Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,028,049	A→G	54.2%	V199A (GTT→GCT)	USA300HOU_RS10230 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,028,049	0	A	G	54.2%	8.2 / 68.5	59	V199A (GTT→GCT)	USA300HOU_RS10230	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (16/11);  new base G (12/20);  total (28/31)
Fisher's exact test for biased strand distribution p-value = 1.21e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.60e-01

GCATTGAACCAATTGTTCTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATT  >  USA300TCH1516_ALE/2027913‑2028188                                                                                                                                         |                                                                                                                                            gCATTGAACCAATTGTTCTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCttt                                                                                                                                         >  1:278265/1‑141 (MQ=255)    ttGAACCAATTGTTCTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATTTTGTTATTTTAAACTTtata                                                                                                                                      >  1:519130/1‑141 (MQ=255)      gAACCAATTGTTCTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATg                                                                                                                                    <  1:415160/141‑1 (MQ=255)      gAACCAATCGTTCTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATg                                                                                                                                    <  1:415374/141‑1 (MQ=255)        tccAATTGTTCTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGAt                                                                                                                                  <  2:194584/140‑1 (MQ=255)           aaTTGTTCTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGAtttt                                                                                                                               >  1:126740/1‑141 (MQ=255)            aTTGTTCTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGAttttt                                                                                                                              >  2:184290/1‑141 (MQ=255)              tGTTCTAATGTAGTGGTTCATCGATAAGTCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTttca                                                                                                                            <  2:242312/141‑1 (MQ=255)               gTTCTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCCACTTTATATGATTTttcat                                                                                                                           >  1:691671/1‑141 (MQ=255)                ttCTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTttcatt                                                                                                                          >  1:422899/1‑141 (MQ=255)                ttCTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCAACGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTttcatt                                                                                                                          <  2:734078/141‑1 (MQ=255)                  cTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTttcagtcc                                                                                                                        >  1:731841/1‑140 (MQ=255)                     aTGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGt                                                                                                                     <  1:750375/141‑1 (MQ=255)                      tGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTa                                                                                                                    <  2:399347/141‑1 (MQ=255)                      tGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACCGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTa                                                                                                                    <  2:95890/141‑1 (MQ=255)                          gTGGTTCATCGATAAATCAGCTCTACGTCGCCGATACACTTTGATACGGAGATATTATCTGTATAGTTATCCGGTTTCATCATGTCTTTAATATGAATATTTTTATTTTCAGCTTTATATGGTTGTTCATTCACGTAAGTa                                                                                                                <  1:356626/141‑1 (MQ=255)                            ggTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACt                                                                                                              >  2:29067/1‑141 (MQ=255)                                cATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCa                                                                                                          <  2:631697/141‑1 (MQ=255)                                  tCGATAAATCACCTCTACTTCTCCGATAAACGTTGATACGTAGATATTAACGGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCGTTATATGATTTTTCATTCACGTAAGTACTTCCATa                                                                                                        <  2:278324/141‑1 (MQ=255)                                  tCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATa                                                                                                        <  2:569470/141‑1 (MQ=255)                                  tCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATa                                                                                                        <  2:675415/141‑1 (MQ=255)                                   cGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATTATTTTTCATTCACTTAAGTACTTCCAtca                                                                                                       >  2:400082/1‑139 (MQ=255)                                   cGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATaa                                                                                                       >  2:71075/1‑141 (MQ=255)                                         aTCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCCTAAAAagca                                                                                                 >  2:108056/1‑141 (MQ=255)                                         aTCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAagca                                                                                                 <  1:644483/141‑1 (MQ=255)                                          tCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCGCGTAAGTACTTCCATAAGAagcag                                                                                                >  1:587757/1‑141 (MQ=255)                                           cACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAagcagc                                                                                               >  1:719093/1‑141 (MQ=255)                                            aCCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCt                                                                                              <  2:611242/141‑1 (MQ=255)                                                ctACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACAt                                                                                          <  2:743830/141‑1 (MQ=255)                                                 tACGTTTGCTATAAACGTTGATACGTAGATATTAACTGTATAGTTATGCGGTTTCATCATTTCTTCAATATTAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATg                                                                                         <  2:23556/141‑1 (MQ=255)                                                  aCGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGt                                                                                        <  1:633412/141‑1 (MQ=255)                                                   cGTCTCCGATAAACGTAGATACGTTGATATTAACTTTAGAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAGGCAGCTACATGTa                                                                                       >  1:188911/1‑141 (MQ=255)                                                    gTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTaa                                                                                      <  1:678782/141‑1 (MQ=255)                                                       tcCGATAAACTGTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAAtt                                                                                   <  1:565774/141‑1 (MQ=255)                                                             aaaCGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTAATGTAGGTACGTCCATAAAAAGCAGCTACATGTAAATTAATAtt                                                                             >  1:532006/1‑141 (MQ=255)                                                               aCGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATAGTTAGTTGCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAACATCAGCTACATTTAAATTAATAtttt                                                                           >  2:634588/1‑139 (MQ=255)                                                                 tttGATACGGAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTaa                                                                         <  2:442537/140‑1 (MQ=255)                                                                               atTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAatat                                                           <  1:327795/141‑1 (MQ=255)                                                                               atTAACTGTATAGTTATCCGGTTTCATCATTTCTTAAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTAATTCCATAAAAAGCAGCTACATTTAAATTAATATTGTAATTAACAGGCAatat                                                           >  2:104241/1‑141 (MQ=255)                                                                                 tAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATaa                                                         <  1:118095/141‑1 (MQ=255)                                                                                  aaCTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTTTTTTTTTTTATTACTTCCATAAAAAGCAACTACATGTAAATTAATATTGTAATTAACCGGCActatctc                                                        >  2:442192/1‑138 (MQ=255)                                                                                   aCTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTATATTAATATTGTAGTTAACCGGCCATATAAcc                                                       >  1:88856/1‑141 (MQ=255)                                                                                   aCTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAAcc                                                       >  1:93034/1‑141 (MQ=255)                                                                                     tGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAACTTAATATTGTAATTAACCAGCAATATAACCTg                                                     >  2:496296/1‑141 (MQ=255)                                                                                       tataGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATATAAATTAATATTCTAATTAACCGACAATACAAcataca                                                   >  2:17672/1‑136 (MQ=255)                                                                                                ccGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTa                                          >  2:601512/1‑141 (MQ=255)                                                                                                ccGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACAGAAAAAACAACCTGCACTTTACCTa                                          <  2:285363/141‑1 (MQ=255)                                                                                                    tttCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAACATAATCTCCACTTTACATAAAAt                                      >  2:712636/1‑141 (MQ=255)                                                                                                    tttCATCATTTCTTCAATATGAATATTGTTATTGTCAGCCTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAAt                                      <  1:108056/141‑1 (MQ=255)                                                                                                       catcatTTCTTCAATATGAATATTGTTATCTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAAtgtg                                   <  2:584785/141‑1 (MQ=255)                                                                                                          catTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCt                                <  1:436534/141‑1 (MQ=255)                                                                                                              tcttcAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTaaca                            <  2:496782/141‑1 (MQ=255)                                                                                                                 tcAATAGGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTAATTCCATAAAAAGCAGCTACATGTAAATTACTTTTGTAATTAACCGTCAATATAACATGCACTTTACTTAAACTGTGTCTacacaca                         >  2:598972/1‑135 (MQ=255)                                                                                                                  cAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTATAATTAACAGACAATATAACCTACACTTTACCTAAAATGTGTCTAAcaacaa                        >  2:369684/1‑141 (MQ=255)                                                                                                                      atGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGt                    <  2:409677/141‑1 (MQ=255)                                                                                                                                  aTTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCtt        <  2:126740/141‑1 (MQ=255)                                                                                                                                  aTTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAACAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCtt        >  2:502003/1‑141 (MQ=255)                                                                                                                                   ttttCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTa       >  1:30979/1‑141 (MQ=255)                                                                                                                                    tttCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTaa      <  1:471/141‑1 (MQ=255)                                                                                                                                        aaCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATAtt  <  1:761696/141‑1 (MQ=255)                                                                                                                                         |                                                                                                                                            GCATTGAACCAATTGTTCTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATT  >  USA300TCH1516_ALE/2027913‑2028188

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑