Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,064,126 G→C 44.7% Y121* (TAC→TAG)  ywtF ← Putative transcriptional regulator YwtF

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,064,1260GC44.7% ‑4.4 / 34.3 27Y121* (TAC→TAG) ywtFPutative transcriptional regulator YwtF
Reads supporting (aligned to +/- strand):  ref base G (9/6);  new base C (6/6);  total (15/12)
Fisher's exact test for biased strand distribution p-value = 7.07e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.35e-01

CATTTACAGCCTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCCTTTT  >  USA300TCH1516_ALE/1063996‑1064258
                                                                                                                                  |                                                                                                                                    
cATTTACAGCCTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCaa                                                                                                                            >  2:199442/1‑141 (MQ=255)
          cTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCTAAATTTAGGAAt                                                                                                                  >  1:101584/1‑141 (MQ=255)
          cTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGGAAt                                                                                                                  >  1:121274/1‑141 (MQ=255)
          cTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCCTAATAGCCAACTTTAGGAAt                                                                                                                  >  1:117366/1‑141 (MQ=255)
               cAAATGCTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCACATGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGc                                                                                                             <  1:122944/141‑1 (MQ=255)
                        tCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTAt                                                                                                    >  1:199413/1‑141 (MQ=255)
                              tGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCCTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTg                                                                                              <  2:111306/141‑1 (MQ=255)
                              tGACCCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCCTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTg                                                                                              <  2:48311/141‑1 (MQ=255)
                               gACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCCTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTgg                                                                                             >  1:224754/1‑141 (MQ=255)
                                                 aaCAGGTACATTCATTGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAAt                                                                           >  2:209595/1‑141 (MQ=255)
                                                        aaaTTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATAGGCATGTGCATGGGTAATCTTATCCTAATAGCCAACTTTAGGAATGTAGCTGAAAATATCACGTGGAATACTAAGCATCTTAATTGGCTGt                                                                    >  2:185817/3‑141 (MQ=255)
                                                              aTGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCCTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTttgat                                                              <  1:228168/141‑1 (MQ=255)
                                                                    gCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCCTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTa                                                        >  1:263015/1‑141 (MQ=255)
                                                                          ccctaaTCCATTGCCGCAATTGGACCACCATCTGCATGTGCATGGGTAATCTTATCCTAATAGTCAACTTTAGGAATGTAGCTGATAGTATCAACTGGAATACTAAGCATTTTAATTTGATGTTTTGATTGATTAAAagta                                                  <  2:196012/137‑1 (MQ=255)
                                                                                  cATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCCTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAAt                                          <  1:70963/141‑1 (MQ=255)
                                                                                    ttGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCCTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCa                                        >  2:36910/1‑141 (MQ=255)
                                                                                     tGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCCTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCAt                                       <  1:223029/141‑1 (MQ=255)
                                                                                      gCGGCAATTGGACCACCAAACCAGCCTTTATGGGTAATCTTATCCTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATa                                      >  2:270483/1‑141 (MQ=255)
                                                                                       cGGCCATTGGACCACCATATGCATGTGCATGGGTAATCTTATGGGAATAGCCAACTGTAGGAATGTAGCTGATAGTATCACGAGGAATACTAAGCATTCTAATTTGATTTGTTGATTGATTAAAAGTAGTTAAAATCATAg                                     <  2:101584/141‑1 (MQ=255)
                                                                                       cGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAg                                     <  2:121274/141‑1 (MQ=255)
                                                                                            aTTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTCAGCATCCTAATTTGATGTTTTGATTGATTAAAAGTAGTTCAAATCATACCGCCt                                >  2:164834/1‑141 (MQ=255)
                                                                                                 accaccATATGCATGTGCATGGATAATCTTATCGTAATAGCCAACTTTAGGAATTTAGCTGATAGGATCACGGGGAATACTAAGCATTGTAATTTGCTGTTTTTATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCt                           >  2:209333/1‑141 (MQ=255)
                                                                                                        tatGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAgtgt                    <  1:199442/141‑1 (MQ=255)
                                                                                                                   atgGGTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTg         >  1:159923/1‑141 (MQ=255)
                                                                                                                     gggTAATATTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCATGTc       >  2:33142/1‑141 (MQ=255)
                                                                                                                       gTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATGTGATGTTTAAATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCCt     <  1:121525/141‑1 (MQ=255)
                                                                                                                          aTCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCCtttt  <  1:209595/141‑1 (MQ=255)
                                                                                                                                  |                                                                                                                                    
CATTTACAGCCTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCCTTTT  >  USA300TCH1516_ALE/1063996‑1064258

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑