Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 1,613,762 T→C intergenic (‑31/‑37) scpA ← / → USA300HOU_RS08000 Segregation and condensation protein A/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,613,7620TC97.1% 117.4 / NA 34intergenic (‑31/‑37)scpA/USA300HOU_RS08000Segregation and condensation protein A/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base C (19/14);  total (20/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCAAATTTTTGGATAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCATGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACATTTTAGAAGATGCATGGAAAGCTGAAAAT  >  USA300TCH1516_ALE/1613637‑1613897
                                                                                                                             |                                                                                                                                       
tCAAATTTTTGGATAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAAtt                                                                                                                   >  3:49225/1‑148 (MQ=255)
tCAAATTTTTGGATAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAAtt                                                                                                                   >  3:283981/1‑148 (MQ=255)
  aaaTTTTTGGATAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTgg                                                                                                                 >  3:292643/1‑148 (MQ=255)
   aaTTTTTGGATAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTa                                                                                                                       >  2:28902/1‑141 (MQ=255)
           gATAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAAc                                                                                                        <  3:238875/148‑1 (MQ=255)
             tAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCATGAAAATAACTTACTTTTAAATTGGGGTGATAACaa                                                                                                      >  4:363535/1‑148 (MQ=255)
             tAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACaa                                                                                                      >  4:251894/1‑148 (MQ=255)
             tAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACaa                                                                                                      >  4:114724/1‑148 (MQ=255)
             tAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACaa                                                                                                      >  3:355315/1‑148 (MQ=255)
               aGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACaaaa                                                                                                    <  3:121959/148‑1 (MQ=255)
                  tGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGc                                                                                                 >  4:47320/1‑148 (MQ=255)
                  tGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGc                                                                                                 >  4:308667/1‑148 (MQ=255)
                        aaTAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAgg                                                                                           >  3:118909/1‑148 (MQ=255)
                               cTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGAt                                                                                    >  4:81600/1‑148 (MQ=255)
                                   tGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAAt                                                                                >  3:45385/1‑148 (MQ=255)
                                      tCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTc                                                                             <  3:139678/148‑1 (MQ=255)
                                       ccATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCt                                                                            <  3:309300/148‑1 (MQ=255)
                                         aTTGAGAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCtat                                                                          <  4:269435/148‑1 (MQ=255)
                                         aTTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCtat                                                                          <  3:304388/148‑1 (MQ=255)
                                         aTTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCtat                                                                          <  4:61846/148‑1 (MQ=255)
                                         aTTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCtat                                                                          <  4:264284/148‑1 (MQ=255)
                                          ttGAAAGCATTTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAAt                                                                                <  2:16456/141‑1 (MQ=255)
                                             aaaGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTAAAGCACGAAAATAACTTACTTTTAAAATAAAAAAAAAAAAAAATGCAACAGGCACTGATAAATTTCtattata                                                                      <  4:347368/148‑2 (MQ=255)
                                                gCATCTAATTTAACTTCATACCTAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCtat                                                                          <  1:12458/141‑1 (MQ=255)
                                                             cTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCa                                                      >  4:213215/1‑148 (MQ=255)
                                                                               ccTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCa                                    <  4:52880/148‑1 (MQ=255)
                                                                                 tCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATg                                  >  3:203514/1‑148 (MQ=255)
                                                                                        gCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATg                                  <  1:28902/141‑1 (MQ=255)
                                                                                          gTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACATTTTag                         >  4:33494/1‑148 (MQ=255)
                                                                                             atatGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACATTTTagaag                      >  3:287180/1‑148 (MQ=255)
                                                                                                           ctctAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACATTTTAGAAGATGCATGGAAAGCt        >  3:219658/1‑148 (MQ=255)
                                                                                                           ctctAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACATTTTAGAAGATGCATGGAAAGCt        >  3:234427/1‑148 (MQ=255)
                                                                                                             ctAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACATTTTAGAAGATGCATGGa             >  1:18725/1‑141 (MQ=255)
                                                                                                                 aaTATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACATTTTAGAAGATGCATGGAAAGCTGAAAAt  <  3:378681/148‑1 (MQ=255)
                                                                                                                             |                                                                                                                                       
TCAAATTTTTGGATAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCATGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACATTTTAGAAGATGCATGGAAAGCTGAAAAT  >  USA300TCH1516_ALE/1613637‑1613897

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑