Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	111,512	A→G	37.6%	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	37.6%	40.4 / 49.2	52	S194S (TCA→TCG)	USA300HOU_RS00520	putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base A (11/21);  new base G (7/12);  total (19/33)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.93e-01

CTACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAT  >  USA300TCH1516_ALE/111373‑111652                                                                                                                                             |                                                                                                                                             cTACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATCTCAAAAG‑CACTATACATGCCGAGTTATTCAg                                                                                                                                             <  2:388734/141‑1 (MQ=25) cTACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCAg                                                                                                                                             <  2:206317/141‑1 (MQ=255)    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)                                                                                                                                             |                                                                                                                                             CTACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATA‑ATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAT  >  USA300TCH1516_ALE/111373‑111652

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: ‑