Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	110,651	C→T	8.6%	D170D (GAC→GAT)	USA300HOU_0109 →	staphylococcal tandem lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	110,651	0	C	T	8.6%	162.3 / 4.2	58	D170D (GAC→GAT)	USA300HOU_0109	staphylococcal tandem lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (29/24);  new base T (2/3);  total (31/27)
Fisher's exact test for biased strand distribution p-value = 6.56e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.68e-01

AAAAGATATCCGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGT  >  CP000730/110511‑110789                                                                                                                                             |                                                                                                                                            aaaaGATATCCGGTTAAAATGGGCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGAGTTTAAAAATTTGAAAAATTATAAAGAc                                                                                                                                             >  2:102041/1‑141 (MQ=255)     gATATCCGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGgag                                                                                                                                         >  1:238465/1‑141 (MQ=255)      atatCCGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGgaga                                                                                                                                        <  1:165421/141‑1 (MQ=255)       tatCCGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGat                                                                                                                                       >  2:284847/1‑141 (MQ=255)         tCCGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGatat                                                                                                                                     >  1:289477/1‑141 (MQ=255)                 aaaTGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGTAGATATTTCAtata                                                                                                                             >  2:217948/1‑141 (MQ=255)                      gTCGATAATAAAATCAATCCAACAAAAAAAATTAAAGAAGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCa                                                                                                                        <  2:58222/141‑1 (MQ=255)                      agaaataataAAATCAAACCAACAAAAAAAATAAAAGAAGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCa                                                                                                                        <  2:277884/137‑1 (MQ=17)                        cGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCaga                                                                                                                      <  1:53036/141‑1 (MQ=255)                              taaAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGcc                                                                                                                >  1:74776/1‑141 (MQ=255)                                aaaTCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGa                                                                                                              >  1:83937/1‑141 (MQ=255)                                aaaTCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGa                                                                                                              >  2:298870/1‑141 (MQ=255)                                aaaTCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGa                                                                                                              <  2:350605/141‑1 (MQ=255)                                     aTTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTAt                                                                                                        <  1:48190/141‑1 (MQ=255)                                        ccAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCg                                                                                                     >  1:104783/1‑141 (MQ=255)                                            caaAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTa                                                                                                 <  1:116205/141‑1 (MQ=255)                                                aGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAata                                                                                             >  2:181138/1‑141 (MQ=255)                                                aGAAATTAAAGAAGAAAAAAAAAAAAAAAGAATCGAAAAATTTAAGTTTTTTGTTCAATATTGCGAATTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTTATTCGGCTAAat                                                                                              <  2:362279/141‑1 (MQ=17)                                                  aaaTTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATc                                                                                           >  1:86418/1‑141 (MQ=255)                                                       aaaGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTTGGCTAAATATCAATTa                                                                                      >  1:21792/1‑141 (MQ=255)                                                       aaaGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTa                                                                                      >  2:405005/1‑141 (MQ=255)                                                         aGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAAc                                                                                    >  1:415769/1‑141 (MQ=255)                                                               aaaaaTAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAatga                                                                              >  1:326691/1‑141 (MQ=255)                                                                 aaaTAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAatgatg                                                                            <  2:64490/141‑1 (MQ=255)                                                                        aaaaGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATaa                                                                     >  2:411443/1‑141 (MQ=255)                                                                         aaaGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCACAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAAt                                                                    >  1:312006/1‑141 (MQ=255)                                                                              aaTCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTaaa                                                               <  1:455944/141‑1 (MQ=255)                                                                                tCGAAAACTTTAAGTTCTTTGTACAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCAGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAAc                                                             >  2:266937/1‑141 (MQ=255)                                                                                  gAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACaa                                                           >  1:97353/1‑141 (MQ=255)                                                                                        tttAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGc                                                     <  1:327378/141‑1 (MQ=255)                                                                                         ttAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCa                                                    <  1:195689/141‑1 (MQ=255)                                                                                         ttAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGAGCCGAG‑TTATTCGGCTAAATATGAATTAACTAATGATGATTATAATGTAAAACAATTACGCa                                                    >  1:321853/1‑141 (MQ=255)                                                                                           aaGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCaaa                                                  >  1:143894/1‑141 (MQ=255)                                                                                             gTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAg                                                <  1:2228/141‑1 (MQ=255)                                                                                                 tttGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgatat                                            >  1:420857/1‑141 (MQ=255)                                                                                                   tGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgatatga                                          <  2:289477/141‑1 (MQ=255)                                                                                                     ttCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgatatgata                                        <  1:387780/141‑1 (MQ=255)                                                                                                       cAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGAtata                                      >  1:376107/1‑141 (MQ=255)                                                                                                              gCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAGTATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACcgacga                               >  2:437589/1‑141 (MQ=255)                                                                                                                  cTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTaa                           >  2:355963/1‑141 (MQ=255)                                                                                                                        agatttaatgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTcc                     <  2:188347/131‑1 (MQ=14)                                                                                                                           tttGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCaaa                  <  2:21792/141‑1 (MQ=255)                                                                                                                            ttGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAg                 >  2:219195/1‑141 (MQ=255)                                                                                                                              gAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGtt               <  1:119020/141‑1 (MQ=255)                                                                                                                              aatgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGtt               >  2:50053/5‑141 (MQ=255)                                                                                                                               atgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTa              <  1:29057/138‑1 (MQ=255)                                                                                                                                aaaaTTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTAt             <  2:46420/141‑1 (MQ=255)                                                                                                                                aaaaTTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTAt             <  2:179289/141‑1 (MQ=255)                                                                                                                                   aTTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGt          >  1:30162/1‑141 (MQ=255)                                                                                                                                   aTTATAAAGACGGAGATATTTCATATAAACCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGGAAAGCTCCAAAGTTATTGt          <  1:421563/141‑1 (MQ=255)                                                                                                                                    ttATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGtt         <  2:145481/141‑1 (MQ=255)                                                                                                                                     tataAAGATGGAGATATATCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTa        <  1:128955/141‑1 (MQ=255)                                                                                                                                      ataAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTaa       <  1:171481/141‑1 (MQ=255)                                                                                                                                       taAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTaaa      <  1:381198/141‑1 (MQ=255)                                                                                                                                       taAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTaaa      >  1:76919/1‑141 (MQ=255)                                                                                                                                       taAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTaaa      <  1:439940/141‑1 (MQ=255)                                                                                                                                        aaaGATGGAGATATATCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTaaaa     >  2:127806/1‑141 (MQ=255)                                                                                                                                          aGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAgg   >  1:361780/1‑141 (MQ=255)                                                                                                                                           gACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGt  >  1:154881/1‑141 (MQ=255)                                                                                                                                             |                                                                                                                                            AAAAGATATCCGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAG‑TTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGT  >  CP000730/110511‑110789

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: ‑