Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	979,234	G→T	16.2%	M838I (ATG→ATT)	clpB_1 →	Chaperone protein ClpB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	979,234	0	G	T	16.2%	69.5 / 2.0	29	M838I (ATG→ATT)	clpB_1	Chaperone protein ClpB
Reads supporting (aligned to +/- strand):  ref base G (15/9);  new base T (2/3);  total (17/12)
Fisher's exact test for biased strand distribution p-value = 6.22e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGAACAACGAATCTCAATTGAAGTTTCTGATGATGCTAAAGCTTGGCTAGGTCAAGAAGCTTATGAACCTCAATACGGTGCAAGACCATTAAAACGTTTTGTACAACGCCAAATTGAAACACCATTAGCACGTATGATGATTAAAGAGGGATTCCCAGAAGGTACAACGATTAAAGTTAATTTAAATTCAGACAATAACTTAACGTTTAATGTTGAAAAAATTCATGAATAAAATTGAACCAAGAATGTGATGATTAATCGCATTCTTGGTTTTT  >  USA300TCH1516_ALE/979099‑979373                                                                                                                                        |                                                                                                                                            aGAACAACGAATCTGAATTGAAGTTTCTGATGATGCTAAAGCTTGGCTAGGTCAAGAAGCTTATGAACCTCAATACGGTGCAAGACCATTAAAACGTTTTGTACAACGCCAAATTGAAACACCATTAGCACGTAtgatga                                                                                                                                         >  2:242577/1‑140 (MQ=255)   aacaacGAATCTCAATTGAAGTTTCTGATGATGCTAAAGCTTGGCTAGGTCAAGAAGCTTATGAACCTCAATACGGTGCAAGACCATTAAAACGTTTTGTACAACGCCAAATTGAAACACCATTAGCACGTATTATGAtt                                                                                                                                       >  2:88457/1‑140 (MQ=255)   aacaacGAATCTCAATTGAAGTTTCTGATGATGCTAAAGCTTGGCTAGGTCAAGAAGCTTATGAACCTCAATACGGTGCAAGACCATTAAAACGTTTTGTACAACGCCAAATTGAAACACCATTAGCACGTATTATGAtt                                                                                                                                       >  2:88388/1‑140 (MQ=255)           aTCTCAATTGAAGTTTCTGATGATGCTAAAGCTTGGCTAGGTCAAGAAGCTTATGAACCTCAATACGGTGCAAGACCATTAAAACGTTTTGTACAACGCCAAATTGAAACACCATTAGCACGTATGATGATTAACGAggg                                                                                                                               >  1:326761/1‑140 (MQ=255)           aTCTCAATTGAAGTTTCTGATGATGCTAAAGCTTGGCTAGGTCAAGAAGCTTATGAACCTCAATACGGTGCAAGACCATTAAAAAGTTTTGTACAACGCCAAATTGAAACACCATTAGCACGAATGATAATTAAAAAggg                                                                                                                               >  2:155071/1‑140 (MQ=255)           aTCTCAATTGAAGTTCCTGATGATGCTAAAGCTTGGCTAGGTCAAGAAGCTTATGAACCTCAATACGGTGCAAGACCATTAAAACGTTTTGTACAACGCCAAATTGAAACACCATTAGCACGTATGATGATTAAAGAggg                                                                                                                               <  2:327532/140‑1 (MQ=255)            tttcAATTGAAGTTTCTGATGATGCTAAAGCTTGGCTAGGTCAAGAAGCTTATGAACCTCAATACGGTGCAAGACCATTAAAACGTTTTGTACAACGCCAAATTGAAACACCATTAGCACGTATGATGATTAAAGAGGGa                                                                                                                              <  2:66538/138‑1 (MQ=255)                 aTTGAAGTTTCTGATGATGCTAAAGCTTGGCTAGGTCAAGAAGCTTATGAACCTCAATACGGTGCAAGACCATTAAAACGTTTTGTACAACGCCAAATTGAAACACCATTAGCACGTATGATGATTAAAGAGGGATTccc                                                                                                                         <  2:8514/140‑1 (MQ=255)                          tCTGATGATGCTAAAGCTTGGCTAGGTCAAGAAGCTTATGAACCTCAATACGGTGCCAGACCATTAAAACGTTTTGTACAACGCCAAATTGAAACACCATTAGCACGTATGATGATTAAAGAGGGATTCCCAGAAGATAc                                                                                                                >  1:121486/1‑140 (MQ=255)                           cTGATGATGCTAAAGCTTGGCTAGGTCAAGAAGCTTATGAACCTCAATACGGTGCAAGACCATTAAAACGTTTTGTACAACGCCAAATTGAAACACCATTAGCACGTATGATGATTAAAGAGGGATTCCCAGAAGGTACa                                                                                                               <  2:166884/140‑1 (MQ=255)                                    cTAAAGCTTGGCTAGGTCAAGAAGCTTATGAACCTCAATACGGTGCAAGACCATTAAAACGTTTTGTACAACGCCAAATTGAAACACCATTAGCACGTATGATGATTAAAGAGGGATTCCCAGAAGGTACAACGATTaaa                                                                                                      >  1:323678/1‑140 (MQ=255)                                           ttGGCTAGGTCAAGAAGCTTATGAACCTCAATACGGTGCAAGACCATTAAAACGTTTTGTACAACGCCAAATTGAAACACCCTTAGCACGTATGATGATTAAAGAGGGATTCCCAGAAGGTACAACGATTAAAGTTAAtt                                                                                               <  2:95048/140‑1 (MQ=255)                                            tGGCTAGGTCAAGAAGCTTATGAACCTCTATACGGTGCAAGACCATTAAAACGTTTTGTACAACGCCAAATTGGAACACCATTAGCACGTATGATGATTAAAGAGGGATTCCCAGAAGGTACAACGATTAAAGTTAAttt                                                                                              <  1:72090/140‑1 (MQ=255)                                             ggCTAGGTCAAGAAGCTTATGAACCTCAATACGGTGCAAGACCATTAAAACGTTTTGTACAACGCCAAATTGAAACACCATTAGCACGTATGATGATTAAAGAGGGATTCCCAGAAGGTACAACGATTAAAGTTAATTTa                                                                                             >  2:9189/1‑140 (MQ=255)                                                tAGGTCAAGAAGCTAATGAACCTCAATACGGTGCAAGACCATTAAAACGATTTGTACAACGCCAAATTGAAACACCATAAGCACGTATGATGATTAAAGAGGGATTCCCAGAAGGTACAACGATTAAAGTTAATTTAAAt                                                                                          <  1:93879/140‑1 (MQ=255)                                                      aagaagCTTATGAACCTCAATACGTTGCAAGACCATTAAAACGTTTTGTACAACGCCAAATTGAAACACCATTAGCACGTATGATGATTAAAGAGGGATTCCCAGAAGGTACAACGATTAAAGTTAATTTAAATTCAGAc                                                                                    >  2:298720/1‑140 (MQ=255)                                                      aagaagCTTATGAACCTCAATACGGTGCAAGACCATTAAAACGTTTTGTACAACGCCAAATTGAAACACCATTAGCACGTATGATGATTAAAGAGGGATTCCCAGAAGGTACAACGATTAAAGTTAATTTAAATTCAGAc                                                                                    <  1:52882/140‑1 (MQ=255)                                                                tGAACCTCAATACGGTGCAAGACCATTAAAACGTTTTGTACAACGCCAAATTGAAACACCATTAGCACGTATTATGATTAAAGAGGGATTCCCAGAAGGTACAACGATTAAAGTTAATTTAAATTCAGACAATAACTTaa                                                                          <  1:88457/140‑1 (MQ=255)                                                                tGAACCTCAATACGGTGCAAGACCATTAAAACGTTTTGTACAACGCCAAATTGAAACACCATTAGCACGTATTATGATTAAAGAGGGATTCCCAGAAGGTACAACGATTAAAGTTAATTTAAATTCAGACAATAACTTaa                                                                          <  1:88388/140‑1 (MQ=255)                                                                      tCAATACGGTGCAAGACCATTAAAACGTTTTGTACAACGCCAAATTGAAACACCATTAGCACGTATGATGATTAAAGAGGGATTCCCAGAAGGTACAACGATTAAAGTTAATTTAAATTCAGACAATAACTTAACGTTTa                                                                    >  2:264092/1‑140 (MQ=255)                                                                       cAATACGGTGCAAGACCATTAAAACGTTTTGTACAACGCCAAATTGAAACACCATTAGCACGTATGATGATTAAAGAGGGATTCCCAGAAGGTACAACGATTAAAGTTAATTTAAATCCAGACAATAACTTAACGGTTaa                                                                   >  2:90933/1‑140 (MQ=255)                                                                            cGGTGCAAGACCATTAAAACGTTTTGTACAACGCCAAATTGAAACACCATTAGCACGTATGATGATTAAAGAGGGATTCCCAGAAGGTACAACGATTAAAGTTAATTTAAATTCAGACAATAACTTAACGTTTAATGTTg                                                              >  2:44049/1‑140 (MQ=255)                                                                              gTGCAAGACCATTAAAACGTTTTGTACAACGCCAAATTGAAACACCATTAGCACGTATGATGATTAAAGAGGGATTCCCAGAAGGTACAACGATTAAAGTTAATTTAAATTCAGACAATAACTTAACGTTTAATGTTGaa                                                            >  2:153129/1‑140 (MQ=255)                                                                              gTGCAAGACCATTAAAACGTTTTGTACAACGCCAAATTGAAACACCATTAGCACGTATGATGATTAAAGAGGGATTCCCAGAAGGTACAACGATTAAAGTTAATTTAAATTCAGACAATAACTTAACGTTTAATGTTGaa                                                            <  2:54734/140‑1 (MQ=255)                                                                                 cAAGACCATTAAAACGTTTTGTACAACGCCAAATTGAAACACCATTAGCACGTATGATGATTAAAGAGGGATTCCCAGAAGGTACAACGATTAAAGTTAATTTAAATTCAGACAATAACTTAACGTTTAATGTTGaaaaa                                                         >  2:237856/1‑140 (MQ=255)                                                                                               cGTTTTGTACAACGCCAAATTGAAACACCACTAGCACGTATGATGATTAAAGAGGGATTCCCAGAAGGTACAACGGTTAAAGTTAATTTAACTTCCGACAGTAACTTAACGTTTAATGTTGAAAAAATTCATGAATaaaa                                           >  2:38078/1‑140 (MQ=255)                                                                                                 ttttGTACAACGCCAAATTGAAACACCATTAGCACGTATGATGATTAAAGAGGGATTCCCAGAAGGTACAACGATTAAAGTTAATTTAAATTCAGACAATAACTTAACGTTTAATGTTGAAAAAATTCATGAATCAAAtt                                         >  2:211482/1‑140 (MQ=255)                                                                                                        cAACGCCAAATTGAAACACCATTAGCACGTATGATGATTAAAGAGGGATTCCCAGAAGGTACAACGATTAAAGTTAATTTAAATTCAGACAATAACTTAACGTTTAATGTTGAAAAAATTCATGAATAAAATTGaaacca                                  >  2:356653/1‑136 (MQ=255)                                                                                                                aaTTGAAACATCATTAGCACGTATTAATATTAAAGGATGATTCCCAGAATGTACAACGATTAAAGTTAATTTAAATTCAGACAATAACTTAACGTTTAATGTTGAAAAAAGTCATGAATAAAATTGAACCAAGAATGtga                          <  1:159971/140‑1 (MQ=255)                                                                                                                                 cACGTATGATGATTAAAGAGGGATTCCCAGAAGGTACAACGATTAAAGTTAATTTAAATTCAGACAATAACTTAACGTTTAATGTTGAAAAAATTCATGAATAAAATTGAACCAAGAATGTGATGATTAATCGAATTCtt         >  2:334885/1‑140 (MQ=255)                                                                                                                                       tgatgaTTAAAGAGGGATTCCCAGAAGGTACAACGATTAAAGTTAATTTAAATTCAGACAATAACTTAACGTTTAATGTTGAAAAAATTCATGAATAAAATTGAACCAAGAATGTGATGATTAATCGCATTCTTGTtttt   <  1:242577/140‑1 (MQ=255)                                                                                                                                        gatgatTAAAGAGGGATTCCCAGAAGGTACAACGATTAAAGTTAATTTAAATTCAGACAATAACTTAACGTTTAATGTTGAAAAAATTCATGAATAAAATTGAACCAAGAATGTGATGATTAATCGCATTCTTGGttttt  >  1:57895/1‑140 (MQ=255)                                                                                                                                        |                                                                                                                                            AGAACAACGAATCTCAATTGAAGTTTCTGATGATGCTAAAGCTTGGCTAGGTCAAGAAGCTTATGAACCTCAATACGGTGCAAGACCATTAAAACGTTTTGTACAACGCCAAATTGAAACACCATTAGCACGTATGATGATTAAAGAGGGATTCCCAGAAGGTACAACGATTAAAGTTAATTTAAATTCAGACAATAACTTAACGTTTAATGTTGAAAAAATTCATGAATAAAATTGAACCAAGAATGTGATGATTAATCGCATTCTTGGTTTTT  >  USA300TCH1516_ALE/979099‑979373

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑