Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	111,516	C→A	28.5%	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	28.5%	84.8 / 36.4	56	Q196K (CAA→AAA)	USA300HOU_RS00520	putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (15/25);  new base A (7/9);  total (22/34)
Fisher's exact test for biased strand distribution p-value = 7.65e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.96e-01

TGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAT  >  USA300TCH1516_ALE/111377‑111652                                                                                                                                             |                                                                                                                                         tGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAA‑TTTTAAAAATTTAATGAATTATCCTGATTGATATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCa                                                                                                                                         <  2:411421/141‑1 (MQ=21)   aGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAat                                                                                                                                       <  1:59313/141‑1 (MQ=255)   aGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAA‑TTTTAAAGATTTAATGAAATATGAGTATTGACATGTATAATATAATCGAGAGATGTCGAGATATTCGGCTAAat                                                                                                                                       >  2:364236/1‑141 (MQ=18)     aaaataaaaGAAGAAAACATAAATAAAGACAATTATTAATATAAGGTTTTTGCGCAATATAGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAatat                                                                                                                                     <  2:207757/135‑1 (MQ=21)       aGTTAAAGAAGAAAACATAAAAAAAGATATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCa                                                                                                                                   <  1:374103/141‑1 (MQ=255)       aGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCa                                                                                                                                   <  1:141841/141‑1 (MQ=255)            aagaagAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTaa                                                                                                                              >  2:97365/1‑141 (MQ=255)             agaagaAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAAc                                                                                                                             <  1:222906/141‑1 (MQ=255)             agaagaAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAAc                                                                                                                             <  1:330372/141‑1 (MQ=255)             agaagaAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAAc                                                                                                                             <  1:339404/141‑1 (MQ=255)              gaagaaAACACAAAAAAAGAAATCGAAAACTTTAATTGTGTTGCGCAATATAGCAA‑TTTGAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGCGCCGAGTTATTCAGCTCAATATCAATTAACt                                                                                                                            <  1:999/141‑1 (MQ=21)               aagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTa                                                                                                                           <  2:314429/141‑1 (MQ=255)                   aaaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatga                                                                                                                       >  1:323783/1‑141 (MQ=255)                    aaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatgat                                                                                                                      >  2:281671/1‑141 (MQ=255)                      cATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAAtgatga                                                                                                                    <  2:207434/141‑1 (MQ=255)                        tAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGTTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGAtt                                                                                                                  >  2:230821/1‑141 (MQ=255)                           aaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATATCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATtata                                                                                                               <  1:177461/141‑1 (MQ=255)                                  aaTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTaaa                                                                                                        <  1:2234/141‑1 (MQ=255)                                     cGAAAACTTTAAGTTTTTTGCGCAAGATAGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATAATGATTATAATGTactaca                                                                                                     >  2:397025/1‑136 (MQ=255)                                       aaaaCTTTAAGTTTTTTGCGCAATATAGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGTATATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                                   <  2:410356/141‑1 (MQ=255)                                       aaaaCTTTAAGTTTTTTGCGCAATATAGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                                   >  1:186455/1‑141 (MQ=255)                                       aaaaCTTTAAGTTTTTTGCGCAATATAGACG‑TGTGAAATACTTTCTGCAGGATAAAAATGGAGATATATCATATAACCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                                   <  1:96372/141‑1 (MQ=17)                                        aaaCTTTAAGTTTTTTGCGCAATATAGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAAtt                                                                                                  <  2:381855/141‑1 (MQ=255)                                          aCTTTAAGTTGTTTGCGCAATATAGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAc                                                                                                <  2:216353/141‑1 (MQ=255)                                           cTTTAAGTTTTTTGCGCAATATAGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACg                                                                                               >  2:360698/1‑141 (MQ=255)                                            tttAAGTTTTTTGCGCAATATAGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGt                                                                                              <  1:173042/141‑1 (MQ=255)                                            tttAAGATTTTTGCGCAACATACCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACgc                                                                                              <  1:241320/141‑2 (MQ=17)                                              tAAGTTTTTTGCGCAATATAGCAATTTTTCAAGA‑TTAATTAATTATAAAGATGAAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCaa                                                                                            <  1:375943/141‑1 (MQ=14)                                              tAAGTGTTTTGCGCAATATAGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAGTCCAGAGGTTCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTaa                                                                                            <  2:72364/141‑1 (MQ=255)                                                aGTTTTTTGCGCAATATAGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCaaaa                                                                                          >  2:74503/1‑141 (MQ=255)                                                        gcgcAATATAGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGat                                                                                  >  1:382048/1‑140 (MQ=255)                                                           cAATATAGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGAtata                                                                               >  2:109420/1‑141 (MQ=255)                                                              tataGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACca                                                                            <  1:235094/141‑1 (MQ=255)                                                               atatCAA‑TTTTAAAGATTGAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGATGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACcaa                                                                           <  2:81866/141‑1 (MQ=255)                                                                  gCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAccgacga                                                                        >  1:207082/1‑136 (MQ=11)                                                                       ttttAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATaa                                                                    <  2:339831/141‑1 (MQ=255)                                                                        tttAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATaaa                                                                   <  1:190171/141‑1 (MQ=255)                                                                           aaaGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAgcg                                                                <  2:347422/141‑1 (MQ=255)                                                                           aaaGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAgcg                                                                >  1:286755/1‑141 (MQ=255)                                                                             aGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGcc                                                              <  2:220373/141‑1 (MQ=255)                                                                                  tAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAAATATGACATACCAACAAATAAAGCGACGACGc                                                         >  2:23996/1‑141 (MQ=255)                                                                                   aaTGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCt                                                        <  2:369034/141‑1 (MQ=255)                                                                                    aTGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtg                                                       <  1:359851/141‑1 (MQ=255)                                                                                     tGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCCAAGCtgt                                                      <  2:288569/141‑1 (MQ=255)                                                                                       aaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtgttg                                                    <  1:358359/141‑1 (MQ=255)                                                                                                      aatatatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAggg                                     <  2:41172/140‑1 (MQ=255)                                                                                                             cATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCAGTTATTGAAAGGTACAGGGAATTTaa                              >  2:357858/1‑141 (MQ=255)                                                                                                                    tCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtc                       >  1:13072/1‑141 (MQ=255)                                                                                                                     ccAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGAAATTTAAAAGGTtca                      >  2:200865/1‑141 (MQ=255)                                                                                                                        gagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcatca                   >  1:224892/1‑141 (MQ=255)                                                                                                                          ggTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGt                 >  1:406674/1‑141 (MQ=255)                                                                                                                           gTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGCCATACTAACAAATAAAGCACCGAAACTGTTGTTGAAAGGTACAGTGAATTTAAAAGGTtctttcgtt                >  2:84241/1‑134 (MQ=14)                                                                                                                                 aGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGatat          <  2:286755/141‑1 (MQ=255)                                                                                                                                     aTTCAGCTCAATATCAATTAACTAATGCTGCTTATAATGAAAAACAATGACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaa      >  1:82008/1‑141 (MQ=255)                                                                                                                                       tCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCAGTTGTTGAAAGGTACAGGAAATTTACAAGGTTCATCAGTTGGATATaaaaaa    >  2:81661/1‑141 (MQ=255)                                                                                                                                         aGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAt  <  1:67311/141‑1 (MQ=255)                                                                                                                                             |                                                                                                                                         TGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAT  >  USA300TCH1516_ALE/111377‑111652

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: ‑