Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,929,875	T→C	47.5%	intergenic (‑958/‑210)	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	1,929,875	0	T	C	47.5%	0.7 / 71.2	54	intergenic (‑958/‑210)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (14/14);  new base C (7/18);  total (21/33)
Fisher's exact test for biased strand distribution p-value = 1.60e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.36e-01

CAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAAT  >  CP000730/1929738‑1930007                                                                                                                                             |                                                                                                                                       cAATCTATCAGCTAGAATCATATAACTCATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAt‑‑t                                                                                                                                   >  2:245639/1‑141 (MQ=255)   aTCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAt‑‑ttt                                                                                                                                 >  2:132828/1‑141 (MQ=255)                aaTCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATa                                                                                                                    <  2:171573/141‑1 (MQ=255)                         aCTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGtc                                                                                                           >  1:39688/1‑141 (MQ=255)                           ttATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGtcat                                                                                                         <  1:199923/141‑1 (MQ=255)                            tATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGtcatc                                                                                                        <  1:92631/141‑1 (MQ=255)                              tCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAg                                                                                                      >  1:308208/1‑141 (MQ=255)                              tCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAg                                                                                                      <  2:208378/141‑1 (MQ=255)                                   cggaagtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCtg                                                                                                <  1:181312/129‑1 (MQ=255)                                     gaagtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCtgtg                                                                                              <  2:307008/131‑1 (MQ=255)                                      aagtagatatgCTTGTATATTCACAGGTGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGCGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCtgtgt                                                                                             <  1:232817/132‑2 (MQ=255)                                      aaGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCtgtg                                                                                              <  2:254744/141‑1 (MQ=255)                                        gtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGctg                                                                                           >  1:131170/8‑139 (MQ=255)                                          agatatgCTTGTATCTTCACAGAAGGTATAATAATACAGTCTCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGctgtt                                                                                         <  2:14426/136‑5 (MQ=255)                                           aCTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCAtt                                                                                         >  2:222136/1‑141 (MQ=255)                                           aCTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCAtt                                                                                         >  1:22891/1‑141 (MQ=255)                                           aCTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCAtt                                                                                         <  2:95373/141‑1 (MQ=255)                                            cTGTGCGTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTg                                                                                        <  2:78453/141‑1 (MQ=255)                                             tgtgCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCATGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGc                                                                                       <  2:321466/141‑1 (MQ=255)                                             tgtgCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGc                                                                                       <  1:298140/141‑1 (MQ=255)                                             tatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGctgttgcg                                                                                      <  1:315321/139‑8 (MQ=255)                                              atgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCGTAGCACCAGTCATCAGTGGCTGTGCTGTTGCGt                                                                                     >  1:31670/2‑141 (MQ=255)                                                 cTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtatt                                                                                  >  1:15080/1‑141 (MQ=255)                                                          tcacagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCtgtg                                                                                              <  2:250434/115‑1 (MQ=255)                                                          tcacagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCtgtg                                                                                              >  1:250434/6‑120 (MQ=255)                                                           cacagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTg                                                                        >  2:173140/5‑141 (MQ=255)                                                             ccGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTgg                                                                       >  1:60036/1‑141 (MQ=255)                                                             cagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGc                                                                      <  2:215288/139‑1 (MQ=255)                                                              agatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCt                                                                     <  2:316340/140‑1 (MQ=255)                                                                 tggtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCttag                                                                  <  2:115722/138‑4 (MQ=255)                                                                 tgatATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTaa                                                                   >  2:99658/1‑141 (MQ=255)                                                                    tataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTaa                                                               <  1:280839/141‑2 (MQ=255)                                                                       aataatAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACg                                                            >  1:93037/1‑141 (MQ=255)                                                                        ataatagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGc                                                           <  2:301488/137‑1 (MQ=255)                                                                        ataatagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGc                                                           <  2:36173/137‑1 (MQ=255)                                                                        ataatagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGc                                                           <  1:158128/137‑1 (MQ=255)                                                                        ataatagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTA‑C‑TT‑‑TGCTAATCATTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCa                                                          <  2:283603/137‑1 (MQ=255)                                                                         taatagTGTCGCCTATCTTTAAGGCGTCAATT‑‑GAAGAAGAGAGGAGGTGCATTAC‑T‑ATGCTAATCAT‑‑TTTCGTTCAAATCATAGCCCCAGTCATCAGTGGCTGTGCTATTGCGTATTATACTTATTGGCTTAGTAAACGCa                                                          <  2:44104/138‑1 (MQ=255)                                                                            tagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaaca                                                       <  1:304971/141‑3 (MQ=255)                                                                            tagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaaca                                                       <  1:204486/141‑3 (MQ=255)                                                                              gagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaa                                                     >  2:263415/1‑137 (MQ=255)                                                                              gagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTA‑CTTTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaa                                                     <  1:232403/141‑5 (MQ=255)                                                                               agTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCGGTGGCTGTGCTGTTGCAAATTATGCTTATTGGCTTCGTAAACGCaacaaat                                                    <  2:52958/141‑6 (MQ=255)                                                                                gTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGTCTAAGTAGACGCAATACaa                                                    >  2:170569/1‑141 (MQ=255)                                                                                gTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACaa                                                    >  2:170563/1‑141 (MQ=255)                                                                                  cGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCAATTGCGTTTTTTTCTTATTGGCTAAGTACACGCAATACaaaa                                                  >  1:302135/1‑141 (MQ=255)                                                                                       gagagataGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGt                                             >  2:242800/8‑141 (MQ=255)                                                                                                gCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAg                                    >  2:214335/1‑141 (MQ=255)                                                                                                   tCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCg                                 <  1:305019/141‑1 (MQ=255)                                                                                                     aaTTTAGTCGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCa                               <  1:300793/141‑1 (MQ=255)                                                                                                             cGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATaaa                       <  1:245639/141‑1 (MQ=255)                                                                                                              gCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATaaaa                      >  2:47681/1‑141 (MQ=255)                                                                                                                        ggTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCAc            <  1:9449/141‑1 (MQ=255)                                                                                                                                     gTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTatttgcggt  <  2:196222/141‑9 (MQ=255)                                                                                                                                             |                                                                                                                                       CAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAAT  >  CP000730/1929738‑1930007

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: ‑