Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	111,512	A→G	29.0%	S194S (TCA→TCG)	USA300HOU_RS00520 →	putative lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	111,512	0	A	G	29.0%	57.0 / 28.4	45	S194S (TCA→TCG)	USA300HOU_RS00520	putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base A (17/15);  new base G (4/9);  total (21/24)
Fisher's exact test for biased strand distribution p-value = 2.05e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.50e-01

CTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAA  >  USA300TCH1516_ALE/111376‑111651                                                                                                                                         |                                                                                                                                            ctaatgAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCta                                                                                                                                         <  1:166434/136‑2 (MQ=255) atGAGGAAGTGAAAGAAGAAAGGCTAAAAAAAGAAATCGAAAACTTTAAATTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTc                                                                                                                                         <  1:227583/140‑1 (MQ=25)     ggAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAata                                                                                                                                     <  2:131857/141‑1 (MQ=255)        aGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCa                                                                                                                                  >  2:108535/1‑141 (MQ=255)        aGTGAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCa                                                                                                                                  <  2:42659/141‑1 (MQ=255)               gaagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTGTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACt                                                                                                                           <  2:74531/141‑1 (MQ=255)                            aaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGCGTTATTCAGCTCAATATCAATTAAATAATGATGataata                                                                                                              >  1:244126/1‑141 (MQ=255)                             aaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATaa                                                                                                             <  1:240617/141‑1 (MQ=255)                              aaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTGTAAt                                                                                                            >  1:43907/1‑141 (MQ=255)                                aGAAGTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCCTATAATCCAGAGGTGCCGAGTTATTTGGCTAAATATCAATTAACTAATGTTGAttttgttat                                                                                                          >  2:102145/1‑134 (MQ=18)                                  aaaTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATCATGATTATAATGTaa                                                                                                        >  1:58274/1‑141 (MQ=255)                                      cGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAGTGTAAAACa                                                                                                    >  2:58404/1‑141 (MQ=255)                                      cGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGAGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACa                                                                                                    >  1:215145/1‑141 (MQ=255)                                       gAAAAGTTTAAGTTTTTTGGGCAATATAGAAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACaa                                                                                                   <  2:108266/141‑1 (MQ=255)                                        aaaaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATTGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                                  <  1:233624/141‑1 (MQ=255)                                          aaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTa                                                                                                <  1:273862/141‑1 (MQ=255)                                             tttAAGTTTTTTGCGCAATATCGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGt                                                                                             <  1:48050/141‑1 (MQ=255)                                             tttAAGTTTTTTGCGCAATATAGAAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACgc                                                                                             <  1:157523/141‑2 (MQ=255)                                             tttAAGCTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACgc                                                                                             <  1:107894/141‑2 (MQ=255)                                               tAAGTTTTTTGAGCAATATATCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTaa                                                                                           <  1:260995/141‑1 (MQ=255)                                               tAAGTTTTGTGCGAAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATAGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACgcaa                                                                                           <  2:48403/141‑4 (MQ=17)                                                 aGTTTTTTGCGCAATATAGCAATTTTAAAGCTTTAATGCCAGAAAAAGATGGAGATATATCATATAATTCATAGGTGCCGCGGTATTCGGCTAAATATCAATTAACTAATGCTGTTTATAATGTAAATCACTTACGCaaaa                                                                                         >  2:64295/1‑141 (MQ=17)                                                               aataGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACca                                                                           <  1:201839/140‑1 (MQ=255)                                                                ataGCAATTTTAAAGATTTAATGAATTATAAAAATGGAGATATATAAGATAATCCAGAGGTGCCGAGTGATTCGGCTAAATATAAATTAACTAATGATGATTATAACGTAAAACAATTACGCAAAAGATATGATATAccga                                                                          <  2:125118/141‑3 (MQ=14)                                                                   acAATTTTAAAGATTTAATGAATTATAAAGATGGAAATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAccgacga                                                                       <  2:27715/140‑6 (MQ=11)                                                                           aaaGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGACGAGTTCTTCAGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAAATAATAGAAATAACATACTAAAAAATAAAgag                                                               >  2:183147/1‑139 (MQ=17)                                                                           aaaGAATTAATGAAGTAAAAAGATGGAGATAAAGGAGATAATCCAGAGGTGGCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAgcg                                                               <  2:28565/141‑1 (MQ=17)                                                                            aaGATTTAATGAATTATAAAGATTGAGATATATCATATAATCCAGAGGTGCCGAGTTATGCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAgcgc                                                              >  1:211189/1‑141 (MQ=255)                                                                            aaGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATACAgcgc                                                              >  1:251648/1‑141 (MQ=255)                                                                            aaGATTTAATGAACTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAgcgc                                                              <  1:253303/141‑1 (MQ=255)                                                                             aGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTCTAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAACGcc                                                             >  2:96130/1‑141 (MQ=255)                                                                                     tGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtgt                                                     <  1:231350/141‑1 (MQ=255)                                                                                      gAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAACGCGCCGAGGCtgtt                                                    >  1:42881/1‑141 (MQ=255)                                                                                        aTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCagttgt                                                  >  2:112357/1‑141 (MQ=255)                                                                                         ttATAAAGATGGAGATATATCATATAATCCGGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTgttgtt                                                 >  1:91746/1‑141 (MQ=255)                                                                                         ttATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTgttgtt                                                 >  1:99477/1‑141 (MQ=255)                                                                                           ataAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGa                                               <  1:35627/141‑1 (MQ=255)                                                                                              aaGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATCATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAg                                            >  2:178459/1‑141 (MQ=255)                                                                                               aGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAgg                                           >  2:119581/1‑141 (MQ=255)                                                                                                      aatatatTATATAATTCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAggg                                    <  2:235584/140‑1 (MQ=255)                                                                                                            taatatAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAGAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTa                              <  1:287194/139‑1 (MQ=255)                                                                                                               tataATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTCTAGAAAGGTACAGGAAATTTaaaa                           >  2:117833/1‑141 (MQ=255)                                                                                                                     ccAGAGGTGCCGAGTTATTCAGCTCAATATAAATTAAAAAAAGATAATTATAATGTAAAAAAAATACGTAAAAAATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtca                     >  1:280120/1‑141 (MQ=17)                                                                                                                           gTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGtt               >  1:35275/1‑141 (MQ=255)                                                                                                                                        cAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaaaaa  <  1:149865/141‑1 (MQ=255)                                                                                                                                         |                                                                                                                                            CTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAA  >  USA300TCH1516_ALE/111376‑111651

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: ‑