Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,028,191	C→A	72.7%	A152S (GCA→TCA)	USA300HOU_RS10230 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,028,191	0	C	A	72.7%	47.5 / 14.8	34	A152S (GCA→TCA)	USA300HOU_RS10230	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (2/7);  new base A (12/12);  total (14/20)
Fisher's exact test for biased strand distribution p-value = 2.41e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCAT  >  USA300TCH1516_ALE/2028057‑2028328                                                                                                                                       |                                                                                                                                          tGATTTTTCATTCACGTAAGTACGTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCttt                                                                                                                                     <  1:421662/141‑1 (MQ=255)    tttttCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGt                                                                                                                                  <  1:199959/141‑1 (MQ=255)          attcaCGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTc                                                                                                                            >  2:18801/1‑141 (MQ=255)          attcaCGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTc                                                                                                                            <  2:475444/141‑1 (MQ=255)           ttcaCGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTATACCAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCa                                                                                                                           >  1:469984/1‑141 (MQ=255)            tcaCGTAAGTACTACCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATGTGAAGCTTTTGTTACGTCaa                                                                                                                          >  2:357790/1‑141 (MQ=255)                  aaGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATCGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTACCAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCACTCTGTa                                                                                                                    >  2:183528/1‑141 (MQ=255)                   aGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAg                                                                                                                   >  1:449782/1‑141 (MQ=255)                       tttCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAAGCTGTACTTTACCTAAAATGTGTCTAACTACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCg                                                                                                               <  2:117283/140‑1 (MQ=255)                       cTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCg                                                                                                               >  1:419875/1‑141 (MQ=255)                         tCCACAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGcc                                                                                                             <  1:13480/141‑1 (MQ=255)                              aaaaaGCAGCTAAATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTc                                                                                                        >  2:62802/1‑141 (MQ=255)                               aaaaGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTcc                                                                                                       <  1:140994/141‑1 (MQ=255)                                  agcagcTACATGTAAATTAATATTGTAAGTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATGTGCAGGTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATg                                                                                                    <  2:169359/141‑1 (MQ=255)                                                aaTTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGATGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCTATGTTGAATTTGTACAt                                                                                      <  2:84868/141‑1 (MQ=255)                                                  ttAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTATAATGTTTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCt                                                                                    <  1:162244/141‑1 (MQ=255)                                                      tagtttAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTccc                                                                                <  2:121769/136‑1 (MQ=255)                                                                 aCCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTAAATCCGCCCACTTATATACa                                                                     >  2:323182/1‑141 (MQ=255)                                                                   cGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATa                                                                   >  1:64192/1‑141 (MQ=255)                                                                     gCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCATTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTAAATCTTCCCACTTATATACATaaa                                                                 >  2:340435/1‑141 (MQ=255)                                                                       aaTATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACt                                                               <  1:204961/141‑1 (MQ=255)                                                                         tataACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTgg                                                             >  1:317315/1‑141 (MQ=255)                                                                                  cACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTg                                                    >  2:410306/1‑141 (MQ=255)                                                                                   aCTTTACCTAAAATGTGTCTAACCACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGc                                                   <  1:134188/141‑1 (MQ=255)                                                                                   aCTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTGTATACATAAACTGGTGTACGTTGc                                                   <  1:96392/141‑1 (MQ=255)                                                                                       tACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCAc                                               <  2:422158/141‑1 (MQ=255)                                                                                             aaaTGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTTGAGCTTTTGTTAAGTGAATATGTAGGTCGCGAATTCGATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAAcc                                         <  2:125690/141‑1 (MQ=255)                                                                                              aaTGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCa                                        >  1:189970/1‑141 (MQ=255)                                                                                                           acaaTGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTGGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTtaata                           <  1:18801/141‑1 (MQ=255)                                                                                                                ggTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGa                      >  2:271347/1‑141 (MQ=255)                                                                                                                   tttattTTCCGTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATgg                   <  2:468413/140‑1 (MQ=255)                                                                                                                                 tatTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCt     <  1:168592/141‑1 (MQ=255)                                                                                                                                 tatTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCt     <  1:431071/141‑1 (MQ=255)                                                                                                                                    ttGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCAt  <  2:419875/141‑1 (MQ=255)                                                                                                                                       |                                                                                                                                          TGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCAT  >  USA300TCH1516_ALE/2028057‑2028328

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑