Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	111,516	C→A	40.8%	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	40.8%	29.3 / 50.3	49	Q196K (CAA→AAA)	USA300HOU_RS00520	putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (12/17);  new base A (8/12);  total (20/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.11e-02

CTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAA  >  USA300TCH1516_ALE/111376‑111656                                                                                                                                              |                                                                                                                                             cggAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCAGCTc                                                                                                                                              <  2:49928/139‑1 (MQ=255) ataaGGAAGTTAAACAAGAAAACATAAAAAAAGAAATCGAAAGCTTTAAGTTTTTTGCGCAATATAACAATTTTAAAGATTTAATGAATTATAAAGATGGAAATATATAATATA‑ATCCAGATGTGCAGAGTCATTCAGCTc                                                                                                                                              <  2:68659/138‑1 (MQ=21)    aGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCGGCTAAat                                                                                                                                           <  2:225356/141‑1 (MQ=255)     ggAAGTTAAAGAAGAAAACATAAAAAAAGGAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCAGCTCAata                                                                                                                                          >  1:50649/1‑141 (MQ=255)     ggAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCAGCTCAata                                                                                                                                          <  1:153918/141‑1 (MQ=255)        aGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAACGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCAGCTCAATATCa                                                                                                                                       >  1:226725/1‑141 (MQ=255)        aGTTAAAGAAAAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCTAGTTATTCGGCTAAATATCa                                                                                                                                       <  2:55920/141‑1 (MQ=17)           tAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCACTACAGGGAGCCTTGTGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAAtt                                                                                                                                    <  1:289975/141‑1 (MQ=17)           tAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAAtt                                                                                                                                    <  2:1738/141‑1 (MQ=255)             aagaagAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCCGAGGTGCCGAGTTATTCAGCTCAATATCAATTaa                                                                                                                                  >  1:380877/1‑141 (MQ=255)              agaagaAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAAc                                                                                                                                 <  2:390457/141‑1 (MQ=255)               gaagaaAATATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACt                                                                                                                                <  2:125138/141‑1 (MQ=255)                  gaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCTGCTAAATTTTAATGaataaac                                                                                                                             >  1:349368/1‑136 (MQ=18)                  gaaAACATAAAAAAAGAAAACGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAat                                                                                                                             <  1:213715/141‑1 (MQ=255)                  aaaaaaaTAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAat                                                                                                                             <  1:51486/140‑1 (MQ=255)                     aaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatgat                                                                                                                          >  1:326964/1‑141 (MQ=255)                     aaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAatgat                                                                                                                          >  1:47786/1‑141 (MQ=255)                      aCATAAAAAAAGAAATCGAAAACTTTAAGATTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAatgatg                                                                                                                         >  2:301760/1‑141 (MQ=255)                         tAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGAtt                                                                                                                      >  1:195385/1‑141 (MQ=255)                            aaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATtata                                                                                                                   <  1:257184/141‑1 (MQ=255)                              aaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATCT‑ATATATATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAAt                                                                                                                 >  1:289776/1‑141 (MQ=18)                              aaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAAt                                                                                                                 <  1:295323/141‑1 (MQ=255)                                aGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGt                                                                                                               <  1:209031/141‑1 (MQ=255)                                  aaaTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTaa                                                                                                             <  2:2604/141‑1 (MQ=255)                                      cGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACa                                                                                                         >  1:321843/1‑141 (MQ=255)                                         aaaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAAtt                                                                                                      >  2:18625/1‑141 (MQ=255)                                           aCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAc                                                                                                    <  1:343310/141‑1 (MQ=255)                                           aCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAc                                                                                                    <  1:217818/141‑1 (MQ=255)                                             tttAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATTATGATTATCATGTAACACAATTACgc                                                                                                  >  2:269758/1‑140 (MQ=18)                                             tttAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGt                                                                                                  <  2:80303/141‑1 (MQ=255)                                             tttAAGTTTTTTGAGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTATCTCATTCTGTGAAGAATGTAAAACAATTACgc                                                                                                  <  2:222193/141‑2 (MQ=17)                                              ttAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTTGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACgca                                                                                                 <  1:206625/141‑3 (MQ=255)                                                    tttttGCGCTATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGat                                                                                           <  2:168142/141‑1 (MQ=17)                                                     ttttGAGAAAAATAGGAATTTTTGAGGTTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGata                                                                                          <  1:372128/141‑1 (MQ=17)                                                        tGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATCTATAATATA‑ATCTAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAGGCAAAAGATATGa                                                                                       >  2:250930/1‑141 (MQ=17)                                                              atatAGAAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAcc                                                                                 <  2:392442/141‑1 (MQ=255)                                                                  aGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATTATTATAATGTAAAACAATTACGCAAAAGATATGATATAccgacg                                                                             <  1:365033/141‑5 (MQ=11)                                                                   gCAATTTTAAAGATTTAATGAATTATGAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACcaacaa                                                                            <  1:301512/141‑1 (MQ=255)                                                                       atttAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATaa                                                                        <  1:20277/140‑1 (MQ=255)                                                                         ttAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATaaaa                                                                      >  2:324840/1‑140 (MQ=255)                                                                                tttAATGAATTATAATGATGGAGATATATCATATA‑ATCCAGAGGTGTCGAGTTATTCAGATCAATATCAATTAACTAATGATGATTATAATGTAAATCAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGaa                                                               <  2:335531/141‑1 (MQ=255)                                                                                        aTTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtgttgt                                                       <  2:226725/141‑1 (MQ=255)                                                                                        aTTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCACCGAAGCtgttgt                                                       >  2:202233/1‑141 (MQ=255)                                                                                             aaaGATGGAGATATATCATATA‑ATCCAGAAGTGCCGAGTTATTCAACTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAAGTAAAATATATGAAATATCAACAAATAAATAACCGAAACTattgttataa                                                  >  2:54125/1‑137 (MQ=14)                                                                                                      gaTATATCATATA‑ATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAggg                                         >  2:395911/1‑141 (MQ=255)                                                                                                                      ccAGAGGTGCCGAGGTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtca                          <  1:116290/141‑1 (MQ=255)                                                                                                                         gagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATAATGGTTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcatca                       <  1:373931/141‑1 (MQ=255)                                                                                                                          agGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAg                      <  1:263851/141‑1 (MQ=255)                                                                                                                             tGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTACAAGGTTCATCAGTTg                   >  2:288165/1‑141 (MQ=255)                                                                                                                                  aGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGatat              >  1:192711/1‑141 (MQ=255)                                                                                                                                          aGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAt      >  1:143531/1‑141 (MQ=255)                                                                                                                                              cAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGaa  <  1:301760/141‑1 (MQ=255)                                                                                                                                              |                                                                                                                                             CTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAA  >  USA300TCH1516_ALE/111376‑111656

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑