Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	111,512	A→G	31.3%	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	31.3%	57.7 / 37.0	48	S194S (TCA→TCG)	USA300HOU_RS00520	putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base A (17/16);  new base G (8/7);  total (25/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.17e-01

CTACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAA  >  USA300TCH1516_ALE/111373‑111651                                                                                                                                            |                                                                                                                                            cTACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCat                                                                                                                                            >  1:70284/1‑140 (MQ=255)        aaaaGTTAAAAAAGAAAACAAAAAAAAATAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATACATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAata                                                                                                                                     <  2:2593/139‑1 (MQ=18)           aGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCa                                                                                                                                  >  1:183923/1‑141 (MQ=255)              tAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATCAAGAGCAAGACATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAAtt                                                                                                                               >  1:70547/1‑141 (MQ=18)                  gaagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGATATTCGGCTAAATATCAATTAACt                                                                                                                           >  1:55826/1‑141 (MQ=255)                  gaagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCAAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACt                                                                                                                           >  2:212735/1‑141 (MQ=255)                    agaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTAAATATCAATTAAATaa                                                                                                                         >  1:83550/1‑141 (MQ=255)                       aaaCATAAAAAAAGAAATCGAAACAGTGAAGTTTTTTGCGCAATATAGCAAGTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATACAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatga                                                                                                                      >  2:264685/1‑141 (MQ=17)                        aaCAAAAAAACAGAAATCGAAAACTTTAAGTTTTGTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAatgat                                                                                                                     <  1:297468/141‑1 (MQ=255)                         aCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGCCTAAATATAAAATAACTactaata                                                                                                                    >  2:120100/1‑135 (MQ=17)                          cATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAAagatga                                                                                                                   >  2:194781/1‑141 (MQ=255)                           aTAAAAATAGAAATCGAAAACTTTAAGTTTTTTACGCAATATTGCAATTTTAAAGATTTAATGAATTAAAAAGATGGATAAATATCATATAATCCAGACTTGCCGAGTTATTCAGCTCAATATCAACTAACTAATgatgat                                                                                                                  <  1:1519/141‑1 (MQ=18)                              aaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATtat                                                                                                               <  1:235453/141‑1 (MQ=255)                              aaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATtat                                                                                                               <  1:242326/141‑1 (MQ=255)                              aaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATtat                                                                                                               <  2:320855/141‑1 (MQ=255)                                 aaaGAAATCGAAAACTTTAAGTTTTTTTCTTATTTTAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGCTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAAt                                                                                                            >  2:184483/1‑141 (MQ=18)                                 aaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAAt                                                                                                            >  1:17277/1‑141 (MQ=255)                                 aaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAAt                                                                                                            >  2:348885/1‑141 (MQ=255)                                 aaaGAAATCGAAAACTTTAAGTGTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAAt                                                                                                            <  2:334864/141‑1 (MQ=255)                                      aaTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTaaa                                                                                                       >  1:239028/1‑141 (MQ=255)                                       aTCGAGAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTaaaa                                                                                                      <  2:103750/141‑1 (MQ=255)                                       aTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAGGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAACTATCAATTAACTAATAATGATTATAATGTaaaa                                                                                                      >  2:207528/1‑141 (MQ=18)                                          gAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACaa                                                                                                   <  2:929/141‑1 (MQ=255)                                             aaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAAGAGCAATTAACTAATGATGATTATAATGTAAAACAATTa                                                                                                <  2:87241/141‑1 (MQ=255)                                                tttAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACgc                                                                                             <  1:216861/141‑2 (MQ=255)                                                tttAAGTTTTTTGCGCAATATAGCAATTTTAAAGAGGTAATGACTCAACAGGAGGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACgc                                                                                             <  1:175494/141‑2 (MQ=17)                                                   aaGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAAGaaaa                                                                                          >  2:33468/1‑141 (MQ=255)                                                           tGCGCAATATAGCAATTTTAAAGATGTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGa                                                                                  <  2:201941/141‑1 (MQ=255)                                                              gcAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACaa                                                                               >  1:161046/1‑140 (MQ=255)                                                              gcAAAATAGCAATTTTAAAGATTTAATGAATTCTAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGataa                                                                               >  1:267053/1‑138 (MQ=17)                                                                              aaaGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAAATATGACATAACAAAAAATAAAgcg                                                               >  1:139426/1‑141 (MQ=255)                                                                                   tttAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGaa                                                          <  1:61316/141‑1 (MQ=255)                                                                                     tAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGTCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGc                                                        <  1:237742/141‑1 (MQ=255)                                                                                     tAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGc                                                        <  1:54268/141‑1 (MQ=255)                                                                                            ttATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGATgttgtt                                                 >  1:2084/1‑141 (MQ=255)                                                                                                         aatataaCATATAATCCAGAGATGCCTAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAggg                                    <  1:138642/140‑1 (MQ=255)                                                                                                           tatatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGAGATTACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGaa                                  >  1:289823/1‑141 (MQ=255)                                                                                                             tatCATATAATCCAGAGGTGCCGAGGTATTGAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGAATTAACAACAAATAAAGCGTCGAAGATGTTGTTTAAAGGTAAAGGGAAtt                                >  2:73038/1‑141 (MQ=14)                                                                                                              atCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAAttt                               <  2:183923/141‑1 (MQ=255)                                                                                                               tCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTa                              >  1:213538/1‑141 (MQ=255)                                                                                                                aatatAATCCAGAGATTCCGAGTTATTCAGATCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTaa                             <  2:161046/140‑1 (MQ=255)                                                                                                                           gagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcatca                  <  1:133040/141‑1 (MQ=255)                                                                                                                             ggTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGt                >  1:95887/1‑141 (MQ=255)                                                                                                                             ggTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGt                >  1:7897/1‑141 (MQ=255)                                                                                                                                 ccGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAGAGGTTCATCAGTTGGa            <  1:184483/141‑1 (MQ=255)                                                                                                                                 ccGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGa            >  2:138469/1‑141 (MQ=255)                                                                                                                                          tCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATCAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaaaa   <  2:17277/141‑1 (MQ=255)                                                                                                                                          tCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaaaa   <  1:348885/141‑1 (MQ=255)                                                                                                                                           cAGCTCAATATCAATTAACTACTGATGATTATGATGTAAAACAATTACGCAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTAAAGGGAATTTAAAAGGTTCATCAGTTGGATCTaaaaaaa  >  1:34198/1‑141 (MQ=17)                                                                                                                                            |                                                                                                                                            CTACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAA  >  USA300TCH1516_ALE/111373‑111651

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: ‑