Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,530,791 C→T 9.8% intergenic (‑42/+123) USA300HOU_2388 ← / ← USA300HOU_2389 hypothetical protein/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,530,7910CT 9.8% 105.8 / 3.9 41intergenic (‑42/+123)USA300HOU_2388/USA300HOU_2389hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (22/15);  new base T (2/2);  total (24/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.59e-01

AGTAGATGTTACAGTTACCATAACACTATCATCATTTACTTTTGTCATAAGTGCCTTTAAATTCTGTCGAGCGTATGAATAATTTTTAATAATCATATTTATCGCCTCCTTTTAACACACCTCAATTGTACAAATATCTGTACAATAAAACAAGCGACACAGAAAAAAACTACTAATCAAGATTTCGCACGGGGAAGAATCAATACCTATCCTGTACTGATTCCCTACTAAACAATGTTTACATGATAATTTCCACCTATTTAGACTTCATACATTAA  >  CP000730/2530654‑2530931
                                                                                                                                         |                                                                                                                                            
aGTAGATGTTACAGTTACCATAACACTATCATCATTTACTTTTGTCATAAGTGCCTTTAAATTCTGTCGAGCGTATGAATAATTTTTAATAATCATATTTATCGCCTCCTTTTAACACACCTCAATTGTACAGATATTTGt                                                                                                                                           <  1:370769/141‑1 (MQ=255)
 gTAGATGTTACAGTTACCATAACACTATCATCATTTACTTTTGTCATAAGTGCCTTTAAATTCTGTCGAGCGTATGAATAATTTTTAATAATCATATTTATCGCCTCCTTTTAACACACCTCAATTGTACAGATATTTGTa                                                                                                                                          <  2:372617/141‑1 (MQ=255)
    gATGTTACAGTTACCATAACACTATCATCATTTACTTTTGTCATAAGTGCCTTTAAATTCTGTCGAGCGTATGAATAATTTTTAATAATCATATTTATCGCCTCCTTTTAACACACCTCAATTGTACAAATATCTGTACaa                                                                                                                                       <  2:265027/141‑1 (MQ=255)
     aTGTTACAGTTACCATAACACTATCATCATTTACTTTTGTCATAAGTGCCTTTAAATTCTGTCGAGCGTATGAATAATTTTTAATAATCATATTTATCGCCTCCTTTTAACACACCTCAATTGTACAAATATCTGTACAAt                                                                                                                                      >  1:23006/1‑141 (MQ=255)
       gTTACAGTTACCATAACACTATCATCATTTACTTTTGTCATAAGTGCCTTTAAATTCTGTCGAGCGTATGAATAATTTTTAATAATCATATTTATCGCCTCCTTTTAACACACCTCAATTGTACAAATATCTGTACAATaa                                                                                                                                    >  2:406656/1‑141 (MQ=255)
          aCAGTTACCATAACACTATCATCATTTACTTTTGTCATAAGTGCCTTTAAATTCTGTCGAGCGTATGAATAATTTTTAATAATCATATTTATCGCCTCCTTTTAACACACCTCAATTGTACAAATATCTGTACAATAAAAc                                                                                                                                 >  2:480729/1‑141 (MQ=255)
                   aTAACACTATCATCATTTACTTTTGTCATAAGTGCCTTTAAATTCTGTCGAGCGTATGAATAATTTTTAATAATCATATTTATCGCCTCCTTTTAACACACCTCAATTGTACAAATATCTGTACAATAAAACAAGCGacac                                                                                                                        <  2:690143/141‑1 (MQ=255)
                      acacTATCATCATTTACTTTTGTCATAAGTGCCTTTAAATTCTGTCGAGCGTATGAATAATTTTTAATAATCATATTTATCGCCTCCTTTTAACACACCTCAATTGTACAAATATCTGTACAATAAAACAAGCGACACAGa                                                                                                                     >  1:664837/1‑141 (MQ=255)
                      acacTATCATCATTTACTTTTGTCATAAGTGCCTTTAAATTCTGTCGAGCGTATGAATAATTTTTAATAATCATATTTATCGCCTCCTTTTAACACACCTCAATTGTACAAATATCTGTACAATAAAACAAGCGACACAGa                                                                                                                     <  1:186160/141‑1 (MQ=255)
                            tcatcaTTTACTTGTGTCATAAGTGCCTTTAAACTCTGTCGAGCGTATGAATAATCTTTAATAATCATATTTATCGCCTCCTTTTAACACACCTCAATTGTACAAATATCTGTACAATAAAACAAGCGACACAGaaaaaaa                                                                                                               >  2:328916/1‑141 (MQ=255)
                                catTTACTTTTGTCATAAGTGCCTTTAAATTCTGTCGAGCGTATGAATAATTTTTAATAATCATATTTATCGCCTCCTTTTAACACACCTCAATTGTACAAATATCTGTACAATAAAACAAGCGACACAGAAAAAAactac                                                                                                           <  2:196739/141‑1 (MQ=255)
                                          tGTCATAAGTGCCTTTAAATTCTGTCGAGCGTATGAATAATTTTTAATAATCATATTTATCGCCTCCTTTTAACACACCACAATTGAACAAATATCTGTACAATAAAACAAACGACACAGAAAAAAACTACTAATCAAGAt                                                                                                 <  2:66543/141‑1 (MQ=255)
                                                aaGTGCCTTTAAATTCTGTCGAGCGTATGAATAATTTTTAATAATCATATTTATCGCCTCCTTTTAACACACCTCAATTGTACAAATATCTGTACAATAAAACAAGCGACACAGAAAAAAACTACTAATCAAGATTTCGCa                                                                                           >  2:42911/1‑141 (MQ=255)
                                                    gCCTTTAAATTCTGTCGAGCGTATGAATAATTTTTAATAATCATATTTATCGCCTCCTTTTAACACACCTCAATTGTACAAATATCTGTACAATAACACAAGCAACACAGAAAAAAACTACTAATCAAGATTTCGCACggg                                                                                       <  2:622033/141‑1 (MQ=255)
                                                      ctgtAAATTCTGTCGACCGAACGAATACTTTTTAATACGCAAATTTATCGCGTCCTTTTAACACACCTCAATTGTACAAATATCTGTACAATAAAACAAGCGACACAGAATAACACTACTAACCAAGATTTCGCACGAGga                                                                                     >  2:612254/4‑141 (MQ=255)
                                                      cTTTAAATTCTGTCGAGCGTATGAATAATTTTTAATAATCATATTTATCGCCTCCTTTTAACACACCTCAATTGTACAAATATCTGTACAATAATACAAGCGACACAGAAAAAAACTACTAATCAAGATTTCGCACGGGga                                                                                     <  2:505049/141‑1 (MQ=255)
                                                         tgaagccTGCCGAGCGTAGGAATACTGCTTAATTTTCATGTCTATCGCCTCCTTGTAACAGCCCTCAATTGTACAAATATCTGTAAAATACAACAGGCGAGACAGAATAACACTACTGATCAACAGTTCGCCCTGGgcaga                                                                                  >  2:114446/7‑141 (MQ=255)
                                                         tAAATTCTGTCGAGCGTATGAATAATTTTTTTTTTTTTTATTTATCGCCTCCTGTTAACACACCTAAATTGTACAAATATCTGTACAATAAAACAAGCGACACAGAAAAAAACTACTAATCAAGATTTCGCATGGGgaaga                                                                                  >  2:613774/1‑141 (MQ=255)
                                                               cTGTCGAGCGTATGAATAATTTTTAATAATCATATTTATCGCCTCCTTTTAACACACCTCAATTGTACAAATATCTGTACAATAAAACAAGCGACACAGAAAAAAACTACTAATCAAGATTTCGCACGGGGAAGAATCAAt                                                                            >  1:350308/1‑141 (MQ=255)
                                                                tGTCGAGCGTATGAATAATTTTTAATAATCATATTTATCGCCTCCTTTTAACACACCTCAATTGTACAAATATCTGTACAATAAAACAAGCGACACAGAAAAAAACTACTAATCAAGATTTCGCACGGGGAAGAATCAATa                                                                           <  1:223862/141‑1 (MQ=255)
                                                                 gTCGAGCGTATGAATAATTTTTAATAATCATATTTATCGCCTCCTTTTAACACACCTCAATTGTACAAATATCTGTACAATAAAACAAGCGACACAGAAAAAAACTACTAATCAAGATTTCGCACGGGGAAGAATCAATAc                                                                          >  2:116515/1‑141 (MQ=255)
                                                                 gTCGAGCGTATGAATAATTTTTAATAATCATATTTATCGCCTCCTTTTAACACACCTCAATTGTACAAATATCTGTACAATAAAACAAGCGACACAGAAAAAAACTACTAATCAAGATTTCGCACGGGGAAGAATCAATAc                                                                          >  1:347901/1‑141 (MQ=255)
                                                                                   ttttAATAATCATATTTATCGCCTCCTTTTAACACACCTCAATTGTACAAATATCTGTACAATAAAACAAGCGACACAGAAAAAAACTACTAATCAAGATTTCGCACGGGGAAGAATCAATACCTATCCTGTACTGATTcc                                                        >  2:381729/1‑141 (MQ=255)
                                                                                             cATATTTATCGCCTCCTTTTAACACACCTCAATTGTACAAATATCTGTACAATAAAACAAGCGACACAGAAAAAAACTACTAATCAAGATTTCGCACGGGGAAGAATCAATACCTATCCTGTACTGATTCCCTACTAAACa                                              >  2:475124/1‑141 (MQ=255)
                                                                                                          tcctTTTAACACACCTCAATTGTACAAATATCTGTACAATAAAACAAGCGACACAGAAAAAAACTACTAATCAAGATTTCGCACGGGGAAGAATCAATACCTATCCTGTACTGATTCCCTACTAAACAATGTTTACATGAt                                 <  2:246421/141‑1 (MQ=255)
                                                                                                            ctTTTAACACACCTCAATTGTACAAATATCTGTACAATAAAACAAGCGACACAGAAAAAAACTACTAATCAAGATTTCGCACGGGGAAGAATCAATACCTATCCTGTACTGATTCCCTACTAAACAATGTTTACATGATaa                               <  1:562344/141‑1 (MQ=255)
                                                                                                               ttAACACACCTCAATTGTACAAATATCTGTACAATAAAACAAGCGACACAGAAAAAAACTACTAATCAAGATTTCGCACGGGGAAGAATCAATACCTATCCTGTACTGATTCCCTACTAAACAATGTTTACATGATAAttt                            <  1:411922/141‑1 (MQ=255)
                                                                                                                tAACACACCTCAATTGTACAAATATCTGTACAATAAAACAAGCGACACAGAAAAAAACTACTAATCAAGATTTCGCACGGGGAAGAATCAATACCTATCCTGTACTGATTCCCTACTAAACAATGTTTACATGATAATTTc                           <  1:651004/141‑1 (MQ=255)
                                                                                                                 aaCACACCTCAATTGTACAAATATCTGTACAATAAAACAAGCGACACAGAAAAAAACTACTAATCAAGATTTCGCACGGGGAAGAATCACTAAATATCATGTTCTGGGGCCGTACTTGACAGTGTTTACATGAGAATTTcc                          >  1:670759/1‑141 (MQ=255)
                                                                                                                 aaCACACCTCAATTGTACAAATATCTGTACAATAAAACAAGCGACACAGAAAAAAACTACTAATCAAGATTTCGCACGGGGAAGAATCAATACCTATCCTGTACTGATTCCCTACTAAACAATGTTTACATGATAATTTcc                          >  1:167778/1‑141 (MQ=255)
                                                                                                                 aaCACACCTCAATTGTACAAATATCTGTACAATAAAACAAGCGACACAGAAAAAAACTACTAATCAAGATTTCGCACGGGGAAGAATCAATACCTATCCTGTACTGATTCCCTACTAAACAATGTTTACATGATAATTTcc                          >  1:665334/1‑141 (MQ=255)
                                                                                                                     cacCTCAATTGTACAAATATCTGTACAATAAAACAAGCGACACAGAAAAAAACTACTAATCAAGATTTCGCACGGGGAAGAATCAATACCTATCCTGTACTGATTCCCTACTAAACAATGTTTACATGATAATTTCCACCt                      >  1:109723/1‑141 (MQ=255)
                                                                                                                     cacCTCAATTGTACAAATATCTGTACAATAAAACAAGCGACACAGAAAAAAACTACTAATCAAGATTTCGCACGGGGAAGAATCAATACCTATCCTGTACTGATTCCCTACTAAACAATGTTTACATGATAATTTCCACCt                      >  2:182585/1‑141 (MQ=255)
                                                                                                                      acCTCAATTGTACAAATATCTGTACAATAAAACAAGCGACACAGAAAAAAACTACTAATCAAGATTTCGCACGGGGAAGAATCAATACCTATCCTGTa                                                                <  2:413689/98‑1 (MQ=255)
                                                                                                                      acCTCAATTGTACAAATATCTGTACAATAAAACAAGCGACACAGAAAAAAACTACTAATCAAGATTTCGCACGGGGAAGAATCAATACCTATCCTGTa                                                                >  1:413689/1‑98 (MQ=255)
                                                                                                                      acCTCAATTGTACAAATATCTGTACAATAAAACAAGCGACACAGAAAAAAACTACTAATCAAGATTTCGCACGGGGAAGAATCAATACCTATCCTGTACTGATTCCCTACTAAACAATGTTTACATGATAATTTCCACCTa                     >  1:280211/1‑141 (MQ=255)
                                                                                                                           aaTTGTACAAATATCTGTACAATAAAACAAGCGACACAGAAAAAAACTACTAATCAAGATTTCGCACGGGGAAGAATCAATACCTATCCTGTACTGATTCCCTACTAAACAATGTTTACATGATAATTTCCACCTATTTAg                <  1:26621/141‑1 (MQ=255)
                                                                                                                             ttGTACAGATATTTGTACAATAAAACAAGCGACACAGAAAAAAACTACTAATCAAGATTTCGCACGGGGAAGAATCAATACCTATCCTGTACTGATTCCCTACTAAACAATGTTTACATGATAATTTCCACCTATTTAGAc              >  2:458433/1‑141 (MQ=255)
                                                                                                                             ttGTACAAATATCTGTACAATAAAACAAGCGACACAGAAAAAAACTACTAATCAAGATTTCGCACGGGGAAGAATCAATACCTATCCTGTACTGATTCCCTACTAAACAATGTTTACATGATAATTTCCACCTATTTAGAc              >  2:488280/1‑141 (MQ=255)
                                                                                                                                     atatTTGTACAATAAAACAAGCGACACAGAAAAAAACTACTAATCAAGATTTCGCACGGGGAAGAATCAATACCTATCCTGTACTGATTCCCTACTAAACAATGTTTACATGATAATTTCCACATATTTAGACTTCATACa      >  1:464070/1‑141 (MQ=255)
                                                                                                                                        tCTGTACAATAAAACAAGCGACACAGAAAAAAACTACTAATCAAGATTTCGCACGGGGAAGAATCAATACCTATCCTGTACTGATTCCCTACTAAACAATGTTTACATGATAATTTCCACCTATTTAGACTTCATACATTa   <  1:255102/141‑1 (MQ=255)
                                                                                                                                         cTGTACAATAAAACAAGCGACACAGAAAAAAACTACTAATCAAGATTTCGCACGGGGAAGAATCAATACCTATCCTGTACTGATTCCCTACTAAACAATGTTTACATGATAATTTCCACCTATTTAGACTTCATACATTaa  >  2:616533/1‑141 (MQ=255)
                                                                                                                                         |                                                                                                                                            
AGTAGATGTTACAGTTACCATAACACTATCATCATTTACTTTTGTCATAAGTGCCTTTAAATTCTGTCGAGCGTATGAATAATTTTTAATAATCATATTTATCGCCTCCTTTTAACACACCTCAATTGTACAAATATCTGTACAATAAAACAAGCGACACAGAAAAAAACTACTAATCAAGATTTCGCACGGGGAAGAATCAATACCTATCCTGTACTGATTCCCTACTAAACAATGTTTACATGATAATTTCCACCTATTTAGACTTCATACATTAA  >  CP000730/2530654‑2530931

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: ‑