Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 942,221 T→A 10.0% intergenic (‑192/+57) USA300HOU_0905 ← / ← mnhG2 hypothetical protein/CPA3 family monovalent cation:proton (H+) antiporter‑3 subunit G

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730942,2210TA10.0% 115.4 / 4.1 40intergenic (‑192/+57)USA300HOU_0905/mnhG2hypothetical protein/CPA3 family monovalent cation:proton (H+) antiporter‑3 subunit G
Reads supporting (aligned to +/- strand):  ref base T (13/23);  new base A (2/2);  total (15/25)
Fisher's exact test for biased strand distribution p-value = 6.22e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.70e-01

TTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAGAAAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATAATCTACAATTTTGTGTCTTTTAAGTCTTCCGAAATTTCATCGACTTTAGTCTTTTTAGTATAAGGCGTTTTAATATTATATGCTG  >  CP000730/942081‑942360
                                                                                                                                            |                                                                                                                                           
ttatCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAGAAAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAAttt                                                                                                                                             <  1:345500/141‑1 (MQ=255)
      taataaATAACGACATGAAAGGAAATTAAATTAAAGAAATATATGTAGATAGGGCGAATATAAAAAAAAAAAAAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAatc                                                                                                                                       <  2:220694/141‑1 (MQ=255)
            aTAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAGAAAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTa                                                                                                                                 <  1:215601/141‑1 (MQ=255)
             tAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAGAAAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAGATGATTCCAAATTAGGAATGATTTTAc                                                                                                                                <  2:131491/141‑1 (MQ=38)
               aCGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAGAAAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTActg                                                                                                                              <  1:204046/141‑1 (MQ=255)
               aCGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAGAAAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTActg                                                                                                                              <  1:106191/141‑1 (MQ=255)
                cGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAGAAAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTActgc                                                                                                                             <  1:37287/141‑1 (MQ=255)
                 gACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAGAAAAAATCATTGAAAAAGAGGTAAGAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTActgct                                                                                                                            <  2:447180/141‑1 (MQ=255)
                     tGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAGAAAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGTATCATCTTACTGCtgttt                                                                                                                        <  1:171914/141‑1 (MQ=255)
                     tGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAGAAAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCtgttt                                                                                                                        <  2:17175/141‑1 (MQ=255)
                       aaaGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAGAAAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCtgtttgt                                                                                                                      <  1:445091/141‑1 (MQ=255)
                                   aataaaGAGGTATATGTAGGGAGGGCGAATCTGTAGTCAAAGAAAAGAACATTGAAAAAGAATTAACAATTTCAAAAGAAAGCAGCAGTCAAATAATTCCTTATTTGGAATCAGCTTACTGCTGTTTGTTGTTGAATtata                                                                                                          <  2:215943/139‑1 (MQ=255)
                                      aaaGAGATATATGTAGATAGGGCGGATCTGTAGTCAAAGAAAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTc                                                                                                       >  1:362076/1‑141 (MQ=255)
                                        agagATATATGTAGATAGGGCGAATCTGTAGTCAAAGAAAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCAt                                                                                                     <  1:232366/141‑1 (MQ=255)
                                           gaTATATGTAGATAAGGACAATCAGTAGTCAAAGAAAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGAt                                                                                                  <  2:18749/141‑1 (MQ=255)
                                               tatGTAGATAGGGCGAATCTGTAGTCAAAGAAAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTg                                                                                              <  1:203940/141‑1 (MQ=255)
                                                aagTAGATAGGGCGAATCTGTAGTCAAAGAAAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGt                                                                                             <  1:216705/139‑1 (MQ=255)
                                                           ccgagaaaaaaacaaaaGAAAAAATCCTTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATAATCTa                                                                                  <  2:220269/127‑1 (MQ=255)
                                                                taaatAGTAAAAAAAAAAATCATAGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATAATCTACAAtt                                                                             <  2:65434/137‑1 (MQ=255)
                                                                 cTGTAGTCAAAGAAAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATAATCTACAAttt                                                                            <  2:242593/141‑1 (MQ=255)
                                                                   gTAGTCAAAGAAAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATAATCTACAATTTtg                                                                          >  1:392516/1‑141 (MQ=255)
                                                                    tAGTCAAAGAAAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATAATCTACAATTTtgt                                                                         <  1:410490/141‑1 (MQ=255)
                                                                     aGTCAAAGAAAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATAATCTACAATTTtgtg                                                                        >  1:322954/1‑141 (MQ=255)
                                                                      gTCAAAGAAAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATAATCTACAATTTTgtgt                                                                       >  1:452388/1‑141 (MQ=255)
                                                                      gTCAAAGAAAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATAATCTACAATTTTgtgt                                                                       >  1:312289/1‑141 (MQ=255)
                                                                           aGAAAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATAATCTACAATTTTGTGTCtttt                                                                  >  2:359037/1‑141 (MQ=255)
                                                                            gAAAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAGATGATTCCAAATTAGGAatgat                                                                                                                                     <  2:162191/73‑4 (MQ=18)
                                                                            gAAAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAGATGATTCCAAATTAGGAatgat                                                                                                                                     >  1:162191/1‑70 (MQ=18)
                                                                                   tCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATAATCTACAATTTTGTGTCTTTTAAGTCTTc                                                          <  2:21859/141‑1 (MQ=255)
                                                                                    aagtGAAAATGAGGTAAGTATTTCAAGAGAAATCAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTGTTTGATTTATATTCATGATTTTGTTATATAATCTACTATTTTGTGTCTTTTAAGTCTTcc                                                         <  2:108748/138‑1 (MQ=255)
                                                                                       tGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATAATCTACAATTTTGTGTCTTTTAAGTCTTCCGaa                                                      >  1:400330/1‑141 (MQ=255)
                                                                                             agagGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATAATCTACAATTTTGTGTCTTTTAAGTCTTCCGAAATTTCa                                                <  2:58002/141‑1 (MQ=255)
                                                                                                ggTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATAATCTACAATTTTGTGTCTTTTAAGTCTTCCGAAATTTCATCg                                             <  2:52020/141‑1 (MQ=255)
                                                                                                 gTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGCATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATAATCTACAATTTTGTGTCTTTTAAGTCTTCCGAAATTTCATCGa                                            >  1:374343/1‑141 (MQ=255)
                                                                                                      aaTGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATAATCTACAATTTTGTGTCTTTTAAGTCTTACGAAATTTCATCGACTTTa                                       >  2:53259/1‑141 (MQ=255)
                                                                                                       aTGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATAATCTACAATTTTGTGTCTTTTAAGTCTTCCGAAATTTCATCGACTTTAg                                      >  2:340207/1‑141 (MQ=255)
                                                                                                            aaaaGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATAATCTACAATTTTGTGTCTTTTAAGTCTTCCGAAATTTCATCGACTTTAGTCttt                                 >  2:108889/1‑141 (MQ=255)
                                                                                                                 aaaaCAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATCACTGATTTAGTTATATAATCTACACCTTTGTGCCTTTTAAGTCTTCCGAAATTTCATAGCCTTTAGTCTTTTTAGt                            >  1:223167/1‑141 (MQ=255)
                                                                                                                      agcagTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATATTCTACAATTTTGTGTCTTTTAAGTCTTCCGAAATTTCATCGACTTTAGTCTTTTTAGTATAAg                       >  2:109974/1‑141 (MQ=255)
                                                                                                                        cagTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATAATCTACAATTTTGTGTCTTTTAAGTCTTCCGACATTTCATCGACTTTAGTCTTTTTAGTATAAGGc                     <  2:273109/141‑1 (MQ=255)
                                                                                                                             agatgaTTCCAAATTAGGAATGATTTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATAATCTACAATTTTGTGTCTTTTAAGTCTTCCGAAATTTCATCGACTTTAGTCTTTTTAGTATAAGGCGtttt                >  2:266396/6‑141 (MQ=38)
                                                                                                                                           ttGGAATCATCTTACTGCTGTTTGTTGTTGATTTATCTTCATGATTTTGTTATATAATCTACAATTTTGTGTCTTTTAAGTCTTCCGAAATTTCATCGACTTTAGTCTTTTTAGTATAAGGAGTTTTAATATTATAtgctg  >  2:320415/1‑141 (MQ=255)
                                                                                                                                            |                                                                                                                                           
TTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAGAAAAAATCATTGAAAAAGAGGTAACAATGTCAAAAGAAAACAGCAGTAAAATCATTCCTAATTTGGAATCATCTTACTGCTGTTTGTTGTTGATTTATATTCATGATTTTGTTATATAATCTACAATTTTGTGTCTTTTAAGTCTTCCGAAATTTCATCGACTTTAGTCTTTTTAGTATAAGGCGTTTTAATATTATATGCTG  >  CP000730/942081‑942360

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: ‑