Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	111,512	A→G	36.6%	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	36.6%	61.2 / 52.1	60	S194S (TCA→TCG)	USA300HOU_RS00520	putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base A (16/21);  new base G (8/13);  total (24/36)
Fisher's exact test for biased strand distribution p-value = 7.86e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

CTACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGT  >  USA300TCH1516_ALE/111373‑111637                                                                                                                                            |                                                                                                                              cTACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGAAATATAGCAATTTTAAAGAATTAATAAATTATAAAGATAGTAATATATCATATAATAAAGAGGTGCCGAGTTATTCaa                                                                                                                              >  2:359873/1‑140 (MQ=21)  tACTGAGGAAGTTAAAGAAGAAAGCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCAAGTTATTCGGc                                                                                                                             >  2:363799/1‑141 (MQ=255)  tACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGc                                                                                                                             >  1:13184/1‑141 (MQ=255)    cTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTc                                                                                                                           <  1:6923/141‑1 (MQ=255)      gAGGAAGTTAAATAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCaa                                                                                                                         <  2:334370/141‑1 (MQ=255)       aGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAat                                                                                                                        <  2:222663/141‑1 (MQ=255)        ggAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAata                                                                                                                       <  2:340074/141‑1 (MQ=255)          aaGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATc                                                                                                                     <  1:44947/141‑1 (MQ=255)           aGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTCATTCGGCTAAATATCa                                                                                                                    >  1:305233/1‑141 (MQ=255)             ttAAAAAAGAAAACAAAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAAt                                                                                                                  <  2:352307/141‑1 (MQ=255)               aaaaaaGAAAACATAAAAAAAGAAATCGAAGACCTTAAGTTTTAAAGGATAGATGCCAATGTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTa                                                                                                                <  1:386810/141‑1 (MQ=17)               aaaGAAGAGAGCTGAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAGTGAAGTAGAAATATAGAGATAGATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCTATTa                                                                                                                <  2:47409/141‑1 (MQ=18)                 agaagaAAACATAAAACACGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAAc                                                                                                              <  1:346980/141‑1 (MQ=255)                  ggagaaATCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGTAATATAGCAATTTTAAAGATTTAATGAATTATATAGATGGAGATATAGTATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACt                                                                                                             <  2:172961/139‑1 (MQ=18)                  gaagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACt                                                                                                             <  1:122253/141‑1 (MQ=255)                   aagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTa                                                                                                            >  1:202531/1‑141 (MQ=255)                   aagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGAGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTa                                                                                                            <  2:221612/141‑1 (MQ=255)                     gaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAat                                                                                                          <  1:40563/141‑1 (MQ=255)                     gaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAat                                                                                                          <  1:376485/141‑1 (MQ=255)                        aaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatgat                                                                                                       >  2:1768/1‑141 (MQ=255)                         aCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTTTTTTTTTTAAAAATTTAAAAGATTTAATGAATTATAAAGATGGAAATATATCATATAATCTAGATTTCCTAAGTTATTCGGCTAAATATCAATTAACTActgata                                                                                                      >  2:71660/1‑140 (MQ=9)                         aCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatgatg                                                                                                      <  1:308686/141‑1 (MQ=255)                          cATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATACAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAACATCAATTAACTAAtgatga                                                                                                     >  2:253440/1‑141 (MQ=255)                          cATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATCATCCAGAGCTGCCGAGTTATCCAGCTCACTCTCAATTAACTAAtgctga                                                                                                     >  2:104757/1‑141 (MQ=21)                           aTAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGAAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATgatgat                                                                                                    <  1:131298/141‑1 (MQ=255)                            aaaaaaaaGAAAACGAAAACATTAAGTTTTTTACGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGAtt                                                                                                   <  2:262566/140‑1 (MQ=17)                              aaaaaaTAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATtat                                                                                                 <  1:276077/141‑1 (MQ=255)                                aaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATaa                                                                                               >  1:269684/1‑141 (MQ=255)                                    gAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTa                                                                                           >  1:96088/1‑141 (MQ=255)                                    aaaaTCGAAAAATTCACGTTTTTTGCGCAATATCACACTTTCAAAGATTTAATGAATCATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTAACCCGCCATACCTGAATTAACTAATGATGATTATAATGTa                                                                                           <  2:382713/140‑1 (MQ=17)                                     aaaTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTaa                                                                                          <  1:162864/141‑1 (MQ=255)                                        tCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAAc                                                                                       >  1:179802/1‑141 (MQ=255)                                         cGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATTATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCACTTAACTAATGATTATTATAATGTTTAACa                                                                                      >  2:328288/1‑141 (MQ=21)                                             aaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTa                                                                                  >  1:336992/1‑141 (MQ=255)                                             aaCTTTAAGTTTTTTACGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCTGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTa                                                                                  <  1:317910/141‑1 (MQ=255)                                                tttAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGt                                                                               <  1:180254/141‑1 (MQ=255)                                                    aGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCaaaa                                                                           >  1:299370/1‑141 (MQ=255)                                                      ttttttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGa                                                                         <  2:285427/141‑1 (MQ=255)                                                        ttttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATAACAACCAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGata                                                                       <  1:143423/141‑1 (MQ=17)                                                         tttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGatat                                                                      >  1:118087/1‑141 (MQ=255)                                                                  tataGCAATTTTAAAGAATTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAccg                                                             <  1:247611/141‑2 (MQ=14)                                                                      gCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAccgacga                                                         <  1:199392/141‑6 (MQ=11)                                                                                aGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAATAGTTTACATACCAACAAATAAAGCGcc                                               <  1:76759/141‑1 (MQ=255)                                                                                aGATGTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGcc                                               <  2:351017/141‑1 (MQ=255)                                                                                       atggagtataAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAAGTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtg                                        <  2:269822/135‑1 (MQ=255)                                                                                       aTGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtg                                        >  1:20040/1‑141 (MQ=255)                                                                                        ggAAGTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtgt                                       <  2:113830/140‑1 (MQ=255)                                                                                         gAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtgtt                                      >  1:207133/1‑141 (MQ=255)                                                                                              ataAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGa                                 <  2:96088/141‑1 (MQ=255)                                                                                                aaaGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGaaa                               >  2:336501/1‑141 (MQ=255)                                                                                                  aGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAgg                             <  2:299894/141‑1 (MQ=255)                                                                                                  aGATAGAAATATATCATATAAGCCAGACGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAgg                             <  2:115119/141‑1 (MQ=255)                                                                                                   gATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGt                            >  1:345165/1‑141 (MQ=255)                                                                                                    aTGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAGTTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTa                           <  1:336739/141‑1 (MQ=255)                                                                                                         gaTATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAggg                      >  2:91614/1‑141 (MQ=255)                                                                                                                        acAGAGGTGACGAGTTATTCAGATCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtca       <  2:268287/140‑1 (MQ=255)                                                                                                                          agagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcatc     <  2:218628/141‑1 (MQ=255)                                                                                                                            agGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAg   >  1:374759/1‑141 (MQ=255)                                                                                                                            agGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAg   >  1:257164/1‑141 (MQ=255)                                                                                                                            agGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATAAg   >  1:315016/1‑141 (MQ=255)                                                                                                                             ggTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGt  >  2:224981/1‑141 (MQ=255)                                                                                                                                            |                                                                                                                              CTACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGT  >  USA300TCH1516_ALE/111373‑111637

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑