Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	111,512	A→G	28.5%	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	28.5%	82.9 / 35.4	56	S194S (TCA→TCG)	USA300HOU_RS00520	putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base A (16/24);  new base G (7/9);  total (23/33)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.68e-01

TCTACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAT  >  USA300TCH1516_ALE/111372‑111652                                                                                                                                              |                                                                                                                                             tCTACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATAGAAAACTTTAAGTTTTTTCCGCAATATAGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATTAAAAGGTGCCCGGTTATTCa                                                                                                                                              >  2:195957/1‑141 (MQ=255)    aCTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAACTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCt                                                                                                                                           >  2:235094/1‑141 (MQ=255)      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                                                                                                                             <  1:339404/141‑1 (MQ=255)                  agaagaAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAAc                                                                                                                             <  1:330372/141‑1 (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                                                                >  1:286755/1‑141 (MQ=255)                                                                                aaaGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAgcg                                                                <  2:347422/141‑1 (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)                                                                                                                                              |                                                                                                                                             TCTACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAA‑TTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAT  >  USA300TCH1516_ALE/111372‑111652

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: ‑