Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,647,664	A→T	12.9%	Y267* (TAT→TAA)	lipM ←	Octanoyltransferase LipM

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,647,664	0	A	T	12.9%	78.7 / 4.8	31	Y267* (TAT→TAA)	lipM	Octanoyltransferase LipM
Reads supporting (aligned to +/- strand):  ref base A (15/12);  new base T (2/2);  total (17/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.26e-01

ATCGCAAAGCAATGCGTAAGTATAAAAGAAATCAAAGAAGAAAATAGATAAAAAAACGGAAGCACTTGTAGGTAAAATAGTCTACGTGCTTCCATTTTTTATTCTAAAAACTACTTTCTAAACATCCATTCATCTGAACGATATTTTTCAGTTAATTCTTCCACTTCTGCCAATTGAGCTTCTGTTAATTCAAGTGGCTTAAATTCTATATTTAAACCTTTCTTAAAACCTTTCTCGAAAGCTTCTTCCATTTGACTAATAGTAATGTGTTCATCTG  >  USA300TCH1516_ALE/1647524‑1647800                                                                                                                                             |                                                                                                                                         atCGCAAAGCAATGCGTAAGTATAAAAGAAATCAAAGAAGAAAATAGATAAAAAAACGGAAGCACTTGTAGGTAAAATAGTCTACGTGCTTCCATTTTTTATTCTAAAAACTACTTTCTAAACATCCATTCATCTGAACGa                                                                                                                                          <  1:38291/141‑1 (MQ=255)           aaTGCGTAAGTATAAAAGAAATCAAAGAAGAAAATAGATAAAAAAACGGAAGCACTTGTAGGTAAAATAGTCTACGTGCTTCCATTTTTTATTCTAAAAACTACTTTCTAACCTTCCATTCATCTGAACGATATTTTTCAg                                                                                                                                <  2:171037/141‑1 (MQ=255)           aaTGCGTAAGTATAAAAGAAATCAAAGAAGAAAATAGATAAAAAAACGGAAGCACTTGTAGGTAAAATAGTCTACGTGCTTCCATTTTTTATTCTAAAAACTACTTTCTAAACATCCATTCCTCTGACCGATATTTTTCAg                                                                                                                                >  2:29005/1‑141 (MQ=255)                   aGTATAAAAGAAATCAAAGAAGCAACAACTTGTAAAAACGGAAGCACTTGTAGGTAAAATAGTCTACGTGCTTCCATTTTTTATTCTAAAAACTACTTTCTAAACATCCATTCATCTGAACGATATTTTTCAGTTAAttct                                                                                                                        >  1:274332/1‑141 (MQ=255)                   aGTATAAAAGAAATCAAAGAAGAAAATAGATAAAAAAACGGAAGCACTTGTAGGTAAAATAGTCTACGTGCTTCCATTTTTTATTCTAAAAACTACTTTCTAAACATCCATTCATCTGAACGATATTTTTCAGTTAAttct                                                                                                                        >  2:340802/1‑141 (MQ=255)                     tataAAAGAAATCAAAGAAGAAAATAGATAAAAAAACGGAAGCACTTGTAGGTAAAATAGTCTACGTGCTTCCATTTTTTATTCTAAAAACTACTTTCTAAACATCCATTCATCTGAACGATATTTTTCAGTTAAttcttc                                                                                                                      <  1:114546/141‑1 (MQ=255)                      ataaaagaaataaaagaaGAAAATAGATAAAAAAACGGAAGCACTTGTAGGTAAAATAGTCTACGTGCTTCCATTTTTTATTCTAAAAACTACTTTCTAAACATCCATTCATCTGAACGATATTTTTCAGTTAATTCTTcc                                                                                                                     <  2:337785/141‑1 (MQ=255)                          aaGAAATCAAAGAAGAAAATAGATAAAAAAACGGAAGCACTTGTAGGTAAAATAGTCTACGTGCTTCCATTTTTTATTCTAAAAACTACTTTCTAAACATCCATTCATCTGAACGATATTTTTCAGTTAATTCTTCCACtt                                                                                                                 <  1:222057/141‑1 (MQ=255)                                         aaaaTAGATAAAAAAACGGAAGCACTTGTAGGTAAAATAGTCTACGTGCTTCCATTTTTTATTCTAAAAACTACTTTCTAAACATCCATTCATCTGAACGATATTTTTCAGTTAATTCTTCCACTTCTGCCAATTGAGCtt                                                                                                  >  1:283166/1‑141 (MQ=255)                                         aaaaTAGATAAAAAAACGGAAGCACTTGTAGGTAAAATAGTCTACGTGCTTCCATTTTTTATTCTAAAAACTACTTTCTAAACATCCATTCATCTGAACGATATTTTTCAGTTAATTCTTCCACTTCTGCCAATTGAGCtt                                                                                                  >  1:81027/1‑141 (MQ=255)                                          aaaTAGATAAAAAAACGGAAGCACTTGTAGGTAAAATAGTCTACGTGCTTCCATTTTTTATTCTAAAAACTACTTTCTAAACATCCATTCATCTGAACGATATTTTTCAGTTAATTCTTCCACTTCTGCCAATTGAGCTTc                                                                                                 <  1:53608/141‑1 (MQ=255)                                            aTAGATAAAAAAACGGAAGCACTTGTAGGTAAAATAGTCTACGTGCTTCCCTTTTTTATTCTAAAAACTACTTTCTAAACATCCATTCATCTGAACGATATTTTTCAGTTAATTCTTCCACTTCTGCCAATTGAGCTTCTg                                                                                               <  1:176422/141‑1 (MQ=255)                                                                  ttGTAGGTAAAATAGTCTACGTTCTTCCATTTTTTATTCTAAAAACTACTTTCTAAGCACCTAGTTAGCTGAACGATATTTTTCAGTTAATTCTTCCACTTCTGCCAATTGAGCTTCTGTTAATTCAAGTGGCTTAAATTc                                                                         <  1:86053/141‑1 (MQ=255)                                                                                gTCTACGTGCTTCCATTTTTTATTCTAAAAACTACTTTCTAAACATCCATTCATCTGAACGATATTTTTCAGTTAATTCTTCCACTTCTGCCAATTGAGCTTCTGTTAATTCAAGTGGCTTAAATTCTATATTTAAACCtt                                                           >  2:131259/1‑141 (MQ=255)                                                                                 tCTACGTGCTTCCATTTTTTTTTTTTTTTTCTACTTTATAAACGCCCATTCATCTGAACGATATTTTTCAGTTAATTCTTCCTCTTCTGCCAATTGAGCTTCTGTTAATTCAAGTGTCTTACTTTCTTTTTTTTTACCttt                                                          >  2:136355/1‑141 (MQ=255)                                                                                    aCGTGCTTCCATTTTTTATTCTAAAAACTACTTTCTAAACATCCATTCATCTGAACGATATTTTTCAGTTAATTCTTCCACTTCTGCCAATTGAGCTTCTGTTAATTCAAGTGGCTTAAATTCTATATTTAAACCTTTCtt                                                       >  2:261371/1‑141 (MQ=255)                                                                                       tGCTTCCATTTTTTATTCTAAAAACTACTTTCTAAACATCCATTCATCTGAACGATATTTTTCAGTTAATTCTTCCACTTCTGCCAATTGAGCTTCTGTTAATTCAAGTGGCTTAAATTCTATATTTAAACCTTTCTTaaa                                                    >  1:47716/1‑141 (MQ=255)                                                                                       tGCTTCCATTTTTTATTCTAAAAACTACTTTCTAAACATCCATTCATCTGAACGATATTTTTCAGTTAATTCTTCCACTTCTGCCAATTGAGCTTCTGTTAATTCAAGTGGCTTAAATTCTATATTTAAACCTTTCTTaaa                                                    >  1:347255/1‑141 (MQ=255)                                                                                              aTTTTTTATTCTAAAAACTACTTTCTAAACATCCATTCATCTGAACGATATTTTTCAGTTAATTCTTCCACTTCTGCCAATTGACCTTCTGTTAATTCAAGTGGCTTAAATTCTATATTTCAACCTTTCTTCAAACCtttt                                             >  2:85114/1‑140 (MQ=255)                                                                                              aTTTTTTATTATAAAAACTACTTTCTAAACATCCATTCATCTGAACGATATTTTTCAGTTAATTCTTCCACTTCTGCCAATTGAGCTTCTGTTAATTCAAGTGGCTTAAATTCTATATTTAAACCTTTCTTAAAACCTTtc                                             >  2:81678/1‑141 (MQ=255)                                                                                               ttttttATTCTAAAAACTACTTTCTAAACATCCATTCATCTGAACGATATTTTTCAGTTAATTCTTCCACTTCTGCCAATTGAGCTTCTGTTAATTCAAGTGGCTTAAATTCTATATTTAAACCTTTCTTAAAACCTTtct                                            >  2:135447/1‑141 (MQ=255)                                                                                                     tttCTAAAAACTACTTTCCAAACATCCATTCATCTGAACGATATTTTTCAGTTAATTCTTCCACTTCTGCCAATTGAGCTTCTGTTAATTCAAGTGGCTTAAATTCTATATTTAAACCTTTCTTAAAACCTTTCTCGAAAg                                      <  1:364174/140‑1 (MQ=255)                                                                                                     aTTCTAAAAACTACTTTCTAAACATCCATTCATCTGAACGTTATTTTTCAGTTAATTCTTCCACTTCTGCCAATTGAGCTTCTGTTAATTCAAGTGGCTTAAATTCTATATTTAAACCTTTCTTAAAACCTTTCTCGAAAg                                      >  2:283296/1‑141 (MQ=255)                                                                                                     aTTCTAAAAACTACTTTCTAAACATCCATTCATCTGAACGTTATTTTTCAGTTAATTCTTCCACTTCTGCCAATTGAGCTTCTGTTAATTCAAGTGGCTTAAATTCTATATTTAAACCTTTCTTAAAACCTTTCTCGAAAg                                      >  2:283244/1‑141 (MQ=255)                                                                                                               ctactTTCTAAACACCCATTCATCTGAACGATATTTTTCAGTTAATTCTTCCACTTCTGCCAATTGAGCTTCTGTTAATTCAAGTGGCTTAAATTCTATATTTAAACCTTTCTTAAAACCTTTCTCGAAAGCTTCTTCCAt                            <  1:358694/141‑1 (MQ=255)                                                                                                                tactTTCTAAACATCCATTCATCTGAACGATATTTTTCAGTTAATTCTTCCACTTCTGCCAATTGAGCTTCTGTTAATTCAAGTGGCTTAAATTCTATATTTAAACCTTTCTTAAAACCTTTCTCGAAAGCTTCTTCCAtt                           >  1:188166/1‑141 (MQ=255)                                                                                                                              ccATTCATCTGAACGATATTTTTCAGTTAATTCTTCCACTTCTGCCAATTGAGCTTCTGTTAATTCAAGTGGCTTAAATTCTATATTTAAACCTTTCTTAAAACCTTTCTCGAAAGCTTCTTCCATTTGACTAATAGTAAt             >  1:4133/1‑141 (MQ=255)                                                                                                                                   cATCTGAACGTTATTTTTCAGTTAATTCTTCCACTTCTGCCAATTGAGCTTCTGTTAATTCAAGTGGCTTAAATTCTATATTTAAACCTTTCTTAAAACCTTTCTCGAAAGCTTCTTCCATTTGACTAATAGTAATGTGtt        <  1:283296/141‑1 (MQ=255)                                                                                                                                   cATCTGAACGTTATTTTTCAGTTAATTCTTCCACTTCTGCCAATTGAGCTTCTGTTAATTCAAGTGGCTTAAATTCTATATTTAAACCTTTCTTAAAACCTTTCTCGAAAGCTTCTTCCATTTGACTAATAGTAATGTGtt        <  1:283244/141‑1 (MQ=255)                                                                                                                                       tGAACGATATTTTTCAGTTAATTCTTCCACTTCTGCCAATTGAGCTTCTGTTAATTCAAGTGGCTTAAATTCTATATTTAAACCTTCCTTAAAATCTTTCTCGAAAGCTTCTTCCATTTGACTAATAGCAATGTGTTCATc    <  1:191369/141‑1 (MQ=255)                                                                                                                                         aaCGATATTTTTCAGTTAATTCTTCCACTTCTGCCAATTGAGCTTCTGTTAATTCAAGTGGCTTAAATTCTATATTTAAACCTTTCTTAACACCTTTCTCGAAAGATTCTTCCCCTTGACTAATAGTAATGTTTTCATCTg  <  2:274332/141‑1 (MQ=255)                                                                                                                                         aaCGATATTTTTCAGTTAATTCTTCCACTTCTGCCAATTGAGCTTCTGTTAATTCAAGTGGCTTAAATTCTATATTTAAACCTTTCTTAAAACCTTTCTCGAAAGCTTCTTCCATTTGACTAATAGTAATGTGTTCATCTg  <  1:340802/141‑1 (MQ=255)                                                                                                                                             |                                                                                                                                         ATCGCAAAGCAATGCGTAAGTATAAAAGAAATCAAAGAAGAAAATAGATAAAAAAACGGAAGCACTTGTAGGTAAAATAGTCTACGTGCTTCCATTTTTTATTCTAAAAACTACTTTCTAAACATCCATTCATCTGAACGATATTTTTCAGTTAATTCTTCCACTTCTGCCAATTGAGCTTCTGTTAATTCAAGTGGCTTAAATTCTATATTTAAACCTTTCTTAAAACCTTTCTCGAAAGCTTCTTCCATTTGACTAATAGTAATGTGTTCATCTG  >  USA300TCH1516_ALE/1647524‑1647800

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: ‑