Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 949,407 G→T 12.5% intergenic (+194/‑222) USA300HOU_RS04730 → / → yugI_2 Putative peptidyl‑prolyl cis‑trans isomerase/General stress protein 13

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE949,4070GT12.5% 108.0 / 5.0 32intergenic (+194/‑222)USA300HOU_RS04730/yugI_2Putative peptidyl‑prolyl cis‑trans isomerase/General stress protein 13
Reads supporting (aligned to +/- strand):  ref base G (16/12);  new base T (2/2);  total (18/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.65e-01

GAATGGATTAGTATATATTCCAACGAAAATAAATAAACTAATATGATGAGCAATCTCAATATATTTATCAAGAAAGCACAGTTTTTAAATAGATGTGTATTTTAAAGATAATAGTTGAGGTTGCTTTTTATGTTTTTACAGAGAATTGCTATTCAAATAGTAAATAAATTGAAAACAAAGTAGCTGGATATCATATTGATTTAGATAGGAATTTGTTGCTAATTTTATTTGTAAATCCAAGTTTGTAGAATTCTTATTCATTTATAAAATAATATTCGTAT  >  USA300TCH1516_ALE/949267‑949547
                                                                                                                                            |                                                                                                                                            
gAATGGATTAGTATATATTCCAACGAAAATAAATAAACTAATATGATGAGCAATCTCAATATATTTATCAAGAAAGCACAGTTTTTAAATAGATGTGTATTTTAAAGATAATAGTTGAGGTTGCTTTTTATGTTTTTACag                                                                                                                                              >  1:192336/1‑141 (MQ=255)
gAATGGATTAGTATATATTCCAACGAAAATAAATAAACTAATATGATGAGCAATCTCAATATATTTATCAAGAAAGCACAGTTTTTAAATAGATGTGTATTTTAAAGATAATAGTTGAGGTTGCTTTTTATGTTTTTACag                                                                                                                                              >  1:192340/1‑141 (MQ=255)
       ttAGTATATATTCCAACGAAAATAAATACACGAATATGATGAGCAAACTCAATATATTTATCAAGAATGCACAGTTTTTAAATAGATGTGTATTTTAAAGATAATAGTTGAGGTTGCTTTTTATGTTTTTACAGAGAATTg                                                                                                                                       <  2:189538/141‑1 (MQ=255)
                   ccAACGAAAATAAATAAACTAATATGATGAGCAATCTCAATATATTTATCAAGAAAGCACAGTTTTTAAATAGATGTGTATTTTAAAGATAATAGTTGAGGTTGCTTTTTATGTTTTTACAGAGAATTGCTATTCAAATAg                                                                                                                           >  2:51955/1‑141 (MQ=255)
                   ccAACGAAAATAAATAAACTAATATGATGAGCAATCTCAATATATTTATCAAGAAAGCACAGTTTTTAAATAGATGTGTATTTTAAAGATAATAGTTGAGGTTGCTTTTTATGTTTTTACAGAGAATTGCTATTCAAATAg                                                                                                                           >  1:151846/1‑141 (MQ=255)
                   ccAACGAAAATAAATAAACTAATATGATGAGCAATCTCAATATATTTATCAAGAAAGCACAGTTTTTAAATAGATGTGTATTTTAAAGATAATAGTTGAGGTTGCTTTTTATGTTTTTACAGAGAATTGCTATTCAAATAg                                                                                                                           >  2:217787/1‑141 (MQ=255)
                   ccAACGAAAATAAATAAACTAATATGATGAGCAATCTCAATATATTTATCAAGAAAGCACAGTTTTTAAATAGATGTGTATTTTAAAGATAATAGTTAAGGTTGCTCTTTATGTTTTTACAGAGAATTGATATTCAAATat                                                                                                                           >  2:94538/1‑140 (MQ=255)
                              aaataaaCTAATATGATGAGCAATCTCAATATATTTATCAAGAAAGCACAGTTTTTAAATAGATGTGTATTTTAAAGATAATAGTTGAGGTTGCTTTTTATGTTTTTACAGAGAATTGCTATTCAAATAGTAAATAAATTg                                                                                                                >  2:103770/1‑141 (MQ=255)
                               aataaaCTAATATGATGAGCAATCTCAATATATTTATCAAGAAAGCACAGTTTTTAAATAGATGTGTATTTTAAAGATAATAGTTGAGGTTGCTTTTTATGTTTTTACATAGAATTGCTATTCAAATAGTAAATAAATTGa                                                                                                               >  1:250901/1‑141 (MQ=255)
                               aataaaCTAATATGATGAGCAATCTCAATATATTTATCAAGAAAGCACAGTTTTTAAATAGATGTGTATTTTAAAGATAATAGTTGAGGTTGCTTTTTATGTTTTTACATAGAATTGCTATTCAAATAGTAAATAAATTGa                                                                                                               >  1:250991/1‑141 (MQ=255)
                               aataaaCTAATATGATGAGCAATCTCAATATATTTATCAAGAAAGCACAGTTTTTAAATAGATGTGTATTTTAAAGATAATAGTTGAGGTTGCTTTTTATGTTTTTACAGAGAATTGCTATTCAAATAGTAAATAAATTGa                                                                                                               >  1:128953/1‑141 (MQ=255)
                                ataaaCTAATATGATGAGCAATCTCAATATATTTATCAAGAAAGCACAGTTTTTAAATAGATGTGTATTTTAAAGATAATAGTTGAGGTTGCTTTTTATGTTTTTACAGAGAATTGCTATTCAAATAGTAAATAAATTGaa                                                                                                              >  2:43062/1‑141 (MQ=255)
                                ataaaCTAATATGATGAGCAATCTCAATATATTTATCAAGAAAGCACAGTTTTTAAATAGATGTGTATTTTAAAGATAATAGTTGAGGTTGCTTTTTATGTTTTTACAGAGAATTGCTATTCAAATAGTAAATAAATTGaa                                                                                                              <  1:124208/141‑1 (MQ=255)
                                             atgaGCAATCTCAATATATTTATCAAGAAAGCACAGTTTTTAAATAGATGTGTATTTTAAAGATAATAGTTGAGGTTGCTTTTTATGTTTTTACAGAGAATTGCTATTCAAATAGTAAATAAATTGAAAACAAAGTAGCTg                                                                                                 >  1:113333/1‑141 (MQ=255)
                                             atgaGCAATCTCAATATATTTATCAAGAAAGCACAGTTTTTAAATAGATGTGTATTTTAAAGATAATAGTTGAGGTTGCTTTTTATGTTTTTACAGAGAATTGCTATTCAAATAGTAAATAAATTGAAAACAAAGTAGCTg                                                                                                 >  1:219550/1‑141 (MQ=255)
                                                 gCAATCTCAATATATTTATCAAGAAAGCACAGTTTTTAAATAGATGTGTATTTTAAAGATAATAGTTGAGGTTGCTTTTTATGTTTTTACAGAGAATTGCTATTCAAATAGTAAATAAATTGAAAACAAAGTAGCTGGata                                                                                             >  1:84452/1‑141 (MQ=255)
                                                    aTCTCAATATATTTATCAAGAAAGCACAGTTTTTAAATAGATGTGTATTTTAAAGATAATAGTTGAGGTTGCTTTTTATGTTTTTACAGAGAATTGCTATTCAAATAGTAAATAAATTGAAAACAAAGTAGCTGGATATCa                                                                                          >  2:33065/1‑141 (MQ=255)
                                                     tctcAATATATTTATCAAGAAAGCACAGTTTTTAAATAGATGTGTATTTTAAAGATAATAGTTGAGGTTGCTTTTTATGTTTTTACAGAGAATTGCTATTCAAATAGTAAATAAATTGAAAACAAAGTAGCTGGATATCat                                                                                         <  2:192336/141‑1 (MQ=255)
                                                     tctcAATATATTTATCAAGAAAGCACAGTTTTTAAATAGATGTGTATTTTAAAGATAATAGTTGAGGTTGCTTTTTATGTTTTTACAGAGAATTGCTATTCAAATAGTAAATAAATTGAAAACAAAGTAGCTGGATATCat                                                                                         <  2:192340/141‑1 (MQ=255)
                                                          atatatTTATCAAGAAAGCACAGTTTTTAAATAGATGTGTATTTTAAAGATAATAGTTGAGGTTGCTTTTTATGTTTTTACAGAGGATTGCTATTCAAATAGTAAATAAATTGAAAACAAAGTAGCTGGATATCATATTGa                                                                                    >  2:87802/1‑141 (MQ=255)
                                                          atatatTTATCAAGAAAGCACAGTTTTTAAATAGATGTGTATTTTAAAGATAATAGTTGAGGTTGCTTTTTATGTTTTTACAGAGAATTGCTATTCAAATAGTAAATAAATTGAAAACAAAGTAGCTGGATATCATATTGa                                                                                    >  2:72204/1‑141 (MQ=255)
                                                           tatatTTATCAAGAAAGCACAGTTTTTAAATAGATGTGTATTTTAAAGATAATAGTTGAGGTTGCTTTTTATGTTTTTACAGAGAATTGCTATTCAAATAGTAAATAAATTGAAAACAAAGTAGCTGGATATCATATTGAt                                                                                   >  1:39638/1‑141 (MQ=255)
                                                                                     tAAATAGATGTGTATTTTAAAGATAATAGTTGAGGTTGCTTTTTATGTTTTTACAGAGAATTGCTATTCAAATAGTAAATAAATTGAAAACAAAGTAGCTGGATATCATATTGATTTAGATAGGAATTTGTTGCTAAtttt                                                         >  2:228347/1‑141 (MQ=255)
                                                                                          aGATGTGTATTTTAAAGATAATAGTTGAGGTTGCTTTTTATGTTTTTACAGAGAATTGCTATTCAAATAGTAAATAAATTGAAAACAAAGTAGCTGGATATCATATTGATTTAGATAGGAATTTGTTGCTAATTTTATTTg                                                    <  1:43062/141‑1 (MQ=255)
                                                                                                         aGATAATAGTTGAGGTTGCTTTTTATGTTTTTACAGAGAATTGCTATTCAAATAGTAAATAAATTGAAAACAAAGTAGCTGGATATCATATTGATTTAGATAGGAATTTGTTGCTAATTTTATTTGTAAATCCAAGTTTGt                                     <  1:103770/141‑1 (MQ=255)
                                                                                                                  ttGAGGTTGCTTTTTATGTTTTTACAGAGAATTGCTATTCAAATAGTAAATAAATTGAAAACAAAGTAGCTGGATATCATATTGATTTAGATAGGAATTTGTTGCTAATTTTATTTGTAAATCCAAGTTTGTAGAATTCtt                            <  1:121334/141‑1 (MQ=255)
                                                                                                                  ttGAGGTTGCTTTTTATGTTTTTACAGAGAATTGCTATTCAAATAGTAAATAAATTGAAAACAAAGTAGCTGGATATCATATTGATTTAGATAGGAATTTGTTGCTAATTTTATTTGTAAATCCAAGTTTGTAGAATTCtt                            <  1:113347/141‑1 (MQ=255)
                                                                                                                   tGAGGTTGCTTTTTATGTTTTTACATAGAATTGCTATTCAAATAGTAAATAAATTGAAAACAAAGTAGCTGGATATCATATTGATTTAGATAGGAATTTGTTGCTAATTTTATTTGTAAATCCAAGTTTGTAGAATTCTTa                           <  2:250901/141‑1 (MQ=255)
                                                                                                                   tGAGGTTGCTTTTTATGTTTTTACATAGAATTGCTATTCAAATAGTAAATAAATTGAAAACAAAGTAGCTGGATATCATATTGATTTAGATAGGAATTTGTTGCTAATTTTATTTGTAAATCCAAGTTTGTAGAATTCTTa                           <  2:250991/141‑1 (MQ=255)
                                                                                                                   tGAGGTTGCTTTTTATGTTTTTACAGAGAATTGCTATTCAAATAGTAAATAAATTGAAAACAAAGTAGCTGGATATCATATTGATTTAGATAGGAATTTGTTGCTAATTTTATTTGTAAATCCAAGTTTGTAGAATTCTTa                           >  1:219903/1‑141 (MQ=255)
                                                                                                                   tGAGGTTGCTTTTTATGTTTTTACAGAGAATTGCTATTCAAATAGTAAATAAATTGAAAACAAAGTAGCTGGATATCATATTGATTTAGATAGGAAATTATTGATAAATTTATTTGAAAATCCGATTTAGTAGatcgcttt                           <  2:128953/141‑8 (MQ=255)
                                                                                                                    gAGGTTGCTTTTTATGTTTTTACAGAGAATTGCTATTCAAATAGTAAATAAATTGAAAACAAAGTAGCTGGATATCATATTGATTTAGATAGGAATTTGTTGCTAATTTTATTTGTAAATCCAAGTTTGTAGAATTCTTAt                          <  2:84452/141‑1 (MQ=255)
                                                                                                                    gAGGTTGCTTTTTATGTTTTTACAGAGAATTGCTATTCAAATAGTAAATAAATTGAAAACAAAGTAGCTGGATATCATATTGATTTAGATAGGAATTTGTTGCTAATTTTATTTGTAAATCCAAGTTTGTAGAATTCTTAt                          <  1:108647/141‑1 (MQ=255)
                                                                                                                          gCTTTTTATGTTTTTACAGAGAATTGATATTCAAATAGTAAATAAATTGACACCACAGTAGCTGGATATCACGTTGATTTAGATAGGAATTTGTTGCTAATTTTATTTGTAAATCCAAGTTTGTAGAATTCTTATTCAttt                    <  1:91109/141‑1 (MQ=255)
                                                                                                                                            gagaATTGCTATTCAAATAGTAAATAAATTGAAAACAAAGTAGCTGGATATCATATTGATTTAGATAGGAATTTGTTGCTAATTTTATTTGTAAATCCAAGTTTGTAGAATTCTTATTCATTTATAAAATAATATTCGTAt  <  1:80807/141‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                            
GAATGGATTAGTATATATTCCAACGAAAATAAATAAACTAATATGATGAGCAATCTCAATATATTTATCAAGAAAGCACAGTTTTTAAATAGATGTGTATTTTAAAGATAATAGTTGAGGTTGCTTTTTATGTTTTTACAGAGAATTGCTATTCAAATAGTAAATAAATTGAAAACAAAGTAGCTGGATATCATATTGATTTAGATAGGAATTTGTTGCTAATTTTATTTGTAAATCCAAGTTTGTAGAATTCTTATTCATTTATAAAATAATATTCGTAT  >  USA300TCH1516_ALE/949267‑949547

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: