Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 110,660 T→A 19.0% I173I (ATT→ATA USA300HOU_0109 → staphylococcal tandem lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730110,6600TA19.0% 98.7 / 15.6 46I173I (ATT→ATAUSA300HOU_0109staphylococcal tandem lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (20/17);  new base A (5/4);  total (25/21)
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

GTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGG  >  CP000730/110532‑110794
                                                                                                                                |                                                                                                                                      
gTCGCTAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTATTCAATATGGCGACTTTAAAAATTCGAAAAATTATAAAGACGGAGATATATAATAAAATCCa                                                                                                                            >  2:370290/1‑141 (MQ=17)
             tCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGtt                                                                                                               >  1:22875/1‑141 (MQ=255)
               aTTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCAGAGTTAt                                                                                                             >  1:19202/1‑141 (MQ=255)
                     acaaAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCAAGAGGTGCCGAGTTATTCggat                                                                                                       >  2:64351/1‑139 (MQ=255)
                          aaaaaTTGAAAACGAAAAAATAAAAAACGAAGTCTAAATCTTTAAGTTCTTTTGTCAATATGGCGACGTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGATGCGCCTAGCTATTCGGCTAAata                                                                                                  <  2:262370/139‑1 (MQ=17)
                          aGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAata                                                                                                  <  2:19446/141‑1 (MQ=255)
                          aGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAata                                                                                                  <  1:380076/141‑1 (MQ=255)
                                  aaGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGATTTATTCGGCTAAATATCAATTaa                                                                                          >  2:301382/1‑141 (MQ=255)
                                  aaGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAAGTACCGAGTTATTCGGCTAAATATCAATTaa                                                                                          >  2:84638/1‑141 (MQ=255)
                                          aaaaTAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatgat                                                                                  <  2:22875/141‑1 (MQ=255)
                                            aaTAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAAtgatga                                                                                >  1:92207/1‑141 (MQ=255)
                                                       aaaTCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGTAGATATTTCATATTATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTaa                                                                     <  2:41654/141‑1 (MQ=255)
                                                       aaaTCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGCTGATTATAATGTaa                                                                     <  1:249995/141‑1 (MQ=255)
                                                         agcGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTaaaa                                                                   <  2:234301/139‑1 (MQ=255)
                                                           cGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACa                                                                 <  1:100120/141‑1 (MQ=255)
                                                                         tCTTGGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGATATTTTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgat                                                   <  1:336089/141‑1 (MQ=255)
                                                                              gTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgatatgat                                              >  2:41311/1‑141 (MQ=255)
                                                                              gTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgatatgaa                                              >  2:253894/1‑140 (MQ=255)
                                                                              gTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCAAGAGGTGCCGAGTTATTCGGCTAAATATAAATTTACTAATGATGATTATAATGTAAAACAATTACGCAAAGgatatgat                                              >  2:103011/1‑141 (MQ=255)
                                                                                        gCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACcgacga                                    >  1:96324/1‑141 (MQ=255)
                                                                                        gCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATAAGATATACcgacga                                    >  1:237991/1‑141 (MQ=255)
                                                                                          gACTTTAAAAATTGTAAGAATTATAAAGACGGATATATTTCATATAATCCAGAGGTGGCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGGAAAACAATTACGCAAAAGATATGATATAACGAGGAGt                                  >  2:99031/1‑141 (MQ=17)
                                                                                            cTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCACAGCAGAGGATATACCGACGAGTaa                                <  2:369273/141‑1 (MQ=18)
                                                                                            cTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTaa                                <  1:210929/141‑1 (MQ=255)
                                                                                             tttAAAAATTTGAACAATTATAAAGACGGAGATATTTCATATAATCCATAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATTTAAAACAATTACGCAAAAGATATGATATAACGACGAggaca                               >  1:168143/1‑137 (MQ=17)
                                                                                              ttAAAAAATTGAAAAATTTGAATGTCGGGGATATTTTAGATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATTATTATAATGTAAAACAATTACGCAAAAGATATGAGATACCGACGAGTAAAg                              <  2:13188/141‑1 (MQ=17)
                                                                                                 aaaaTTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGGGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTc                           <  2:168143/141‑1 (MQ=255)
                                                                                                  agatttaatgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCtac                          >  1:143093/11‑139 (MQ=11)
                                                                                                  aaaTTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATCATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTcc                          <  1:12742/141‑1 (MQ=255)
                                                                                                   aaTTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCa                         <  2:14124/141‑1 (MQ=255)
                                                                                                   aaTTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCa                         <  2:355220/141‑1 (MQ=255)
                                                                                                     tttaatgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCAGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCaaa                       >  2:247088/8‑141 (MQ=14)
                                                                                                        aatgaaTTATAAAGATGGAGATATATCATATAATCCGGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGtt                    <  1:222108/137‑1 (MQ=17)
                                                                                                           gaagtataAAGATGGATATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTAtt                 <  2:97702/137‑1 (MQ=255)
                                                                                                           gaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATGAACTAATGATGATTATAATGTAAAACCATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTAtt                 <  2:190692/140‑1 (MQ=255)
                                                                                                             aTTATAAAGACGGAGATATTTCATATCATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCacacgaatagg               >  2:228679/1‑131 (MQ=255)
                                                                                                             aTTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGt               <  1:27131/141‑1 (MQ=255)
                                                                                                              ttAAAAAGATGGAGATATATTATATAATCCAGAGGTGCCTAGTTCTTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGtt              <  2:174029/141‑1 (MQ=18)
                                                                                                                 taAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCCATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCACAGTTATTGTTaaa           >  1:172145/1‑141 (MQ=255)
                                                                                                                  aaaGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTaaaa          >  1:63889/1‑141 (MQ=255)
                                                                                                                  aaaGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTAaaaa          >  2:13001/1‑141 (MQ=255)
                                                                                                                   aaGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGCCGAGTAAAGCTCCCAAGTTATTGTTAAAAg         >  2:358098/1‑141 (MQ=255)
                                                                                                                   aaGACGGAGATATTTCATATAAGCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGCCAAATTCCAAAgccactgcgaaaag         >  2:95478/1‑128 (MQ=14)
                                                                                                                       tggAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTc     >  2:135466/2‑141 (MQ=255)
                                                                                                                       cGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAATGGGttg     >  1:302121/1‑140 (MQ=255)
                                                                                                                          agaTATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATGAATTAATTAATGATGATGATAATGTAAAACAATGACGCAAAAGATATGATATACCGAGGAGTAGAGCTCCAAAGTTATTGTTAAAAAGTTCAgg  >  2:31130/1‑141 (MQ=18)
                                                                                                                                |                                                                                                                                      
GTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGG  >  CP000730/110532‑110794

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: