Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,929,928	T→A	36.6%	intergenic (‑1011/‑157)	USA300HOU_1794 ← / → USA300HOU_1796	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,929,928	0	T	A	36.6%	52.0 / 65.3	52	intergenic (‑1011/‑157)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (13/20);  new base A (11/8);  total (24/28)
Fisher's exact test for biased strand distribution p-value = 2.53e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.15e-01

GTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑GG‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCTAATT  >  CP000730/1929789‑1930068                                                                                                                                               |                                                                                                                                             gTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑GG‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCNGTGCCATTGCGtttttt                                                                                                                                             <  1:163016/141‑1 (MQ=255)   atatTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑GG‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTc                                                                                                                                           <  2:202683/141‑1 (MQ=255)           agatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑TT‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCt                                                                                                                                  <  1:240799/140‑1 (MQ=255)            gatgatATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑GG‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCt                                                                                                                                  <  1:95512/141‑1 (MQ=255)            gatgatATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑GG‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCt                                                                                                                                  >  1:168172/1‑141 (MQ=255)            gatgatATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGGGTA‑TAA‑GG‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCt                                                                                                                                  >  1:84937/1‑141 (MQ=255)              tggtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑TT‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCttag                                                                                                                               >  1:257892/4‑138 (MQ=255)              tggtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑TT‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCttag                                                                                                                               <  2:195061/138‑4 (MQ=255)               gatATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑GG‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAg                                                                                                                               >  2:27327/1‑141 (MQ=255)                   taataaTAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑TT‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTaaac                                                                                                                          <  2:93610/141‑4 (MQ=255)                   taataGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑GG‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGa                                                                                                                           <  1:87025/141‑1 (MQ=255)                    aataatAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑TT‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACg                                                                                                                         >  2:184121/1‑141 (MQ=255)                      taatagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACTT‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCa                                                                                                                       >  2:116085/4‑141 (MQ=255)                        atagAGTCGCCGATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑TT‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaac                                                                                                                     >  2:127504/2‑140 (MQ=255)                         aagagTCGCCTATCTCTCAGACGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTA‑CTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaaca                                                                                                                    <  1:193086/140‑3 (MQ=255)                           gagTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑GG‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATAc                                                                                                                   <  1:168121/141‑1 (MQ=255)                           gagTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑GG‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATAc                                                                                                                   >  2:39591/1‑141 (MQ=255)                            agTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑TT‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaat                                                                                                                 <  1:119610/141‑6 (MQ=255)                              tCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑GG‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACaaa                                                                                                                <  2:107334/141‑1 (MQ=255)                              tCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCG‑TTACTT‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataa                                                                                                               >  1:227712/1‑134 (MQ=255)                              tCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑TT‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataa                                                                                                               >  1:167132/1‑134 (MQ=255)                                gCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑GG‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAAt                                                                                                              >  1:125478/1‑141 (MQ=255)                                 ccTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACTT‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataatta                                                                                                            >  2:57887/1‑131 (MQ=255)                                  cTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑TT‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaa                                                                                                           >  2:172635/1‑130 (MQ=255)                                   tATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGTAGGTGCATTAC‑TT‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaat                                                                                                          <  2:200161/141‑13 (MQ=255)                                    aTCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑TT‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaata                                                                                                         >  1:94316/1‑128 (MQ=255)                                    aTCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑TT‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaata                                                                                                         <  2:242604/141‑14 (MQ=255)                                    aTCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑TT‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaata                                                                                                         >  1:144161/1‑128 (MQ=255)                                    aTCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑TT‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaata                                                                                                         <  1:188146/141‑14 (MQ=255)                                     tctctcAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑TT‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaatag                                                                                                        >  2:211219/1‑127 (MQ=255)                                                  aaTTTAGACGCAGAGAGGAGGTGTA‑TAA‑GG‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCa                                                                                            >  1:214933/1‑141 (MQ=255)                                                                caggaggTGTA‑TAA‑CG‑AGATGCGTAATCTCAACCTTAAAATATCACCACGCAGCAGTTGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATccc                                                                              <  1:184352/140‑1 (MQ=255)                                                                 aggaggTGTA‑TAA‑GG‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATcccc                                                                             <  1:224027/141‑1 (MQ=255)                                                                    aggTGTA‑TAA‑GG‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAACATCCCCTcc                                                                          >  2:125303/1‑140 (MQ=255)                                                                    aggTGTA‑TAA‑GG‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGACACACCAATAAAAATctcctcc                                                                          >  2:99968/1‑140 (MQ=255)                                                                         ta‑taA‑GG‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTAcc                                                                     <  1:218400/141‑1 (MQ=255)                                                                         ta‑taA‑GG‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTAcc                                                                     <  1:39591/141‑1 (MQ=255)                                                                             aa‑GG‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTatttgc                                                                  <  2:73530/141‑6 (MQ=255)                                                                                gg‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAGTCCCCTCACTACCGCaaa                                                                <  1:46547/141‑1 (MQ=255)                                                                                        tttATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAg                                                         <  1:97535/140‑1 (MQ=255)                                                                                        cTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAg                                                         >  1:106585/1‑141 (MQ=255)                                                                                          tATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAggg                                                       >  2:219901/1‑141 (MQ=255)                                                                                             tttCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGAt                                                    <  2:168007/141‑1 (MQ=255)                                                                                                cGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTgg                                                 <  1:40339/141‑1 (MQ=255)                                                                                                cGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTgg                                                 >  2:109101/1‑141 (MQ=255)                                                                                                       atcatAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATaa                                          <  2:214933/141‑1 (MQ=255)                                                                                                        tcatAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTTTTTTTTTTTAAGTAGACGCAATACAAAATAGGTTACATATAGCCGCACCGATAAAAATCGCCTCCCTACCGCCATTCGTGCGGGGATTGGTGTATAAg                                         >  2:178994/1‑141 (MQ=255)                                                                                                                ccAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACt                                 <  1:27327/141‑1 (MQ=255)                                                                                                                   gTCATCATTGGCTGTGCTATTTCGTTTTTTTCTTATTGGCTAAGTATACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAANAGTGAGGGGATTGGTNTATAAGTAAATACTTAt                              <  1:142183/141‑1 (MQ=255)                                                                                                                           tGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTg                      >  1:87000/1‑141 (MQ=255)                                                                                                                                      ttGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATtata           <  2:168172/141‑1 (MQ=255)                                                                                                                                      ttGCGTTTTTTGCGTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTGCCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATtata           <  2:84937/141‑1 (MQ=255)                                                                                                                                       tGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCATAATTATAc          <  1:233101/141‑1 (MQ=255)                                                                                                                                               tttCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCTAAtt  <  1:27677/141‑1 (MQ=255)                                                                                                                                               |                                                                                                                                             GTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑GG‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCTAATT  >  CP000730/1929789‑1930068

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑