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%	77.7 / 28.8	51	S194S (TCA→TCG)	USA300HOU_RS00520	putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base A (18/18);  new base G (7/8);  total (25/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAA  >  USA300TCH1516_ALE/111379‑111647                                                                                                                                      |                                                                                                                                        aGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATACAGAGGTGCCGAGTTATTCAGCTCaa                                                                                                                                   >  1:34960/1‑140 (MQ=255)  ggAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAat                                                                                                                                  <  1:15796/140‑1 (MQ=255)  ggAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAat                                                                                                                                  <  1:316510/140‑1 (MQ=255)   gAAGTTAAAGAAGAAAACATAAAAAAATTAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAata                                                                                                                                 <  1:629173/140‑1 (MQ=255)   gAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGATGCCGAGTTATTCAGCTCAata                                                                                                                                 >  1:681911/1‑140 (MQ=255)    aaattAAAGAAGAAAACATAAAAAAAGAAATCGAATACTTTTAGTTTTTTGCGCAATATAGTAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAatat                                                                                                                                <  1:103618/137‑1 (MQ=17)     aGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGAAGATATATCATATAATTCAGAGATACCGAGTTATTCAGCTCAATATc                                                                                                                               >  1:247462/1‑140 (MQ=255)      gTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCa                                                                                                                              <  1:524963/140‑1 (MQ=255)      gTTAAAGAAGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGGGATAAATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCa                                                                                                                              <  1:147450/140‑1 (MQ=255)         aaaGAAGAGAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCATTTTAGCAATTTTAAAGATTTTATGATTTTTTATGTTGGTGGTATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAAtt                                                                                                                           <  1:56802/140‑1 (MQ=17)         aaaGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTACCGAGTTATTCGGCTAAATATCAAtt                                                                                                                           >  1:276544/1‑140 (MQ=255)          aagaagAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTa                                                                                                                          >  1:470068/1‑140 (MQ=255)            gaagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAAc                                                                                                                        <  1:73499/140‑1 (MQ=255)            gaagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAAc                                                                                                                        <  1:632397/140‑1 (MQ=255)               gaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAACATGGAGATATATCATATAATCCAGAGATGCCGAGTTATTCGGCTCAATATCAATTAACTaa                                                                                                                     >  1:488842/1‑140 (MQ=255)                aaaaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATAAATTAACTAat                                                                                                                    >  1:766647/1‑140 (MQ=255)                      tAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATtatgat                                                                                                              >  1:435829/1‑140 (MQ=255)                         aaaaaGAAATCGAAAACTTTACGTTTTTTGCGCAATATAGCTATTTTAAAGATTTAATGAATTATAAATATGGAGATATATAATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATtat                                                                                                           <  1:219358/140‑1 (MQ=255)                         aaaaaGAAATCGAAAACTTTAAGTTTTTTGCGTAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATtat                                                                                                           <  1:436105/140‑1 (MQ=255)                            aaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATACAAATTATAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAAt                                                                                                        <  1:328974/140‑1 (MQ=255)                              gAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTGATGATGATTATAATGt                                                                                                      >  1:513308/1‑140 (MQ=255)                                aaTCGAATACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTCAATGAATCATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATCATGATTATAATGTaa                                                                                                    <  1:564940/140‑1 (MQ=17)                                aaTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATAGCAATTAACTAATGATGATTATAATGTaa                                                                                                    <  1:150677/140‑1 (MQ=255)                                  tCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAATGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTaaaa                                                                                                  <  1:436538/140‑1 (MQ=255)                                      aaaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAAATATAAAGAAGGTTAAAGATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                              <  1:752749/140‑1 (MQ=18)                                       aaCTTTAAGTTTTTTGCGCAATATAGTAATTTTAAAGATTTGATGTATTATAAAGTTGGAGATATATCATATAATCTAGAGGTGCCGAGTTATTCAGCTCAATATCAATTATTTAATGATGATTATAATGTAAAACAttt                                                                                             >  1:209213/1‑140 (MQ=18)                                               gTTTTTTTCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCACAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTaaaa                                                                                     <  1:202932/140‑1 (MQ=255)                                                         gaaTATAGCAATCTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACAt                                                                           <  1:62874/139‑1 (MQ=255)                                                               aGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACcaac                                                                     <  1:527598/140‑1 (MQ=255)                                                                 taaTTTTAAACATTTAATGAATTATAAAGATTGATATATATCATATAATCCAGAGGTGCCGAGTTATTCATCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACcaacaa                                                                   <  1:70954/139‑1 (MQ=255)                                                                 cAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACcaacaa                                                                   <  1:75864/140‑1 (MQ=255)                                                                  aaTTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACcgacgag                                                                  >  1:643473/1‑137 (MQ=11)                                                                  aaTTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACaaa                                                                  <  1:706759/140‑1 (MQ=255)                                                                         aaGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAgcg                                                           >  1:416384/1‑140 (MQ=255)                                                                          aGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCAACGAATAAAgctc                                                          >  1:290859/1‑138 (MQ=11)                                                                             tttAATGAATTATAAAGATGGAGATATATCATAGAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATAACATACCAACAAATAAAGCGCCGa                                                       >  1:758307/1‑140 (MQ=255)                                                                                 aTGAATTATAAAGATGGAGATATATCATATAATCCAGAGGCGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAGGCt                                                   >  1:654549/1‑140 (MQ=255)                                                                                            aGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGAAAAAGATATGACATACAAACAAATAAAGCAACAAAGCTATTATTGAAAg                                        >  1:476775/1‑140 (MQ=14)                                                                                                   gaTATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAgg                                 >  1:730978/1‑140 (MQ=255)                                                                                                      atatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGaa                              <  1:730705/140‑1 (MQ=255)                                                                                                      atatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGaa                              <  1:599591/140‑1 (MQ=255)                                                                                                      atatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGATGAAAGGTACAGGGaa                              >  1:129061/1‑140 (MQ=255)                                                                                                      atatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGAAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGaa                              >  1:194550/1‑140 (MQ=255)                                                                                                               aaTCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAACGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAgg                     >  1:56014/1‑140 (MQ=255)                                                                                                                aTCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGCATTTAAAAGGt                    >  1:156990/1‑140 (MQ=255)                                                                                                                 tCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGtt                   >  1:715592/1‑140 (MQ=255)                                                                                                                   caaagGTGCCGAATTATTCAGCTCAATATCAATTAACTAATGAAGAATATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtca                 <  1:725180/137‑1 (MQ=255)                                                                                                                    agagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcat                >  1:208019/1‑140 (MQ=255)                                                                                                                     gagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcatc               >  1:43625/1‑140 (MQ=255)                                                                                                                        gTGCGGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGAACAGGGAATTTAGAAGGTTCATCAGt            >  1:546248/1‑140 (MQ=255)                                                                                                                                  aatCAACTCAATAACAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGAAATGACATACCAACAAATAAAGCGCCGAAGCTGATGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaa  <  1:229474/138‑1 (MQ=14)                                                                                                                                      |                                                                                                                                        AGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAA  >  USA300TCH1516_ALE/111379‑111647

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: ‑