Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,002,200	T→G	M173R (ATG→AGG)	mecA →	Adapter protein MecA 1

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,002,200	0	T	G	95.3%	132.5 / NA	43	M173R (ATG→AGG)	mecA	Adapter protein MecA 1
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base G (15/26);  minor base A (2/0);  total (17/26)
Fisher's exact test for biased strand distribution p-value = 1.51e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

TAAACGTCAAAAGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATATGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTAAATGACT  >  USA300TCH1516_ALE/1002069‑1002331                                                                                                                                    |                                                                                                                                    tcaaCGTCAAAAGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGt                                                                                                                                  >  1:161533/3‑135 (MQ=255)  aaaCGTCAAAAGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTTAAGATTTGTTTTATAGGGtt                                                                                                                                 <  1:306387/135‑1 (MQ=255)  aaaCGTCAAAAGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGtt                                                                                                                                 <  1:84289/135‑1 (MQ=255)       tCAAAAGTCGTCAGCGCGTAAAAATACAAGAACAATCATGGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGATTTTTAAGATTTTTTATATAGGGTTGATgg                                                                                                                            <  1:423394/135‑1 (MQ=255)         aaaaGTCTTCAGCACGTAAAAATACAAGAACCATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTa                                                                                                                          <  2:334368/135‑1 (MQ=255)                                aCAAGAACAATCATTGTGAAATTTAAAGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATAtttt                                                                                                   >  1:59232/1‑135 (MQ=255)                                           cATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGt                                                                                        >  2:171038/1‑135 (MQ=255)                                            aTTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCCTAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGtt                                                                                       <  1:95072/135‑1 (MQ=255)                                              tgtgAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGa                                                                                     <  1:400663/135‑1 (MQ=255)                                               gtgAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGAt                                                                                    <  1:581863/135‑1 (MQ=255)                                                  aaaTTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCaa                                                                                 >  1:394608/1‑135 (MQ=255)                                                  aaaTTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCaa                                                                                 >  1:676778/1‑135 (MQ=255)                                                   aaTTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCaag                                                                                <  2:80027/135‑1 (MQ=255)                                                   aaTTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCaag                                                                                >  2:201831/1‑135 (MQ=255)                                                   aaTTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCaag                                                                                <  1:632287/135‑1 (MQ=255)                                                   aaTTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAAGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCaag                                                                                >  2:545948/1‑135 (MQ=255)                                                   aaTTTAACGATTTAGAAGATGTTATTAATTATGAATATAATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTCTATTTTGATAGTCATGTTGATCaag                                                                                >  1:349141/1‑135 (MQ=255)                                                                 gaagaTGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGTTTAAGAAGTCATTAATGAt                                                                  <  1:487799/135‑1 (MQ=255)                                                                 gaagaTGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGAt                                                                  <  1:642378/135‑1 (MQ=255)                                                                       gTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGTTTAAGAAGTCATTAATGATAGTTAc                                                            <  1:73717/135‑1 (MQ=255)                                                                       gTTATTAATTATGCAGATCATATGAATCCTATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATAGTTTGATAGTCATGTTTATCAAGAAGTCATTAATGATAGTTAc                                                            <  2:361568/135‑1 (MQ=255)                                                                             aattaTTCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCaa                                                      <  2:260152/135‑1 (MQ=255)                                                                               ttgtGCATATCATATTAATCCAATAACTACAGAGTTTGAAAATGTGGTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAAtt                                                    <  2:426812/132‑1 (MQ=255)                                                                                       atCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATCGGACTCGGGATACTTATACGCATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATCAATGATCGTTACAGTAAATTGCTTGAAt                                            >  1:129651/1‑135 (MQ=255)                                                                                         cATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAAttt                                          <  1:422547/135‑1 (MQ=255)                                                                                         cATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAAttt                                          >  2:679064/1‑135 (MQ=255)                                                                                             gCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTGTGATAGTCATGTTGATCAAGAAGTCATTAGTGATAGTTACAGTCAATTGCTTGAATTTGCtt                                      >  1:404000/1‑135 (MQ=255)                                                                                             gCAATCCAATAAATACAGAGTATGAAGATTTGTTATATAGGGTTGATGGTACTTATTATGATGCTGTATATTTTGATGGTGATGTTGATGAAGAAGTTATTAATGATAGTTACAGTCAATTGCTTGAATTTGCta                                      >  2:15688/1‑134 (MQ=255)                                                                                                  ccACTAACTACAGAGTTTGAAGAAATGTTAAAAAAGGAAAATGGTACTTATTATTATGCAGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCa                                 >  1:649119/1‑135 (MQ=255)                                                                                                  ccAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCa                                 >  2:559590/1‑135 (MQ=255)                                                                                                       caCTACAGATTTTGAAGCTTTGTTATATAGGCTTGATTTTACTTACTATTATGCTGTATATTTTGATAGTCATGTTTATCAAGAAGTCATTAATGATAGTTACCTTCAATTGCTTGAATTTGCTTATCCAacata                            <  2:551970/134‑3 (MQ=255)                                                                                                       aaCTACAGAGTTTGAAGATTTGTTTTATAGGGCTGATGGTATTTCTTTGGATGCCTTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAacaga                            <  1:123528/135‑1 (MQ=255)                                                                                                       aaCTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGTTTTTATTTGCTTATCCAacaga                            <  1:1622/135‑1 (MQ=255)                                                                                                       aaCTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGCATTTGCTTATCCAacaga                            >  2:488300/1‑135 (MQ=255)                                                                                                       aaCTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAacaga                            <  2:30823/135‑1 (MQ=255)                                                                                                       aaCTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAacaga                            <  2:534226/135‑1 (MQ=255)                                                                                                        aCTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGTATTTGCTTATCCAacagac                           <  1:171038/135‑1 (MQ=255)                                                                                                            cAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGacagaa                       >  1:433918/1‑135 (MQ=255)                                                                                                             agagTTTGAAGATTTGTTATATAGGATTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGTTTGAATTTGCTTATCCAAcagacagagc                      <  1:459967/135‑3 (MQ=255)                                                                                                                 tttGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGGTTGAATTTTCTTATCCAACAGAcagaaaagaa                  >  2:338017/1‑135 (MQ=255)                                                                                                                        aTTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGtttatt           <  2:169397/135‑1 (MQ=255)                                                                                                                          ttGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGTTTATCCTACAGACAGAACAGAAGtttattta         <  1:244572/135‑1 (MQ=255)                                                                                                                          ttGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATTCAACAGACAGAACAGAAGtttattta         <  1:626130/135‑1 (MQ=255)                                                                                                                                 atatGGTTGATGGTACTTATTATTATGCTGTATATTTTGATATTCATGTGGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTAAATGACt  <  2:383615/135‑1 (MQ=255)                                                                                                                                    |                                                                                                                                    TAAACGTCAAAAGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATATGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTAAATGACT  >  USA300TCH1516_ALE/1002069‑1002331

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: ‑