Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,981,418 C→A 77.9% intergenic (‑17/+339) USA300HOU_RS09870 ← / ← liaR hypothetical protein/Transcriptional regulatory protein LiaR

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,981,4180CA77.9% 44.6 / 11.5 32intergenic (‑17/+339)USA300HOU_RS09870/liaRhypothetical protein/Transcriptional regulatory protein LiaR
Reads supporting (aligned to +/- strand):  ref base C (4/3);  new base A (12/13);  total (16/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.33e-01

TACTAAAGTCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTCTGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACATTTGTATTAAATTTTGATCAAG  >  USA300TCH1516_ALE/1981282‑1981549
                                                                                                                                        |                                                                                                                                   
tACTAAAGTCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGtt                                                                                                                                 <  2:137329/141‑1 (MQ=255)
  ttAAAGTCTTTTTAGAAAGTCCAATTGTTTGCGCCATATTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTCTGTTTg                                                                                                                               <  2:218543/140‑1 (MQ=255)
      aGTCTTTTTATAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGa                                                                                                                           <  1:21969/141‑1 (MQ=255)
              tAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATc                                                                                                                   <  1:7240/141‑1 (MQ=255)
                  aaGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGa                                                                                                               <  2:52363/141‑1 (MQ=255)
                   aGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGCTCAAGTATTTGTATCCGGac                                                                                                              >  2:136877/1‑141 (MQ=255)
                              ttGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGCTTTCTATATATAAACTATTGTTTATCCTTTCTGTTATCTAACTTTATGTTTGTAGAATTTTATCCTGCCACAAAAAttta                                                                                                   >  2:237316/1‑140 (MQ=255)
                                      tAGTATCGTGCGTATAACCAGTCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAataata                                                                                           <  2:4612/141‑1 (MQ=255)
                                         tATCTTGCTTATAACTAGCCTTTATACGATCTATTTTAAATTTGGTTTGAATTAAATCTGTAAAGCTCGTTCGTTCTTTTCTGTTATCTACCTTTCTGTTTGGGGAATTTTATCCAGACACAAGAAATTGCAATAATacac                                                                                        <  2:237856/141‑1 (MQ=255)
                                            cTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTATAAAACTCTGTCTATCCATTCTGTTATCTACCTCTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACAtt                                                                                     >  2:225290/1‑141 (MQ=255)
                                               gcttataACCAGCCGCTATACTAAACCTTTTAAATTTTGTTTGAATTAAATCTGTAAAACGCTGTCTATCCATTCTGTTATCTACCTTTATGTGCGGGGAATTTTAACCGGACACAAGAAATTGCAATAATACACATTTCt                                                                                  <  2:131873/138‑1 (MQ=255)
                                                 gTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTg                                                                                >  1:134174/1‑141 (MQ=255)
                                                            ctctATACGAACCATTTTAAATTTTGTTTGAATTAACTCTGTACAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGCtt                                                                     >  2:1419/1‑141 (MQ=255)
                                                                    aaaCCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTa                                                             <  2:40239/140‑1 (MQ=255)
                                                                         aTTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTCTGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTTAAACACAGATTACATCTTAatata                                                        >  2:369013/1‑141 (MQ=255)
                                                                           tttAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTCTGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATAtt                                                      >  2:185130/1‑141 (MQ=255)
                                                                             tAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATAtttt                                                    <  1:51311/141‑1 (MQ=255)
                                                                                          aaTTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGaaa                                       >  1:354526/1‑141 (MQ=255)
                                                                                               aaTCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTCTGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGt                                  >  1:257244/1‑141 (MQ=255)
                                                                                               aaTCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGt                                  >  2:109621/1‑141 (MQ=255)
                                                                                                 tCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCa                                <  1:353324/141‑1 (MQ=255)
                                                                                                   tGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAAt                              >  1:111063/1‑141 (MQ=255)
                                                                                                   tGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATGGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAAt                              <  2:194816/141‑1 (MQ=255)
                                                                                                    gTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAAGACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAAtt                             <  2:201705/141‑1 (MQ=255)
                                                                                                        aaCTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTcac                         >  2:205137/1‑141 (MQ=255)
                                                                                                          ctctGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACAt                       >  2:170346/1‑141 (MQ=255)
                                                                                                            ctGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACAttt                     >  1:205090/1‑141 (MQ=255)
                                                                                                                         cTGTTATCTACCTTTATGTTTGGGGAATTTTATCCAGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACATTTGTATTAAATTTTg        <  2:350958/141‑1 (MQ=255)
                                                                                                                           gTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACATTTGTATTAAATTTTGAt      >  2:249895/1‑141 (MQ=255)
                                                                                                                               tCTACCTTTCTGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACATTTGTATTAAATTTTGATCAAg  <  1:41530/141‑1 (MQ=255)
                                                                                                                               tCTACCTTTCTGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACATTTGTATTAAATTTTGATCAAg  >  2:232355/1‑141 (MQ=255)
                                                                                                                               tCTAACTTTATGTTTGTGGAATTTTATCCCGACACAAAAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCAAATTTGTATTAAATTTTGATAAAg  <  2:203753/141‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                   
TACTAAAGTCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTCTGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACATTTGTATTAAATTTTGATCAAG  >  USA300TCH1516_ALE/1981282‑1981549

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: ‑