Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 110,660 T→A 19.4% I173I (ATT→ATA USA300HOU_0109 → staphylococcal tandem lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730110,6600TA19.4% 59.6 / 10.3 31I173I (ATT→ATAUSA300HOU_0109staphylococcal tandem lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (10/15);  new base A (2/4);  total (12/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.81e-01

ATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGG  >  CP000730/110529‑110794
                                                                                                                                   |                                                                                                                                      
aaggTCGGTAATAAAATCAATCAAAAAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATaa                                                                                                                                <  2:311468/138‑1 (MQ=17)
               aTCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAg                                                                                                                 <  2:68663/140‑1 (MQ=255)
                              gataTTAAAGATGAAAAAATAAAAAAAGAAATTGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAata                                                                                                  <  2:50294/137‑1 (MQ=255)
                                aaTTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTGTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCTTATAATCAAAAGGTACGTAGTTATTATGCTGAAGATc                                                                                                >  2:33019/1‑140 (MQ=17)
                                aaTTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATc                                                                                                >  1:61781/1‑140 (MQ=255)
                                 aTTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAAAATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCAAGAGTTGCCAAGTTATTAGGCTAAATATCa                                                                                               >  1:125100/1‑140 (MQ=17)
                                                        aGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATg                                                                        <  2:5511/140‑1 (MQ=255)
                                                           aaTCGAATACGTAAAATTCTTTGTTCAATATAGCGAATTTAAAAATTTGAAAAATTATAAAGACGGAGACATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTaa                                                                     <  1:33019/140‑1 (MQ=17)
                                                            aTCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTaaa                                                                    >  2:314129/1‑140 (MQ=255)
                                                                 aaaCTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                               <  1:307677/140‑1 (MQ=255)
                                                                 aaaCTTAAGCTTCTTTGGTTAATATTGTGTCTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCTGAGGTGCCGAGTGATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                               <  1:206704/140‑1 (MQ=17)
                                                                     tttAAGTTCTTTGTTCAATATGGCGCCTTTAAAAATTTGAAAAATTATAAAGACGGAGACATTTTATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACg                                                           <  2:346678/140‑1 (MQ=255)
                                                                                 gTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgatatga                                               <  1:303657/140‑1 (MQ=255)
                                                                                  ttCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgatatgat                                              >  2:273341/1‑140 (MQ=255)
                                                                                      atatGGCGACTTTAAAAATTTGCAACATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAc                                          >  2:176380/1‑140 (MQ=255)
                                                                                           gCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTGTAATGTAAAACAATTACTCAAAAGATATGATATACcgacg                                     >  2:219723/1‑140 (MQ=255)
                                                                                                 ttAAAGATTTAATGAATTAAAAAGATGGAAAAAAATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTaaa                               <  1:330760/140‑1 (MQ=11)
                                                                                                  tAAAGATTTAATGAATTATAAAGATGGAGATATAGCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAg                              <  2:167995/140‑1 (MQ=11)
                                                                                                   aaaaaTTTGAAAAATAATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATCATATACCGACGAGTAAAGc                             >  1:263818/1‑140 (MQ=255)
                                                                                                   aaaaaTTTGAAAAATAATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATAATATACCGACGAGTAAAGc                             >  1:263817/1‑140 (MQ=255)
                                                                                                        tttaatgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCaa                        <  2:256725/133‑1 (MQ=255)
                                                                                                             aaaaTTATAAAGACGGATATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTa                   <  2:323380/140‑1 (MQ=255)
                                                                                                               aaTTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTCACTAATGATGATTATAATGTAAAACAATTACGCAAATGATATGATATACCGACGAGTAAAGCTCCAAAGTTAtt                 <  2:265793/140‑1 (MQ=255)
                                                                                                                  tataAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGtt              <  2:318950/140‑1 (MQ=255)
                                                                                                                    taAAGACGAAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTaa            <  2:149034/140‑1 (MQ=255)
                                                                                                                     aaaGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTaaa           <  2:343423/140‑1 (MQ=255)
                                                                                                                       aGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAg         >  2:66921/1‑140 (MQ=255)
                                                                                                                         aCGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGt       <  2:170300/140‑1 (MQ=255)
                                                                                                                          tggAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAATATATGATATACCGACGAGTAAAGCTACGAAGTTATTGTTAAAAGGtt      >  2:300632/2‑140 (MQ=17)
                                                                                                                          aggacttcttttATATAATCCATTGGTGCCGAGTTATTCGGCTACATATCAACTATCTAATGATGATTAAAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTACAGCTCCAACGTTATTGTTAAAAGGtt      <  2:125100/132‑1 (MQ=18)
                                                                                                                             agaTATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAg   >  1:331753/1‑140 (MQ=255)
                                                                                                                              gaTATTTCATATAATCCAGAGGTTCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAgg  <  1:164033/140‑1 (MQ=255)
                                                                                                                                   |                                                                                                                                      
ATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGG  >  CP000730/110529‑110794

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: