAATTGTACCACCAAGGAAAATAATACCATCAACCTGTTTACTTAATAAGTTATTAAAAATTTCTTTTTCCTTTTCAGGa   <  2:170859/141‑1 (MQ=255)
                                                                                                                              ttGTTCCTGATACTACTACAGGTACAGATGATTGATTTATCAATTCTTTCATTTCTTCAGTAATTGTACCACCAAGGAAAATAATACCATCAACCTGTTTACTTAATAAGTTATTAAAAATTTCTTTTTCCTTTTCAGGAt  >  2:9030/1‑141 (MQ=255)
                                                                                                                                     |                                                                                                                                     
TTTTAGAATGTTCTCCACCTACTAAAGCAAATGATTTAGCGCCTTTTTCAATTAATTCTCCCGTAATTTCTTTCGCAGCTTCAGTAAAATCAATATTAACTGATGCTATATGTGCATCCTTACCATTTGTTCCTGATACTACTACAGGTACAGATGATTGATTTATCAATTCTTTCATTTCTTCAGTAATTGTACCACCAAGGAAAATAATACCATCAACCTGTTTACTTAATAAGTTATTAAAAATTTCTTTTTCCTTTTCAGGAT  >  USA300TCH1516_ALE/1854117‑1854383

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: ‑