Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,680,793	A→G	11.5%	I15I (ATT→ATC)	dgkA ←	Undecaprenol kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,680,793	0	A	G	11.5%	85.4 / 4.6	35	I15I (ATT→ATC)	dgkA	Undecaprenol kinase
Reads supporting (aligned to +/- strand):  ref base A (16/15);  new base G (2/2);  total (18/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.67e-01

TAAAGCTTCAACAGTGAGAACTAATGCAATAGCAATGAGTATAAATATCCACTCAATCCGATTAATATTTAGTACGAGACCAAAGACAATAGCAACAATCATTGCAAACACATGTAAAAGAAATTTATAGTCTTTTTGAATTAAGATTTTCAGCCCATCAAGTGCATATTTAAACCTTTTCATAATTAGTCTCGTGTTAATCCATATGCGTTTAATATTGTATCTTGTCGACCAAACATTTCCTTTTCATCCGCTTCAGTCATATGATCATAACCTAAT  >  USA300TCH1516_ALE/1680655‑1680933                                                                                                                                           |                                                                                                                                             tAAAGCTTCAACAGTGAGAACTAATGCAATAGCAATGAGTATAAATATCCACTCAATCCGATTAATATTTAGTACGAGACCAAAGACAATAGCAACAATCATTGCAAACACATGTAAAAGAAATTTATAGTCTTTTTGAAt                                                                                                                                            >  1:356165/1‑141 (MQ=255)   aaGCTTCAACAGTGAGAACTAATGCAATAGCAATGAGTATAAATATCCACTCAATCCGATTAATATTTAGTACGAGACCAAAGACAATAGCAACAATCATTGCAAACACATGTAAAAGAAATTTATAGTCTTTTTGGATTa                                                                                                                                          >  2:332427/1‑141 (MQ=255)   aaGCTTCAACAGTGAGAACTAATGCAATAGCAATGAGTATAAATATCCACTCAATCCGATTAATATTTAGTACGAGACCAAAGACAATAGCAACAATCATTGCAAACACATGTAAAAGAAATTTATAGTCTTTTTGGATTa                                                                                                                                          >  2:301748/1‑141 (MQ=255)            cAGTGAGAACTAATGCAATAGCAATGAGTATAAATATCCACTCAATCCGATTAATATTTAGTACGAGACCAAAGACAATAGCAACAATCATTGCAAACACATGTAAAAGAAATTTATAGTCTTTTTGAATTAAGATTTTCa                                                                                                                                 >  1:128548/1‑141 (MQ=255)                    aCTAATGCAATAGCAATGAGTATAAATATCCACTCAATCCGATTAATATTTAGTACGAGACCAAAGACAATAGCAACAATCATTGCAAACACATGTAAAAGAAATTTATAGTCTTTTTGAATTAAGATTTTCAGCCCATCa                                                                                                                         >  2:51938/1‑141 (MQ=255)                     cTAATGCAATAGCAATGGGTATAAATATCCACTCAATCCGATTAATATTTAGTACGAGACCAAAGACAATAGCAACAATCATTGCAAACACATGTAAAAGAAATTTATAGTCTTTTTGAATTAAGATTTTCAGCCCATCaa                                                                                                                        <  1:29765/141‑1 (MQ=255)                     cTAATGCAATAGCAATGAGTATAAATATCCACTCAATCCGATTAATATTTAGTACGAGACCAAAGACAATAGCAACAATCATTGCAAACACATGTAAAAGAAATTTATAGTCTTTTTGAATTAAGATTTTCAGCCCATCaa                                                                                                                        <  1:206632/141‑1 (MQ=255)                          gCAATAGCAATGAGTATAAATATCCACTCAATCTGATTAATATTTAGTACGAGACCAAAGACAATAGCAACAATCATTGCAAACACATGTAAAAGAAATTTATAGTCTTTTTGAATTAAGATTTTCAGCCCATCAAGTGCa                                                                                                                   >  1:121138/1‑141 (MQ=255)                             aTAGCAATGAGTATAAATATCCACTCAATCCGATTAATATTTAGTACGAGACCAAAGACAATAGCAACAATCATTGCAAACACATGTAAAAGAAATTTATAGTCTTTTTGAATTAAGATTTTCAGCCCATCAAGTGCatat                                                                                                                <  1:142953/141‑1 (MQ=255)                              tAGCAATGAGTATAAATATCCACTCAATCCGATTAATGTTTAGTACGAGACCAAAGACAGTCTCAACAATCATAGCAGACGCATGTAATAGGAAGCTATGGTCTTTTGGATTTAAGAGTTTACGCCCATCACGTGCATAtt                                                                                                               >  2:8053/1‑141 (MQ=255)                               aGCAATGAGTATAAATATCCACTCAATCCGATTAATATTTAGTACGAGACCAAAGACAATAGCAACAATCATTGCAAACACATGTAAAAGAAATTTATAGTCTTTTTGAATTAAGATTTTCAGCCCATCAAGTGCATAttt                                                                                                              >  2:286749/1‑141 (MQ=255)                                       gTATAAATATCCACTCAATCCGATTAATATTTAGTACGAGACCAAAGACAATAGCAACAATCATTGCAAACACATGTAAAAGAAATTTATAGTCTTTTTGAATTAAGATTTTCAGCCCATCAAGTGCATATTTAAACtttt                                                                                                      >  2:22690/1‑141 (MQ=255)                                         ataAATATCCACTCAATCCGATTAATATTTAGTACGAGACCAAAGACAATAGCAACAATCATTGCAAACACATGTAAAAGAAATTTATAGTCTTTTTGAATTAAGATTTTCAGCCCATCAAGTGCTTATTTAAACCTTTTc                                                                                                    >  2:191606/1‑141 (MQ=255)                                                      cAATCCGATTAATATTTAGTACGAGACCAAAGACAATAGCAACAATCATTGCAAACACACGTAAAAGAAATTTATAGTCTTTTTGAATTAAGATTTTCAGCCCATCAAGTGCATATTTAAACCTTTTCATAATTAGTCTCg                                                                                       >  2:239718/1‑141 (MQ=255)                                                        aTCCGATTAATATTTAGTACGAGACCAAAGACAATAGCAACAATCATTGCAAACACATGTAAAAGAAATTTATAGTCTTTTTGAATTAAGATTTTCAGCCCATCAAGTGCATATTTAAACCTTTTCATAATTAGTCTCgtg                                                                                     >  1:252815/1‑141 (MQ=255)                                                           cGATTAATATTTAGTACGAGACCAAAGACAATAGCAACAATCATTGCAAACACATGTAAAAGAAATTTATAGTCTTTTTGAATTAAGATTTTCAGCCCATCAAGTGCATATTTAGACCTTTTCATAATTAGTCTCGTGTTa                                                                                  >  1:161826/1‑141 (MQ=255)                                                             aTTAATATTTAGTACGAGACCAAAGACAATAGCAACCATCATTGCAAACACATGTAAAAGAAATTTATAGTCTTTTTGAATTAAGATTTTCAGCCCATCAAGTGCATATTTAAACCTTTTCATAATTAGTCTCGTGTTAAt                                                                                <  1:8856/141‑1 (MQ=255)                                                              ttAATATTTAGTACGAGACCAAAGACAATAGCAACAATCATTGCAAACACATGTAAAAGAAATTTATAGTCTTTTTGAATTAAGATTTTCAGCCCATCAAGTGCATATTTAAACCTTTTCATAATTAGTCTCGTGTTAATc                                                                               <  1:242952/141‑1 (MQ=255)                                                                      tAGTACGAGACCAAAGACAATAGCAACAATCATTGCAAACACATGTAAAAGAAATTTATAGTCTTTTTGAATTAAGATTTTCAGCCCATCAAGTGCATATTTAAACCTTTTCATAATTAGTCTCGTGTTAATCCATATGCg                                                                       <  1:326005/141‑1 (MQ=255)                                                                         tACGAGACCAAAGACAATAGCAACAACCATTGTAAACACATGTACCCGAAATTTAGAGTCTTTTTGAATTAAGATTTTCAGCCCATCAAGTGCATATTTAAACCTTTTCATAATTAGTCTCGTGTTAATCTATATGCGttt                                                                    <  1:259248/141‑1 (MQ=255)                                                                              gaCCAAAGACAATAGCAACAATCATTGCAAACACATGTAAAAGAAATTTATAGTCTTTTTGGATTAAGATTTTCAGCCCATCAAGTGCATATTTAAACCTTTTCATAATTAGTCTCGTGTTAATCCATATGCGTTTAatat                                                               <  1:301748/141‑1 (MQ=255)                                                                              gaCCAAAGACAATAGCAACAATCATTGCAAACACATGTAAAAGAAATTTATAGTCTTTTTGGATTAAGATTTTCAGCCCATCAAGTGCATATTTAAACCTTTTCATAATTAGTCTCGTGTTAATCCATATGCGTTTAatat                                                               <  1:332427/141‑1 (MQ=255)                                                                                ccAAAGACAATAGCAACAATCATTGCAAACACATGTAAAAGAAATTTATAGTCTTTTTGAATTAAGATTTTCAGCCCATCAAGTGCATATTTAAACCTTTTCATAATTAGTCTCGTGTTAATCCATATGCGTTTAATATTg                                                             <  1:129125/141‑1 (MQ=255)                                                                                       cAATAGCAACAATCATTGCAAACACATGTAAAAGAAATTTATAGTCTTTTTGAATTAAGATTTTCAGCCCATCAAGTGCATATTTAAACCTTTTCATCATTAGTCTCGTGTTAATCCATATGCGTTTAATATTGTATCTTg                                                      <  1:75506/141‑1 (MQ=255)                                                                                          tAGCAACAATCATTGCAAACACATGTAAAAGAAATTTATAGGCATTTTGAAGTAAGATTTTCAGCCCATCAAGTGCATATTTAAACCTTTTCATAATTAGTCTCGTGTTAATCCATATGCGTTTAATATTGTATCTTGTCg                                                   >  1:246034/1‑141 (MQ=255)                                                                                                      ttGCAAACACATGTAAAAGAAATTTATAGTCTTTTTGAATTAAGATTTTCAGCCCATCAAGTGCATATTTAAACCTTTTCATAATTAGTCTCGTGTTAATCCATATGCGTTTAATATTGTATCTTGTCGACCAAACATTTc                                       <  2:143105/141‑1 (MQ=255)                                                                                                      tggCAAACACATGTAAAACAAATTTAGAGTCTTTTTGAATTAAGATTTTCAGCCCATTAAGTGCATATTTAAACCTTTTCATAATTAGTCTCGTGTTAATCCATATGCGTTTAATATTGTATCTTGTCGACCAAACATTTc                                       <  2:173492/139‑1 (MQ=255)                                                                                                                aTGTAAAAGAAATTTATAGTCTTTTTGAATTAAGATTTTCAGCCCATCAAGTGCATATTTAAACCTTTTCATAATTAGTCTCGTGTTAATCCATATGCGTTTAATATTGTATCTTGTCGACCAAACATTTCCTTTTCATcc                             <  1:215909/141‑1 (MQ=255)                                                                                                                 tGTAAAAGAAATTTATAGTCTTTTTGAATTAAGATTTTCAGCCCATCAAGTGCATATTTAAACCTTTTCATAATTAGTCTCGTGTTAATCCATATGCGTTTAATATTGTATCTTGTCGACCAAACATTTCCTTTTCATCCg                            <  2:159702/141‑1 (MQ=255)                                                                                                                  gTAAAAGAAATTTATAGTCTTTTTGAATTAAGATTTTCAGCCCATCAAGTGCATATTTAAACCTTTTCATAATTAGTCTCGTGTTAATCCATATGCGTTTAATATGGTATCTTTTCGACCAAACATGTCCTTTTGATcctc                           >  1:342777/1‑139 (MQ=255)                                                                                                                   tAAAAGACATTTATAGTCTTTTTGAATTAAGATTTTCAACCCATCAAGTGCATATTTAAACCTTTTCATAATTAGTCTCGTGTTAATCCATATGCGTTTAATATTGTATCTTGTCGACCAAACATTTCCTTTTCATCCGCt                          <  1:239209/141‑1 (MQ=255)                                                                                                                      aaGAAATTTATAGTCTTTTTGAATTAAGATTTTCAGCCCATCAAGTGCATATTTAAACCTTTTCATAATTAGTCTCGTGTTAATCCATATGCGTTTAATATTGTATCTTGTCGACCAAACATTTCCTTTTCATCCGCTTCa                       <  1:239718/141‑1 (MQ=255)                                                                                                                                taGTCTTTTTGAATTAAGATTTTCAGCCCATCAAGTACATATTTAAAACTTTTCATAATTCGTCTCGTGTTAATCCATATGCGTTTAATATTGTATCTTGTCGACCAAGCATTTCCTTCTCATCCGCTTCAGTCATATGAt             >  1:247691/1‑141 (MQ=255)                                                                                                                                      ttttGAATTAAGATTTTCAGCCCATCAAGTGCATATTTAAACCTTTTCATAATTAGTCTCGTGTTAATCCATATGCGTTTAATATTGTATCTTGTCGACCAAACATTTCCTTTTCATCCGCTTCAGTCATATGATCATAAc       >  1:336561/1‑141 (MQ=255)                                                                                                                                          gAATTAAGATTTTCAGCCCATCAAGTGCATATTTAAACCTTTTCATAATTAGTCTCGTGTTAATCCATATGCGTTTAATATTGTATCTTGTCGACCAAACATTTCCTTTTCATCCGCTTCAGTCATATGATCATAACCTaa   >  2:358790/1‑141 (MQ=255)                                                                                                                                           aaTTAAGATTTTCAGCCCATCAAGTGCATATTTAAACCTTTTCATAATTAGTCTCGTGTTAATCCATATGCGTTTAATATTGTATCTTGTCGACCAAACATTTCCTTTTCATCCGCTTCAGTCATATGATCATAACCTAAt  >  2:63766/1‑141 (MQ=255)                                                                                                                                           |                                                                                                                                             TAAAGCTTCAACAGTGAGAACTAATGCAATAGCAATGAGTATAAATATCCACTCAATCCGATTAATATTTAGTACGAGACCAAAGACAATAGCAACAATCATTGCAAACACATGTAAAAGAAATTTATAGTCTTTTTGAATTAAGATTTTCAGCCCATCAAGTGCATATTTAAACCTTTTCATAATTAGTCTCGTGTTAATCCATATGCGTTTAATATTGTATCTTGTCGACCAAACATTTCCTTTTCATCCGCTTCAGTCATATGATCATAACCTAAT  >  USA300TCH1516_ALE/1680655‑1680933

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: ‑