Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	111,516	C→A	27.1%	Q196K (CAA→AAA)	USA300HOU_RS00520 →	putative lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	111,516	0	C	A	27.1%	46.7 / 18.7	37	Q196K (CAA→AAA)	USA300HOU_RS00520	putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (10/17);  new base A (4/6);  total (14/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.44e-01

GAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCT‑CAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAA  >  USA300TCH1516_ALE/111381‑111649                                                                                                                                         |                                                                                                                                      gAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCT‑CAata                                                                                                                                   <  1:39494/140‑1 (MQ=255) gAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCT‑CAata                                                                                                                                   <  1:225672/140‑1 (MQ=255)   aGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCAAGAGGTGCCGAGTTATTCGGCT‑AAATATc                                                                                                                                 >  1:14780/1‑140 (MQ=255)            agaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCT‑CAATATCAATTAACTa                                                                                                                        <  1:187310/140‑1 (MQ=255)             gaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCT‑AAATATCAATTAACTaa                                                                                                                       >  1:142995/1‑140 (MQ=255)                aaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCT‑AAATATCGATTAACTAatga                                                                                                                    <  1:50300/140‑1 (MQ=255)                aaCATAAAAAAAAAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCT‑AAATATCAATTAACTAatga                                                                                                                    <  1:50268/140‑1 (MQ=255)                 aCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCACAGGTGCCGAGTTATTCAGCT‑AAATATCAATTAACTAaagat                                                                                                                   >  1:30080/1‑140 (MQ=255)                   aTAAAAAAATAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTATAGATGTAATGAATTATAAAGATGGAGATATATCTTATGATCCAGAGGTGCCGAGTTATTCAGCT‑CAATATCAATTAACTAAtgatga                                                                                                                 <  2:118290/140‑1 (MQ=21)                       aaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAATATTTAATGAATTATAAAGATGGAGAGATATCATATAATCCATAGGTGCCGAGTTATTCAGCT‑CAATATCAATTAACTAATGATGATtat                                                                                                             <  2:14172/140‑1 (MQ=255)                       aaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCT‑CAATATCAATTAACTAATGATGATtat                                                                                                             <  1:221013/140‑1 (MQ=255)                       aaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCT‑CAATATCAATTAACTAATGATGATtat                                                                                                             <  1:222229/140‑1 (MQ=255)                          aaGAAAGCGACAAATTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATACCATATAATCCAGAGGTGCCGAGTTATTCGGCT‑AAATATCAATTAACTAATGATGATTATAAt                                                                                                          <  2:127091/140‑1 (MQ=17)                           aGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCT‑CAATATCAATTAACTAATGATGATTATAATg                                                                                                         <  1:84299/140‑1 (MQ=255)                              aaTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCT‑CAATATCAATTAACTAATGATGATTATAACGTaa                                                                                                      <  1:207927/140‑1 (MQ=255)                               aTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGAGTTAATGAATTATAAAGATGGAGATATCTCATATAATCTAGAGGTGCCGAGTTATTCTGCT‑AAATATCAATTAACTAATGATGATTATAATGTaaa                                                                                                     >  1:58905/1‑140 (MQ=18)                                 cGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGATAAATTCATCT‑CAATATCAATTAACTAATGATGATTATAATGTAAAAc                                                                                                   >  1:125279/1‑140 (MQ=255)                                    aaaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCT‑AAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                                <  1:81077/140‑1 (MQ=255)                                     atcTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCT‑CAATATCAATTAACTAATGATGATTATAATGTAAAACAAtt                                                                                               <  1:47275/138‑1 (MQ=255)                                         ttAAGTTTTGTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCT‑AAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACgc                                                                                           <  2:272600/140‑2 (MQ=255)                                                    gcgcAATATAGAAATTTTAAAGATTTAGTGGTTTATAAAGATGGAGATAGATCATATAATCCGGAGAGGCAGAGTTATTCAGCG‑CAATATCAATTAACTGATGATGATTATAATGTAAAACAATTACGTTAAAGATATGa                                                                                >  2:5995/1‑140 (MQ=18)                                                     cgcAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCT‑CAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGAc                                                                               >  2:20590/1‑140 (MQ=255)                                                      gcAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCT‑CAATATCAATTAGCTAATGATGATTATAATGTAAAACAATTACTTTAAATATATAACa                                                                              >  1:204032/1‑140 (MQ=21)                                                         attcaGCAATTTTAAAGATTTAATGAATTATAAAGTTGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCT‑AAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgatatgatatcc                                                                           <  2:195207/136‑3 (MQ=11)                                                               cAATTTTAAAGATTTAATGAATTATAAAGTCGCAGATATATGATCAAGAACAGATGTGCCGGGTT‑CTCACCTACGATACCAATTCCATTACTATTATTATAATGTAAAACAATTACGTAAAAGATATGACATACcaacaa                                                                     <  1:287342/140‑1 (MQ=12)                                                               cAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCT‑CAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACcaacaa                                                                     <  1:262677/140‑1 (MQ=255)                                                                            ttAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCT‑CAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGaa                                                        <  1:85343/140‑1 (MQ=255)                                                                                                 gaTATATCATATAATCCAGAGGTGCCGAGTTATTCAGCT‑CAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAgg                                   <  2:63405/140‑1 (MQ=255)                                                                                                      atCATATAATCCAGAGGTGCCGAGTTATTCAGCT‑CAATATCAATTAACTAATGATGATTATAATGTAAATCAATTACGTAAAAGATATGACATACCAACAAATAAAACGCCGAAGCTGTTGTTGAAAGGTACAGGGAAtt                              >  1:8209/1‑140 (MQ=255)                                                                                                                ccAGAGGTGCCGAGTTATTCAGCT‑CAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtc                    <  1:178773/140‑1 (MQ=255)                                                                                                                ccAGAGGTGCCGAGTTATTCAGCT‑CAATATCAATTAACTAATGATGATTATAATGTAAAACAAATACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtc                    >  1:263037/1‑140 (MQ=255)                                                                                                                    agGTGACGAGTTATTCAGCT‑CAATATCAAATAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATAGGACATACTAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcatca                <  2:1016/140‑1 (MQ=255)                                                                                                                       tGCCGAGTTATTCAGCT‑CAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAGGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAACTGTTGTTGAAAGGCACAGAGAAATTAAAAGGTgcatgattg             >  2:239534/1‑135 (MQ=17)                                                                                                                        gCCGAGTTATTCAGCT‑CAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGtgg            >  2:74007/1‑138 (MQ=255)                                                                                                                            aGTTATTCAGCT‑CAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGata        <  1:156043/140‑1 (MQ=255)                                                                                                                               tATTCAGCT‑CAATATCAATTAACTAATGATGATTATAATGTAAAACCATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAACTGTTGGTGAAAGGTACAGGGAATGTAAAAGTGTCATCAGTTGGCAATaa     >  2:14865/1‑140 (MQ=17)                                                                                                                                  tCAGCT‑CAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGAAAAACATATGACATACCAGCACATAAAGCGCCGAAGATGTTGATAAAAGGAACAGGGAATTTAAAAGGCTCATCAGTGAGATATaaaaa  >  2:15500/1‑140 (MQ=14)                                                                                                                                         |                                                                                                                                      GAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCT‑CAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAA  >  USA300TCH1516_ALE/111381‑111649

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑