Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	47,736	G→A	7.5%	R386C (CGC→TGC)	hin_2 ←	DNA‑invertase hin

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	47,736	0	G	A	7.5%	156.4 / 3.5	53	R386C (CGC→TGC)	hin_2	DNA‑invertase hin
Reads supporting (aligned to +/- strand):  ref base G (20/29);  new base A (2/2);  total (22/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.79e-01

AAATAGATTCCTATAAGATTTTTATCTTTCGTAATGTGAATGGTTTCAATATAGGGGTACAATATGTTTAACGTGAAACGTTTTTGAATAATATTTTGAATGATGTGTTGTATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGATGCCTTGTGCCAACTTTTCTATCAGTTGTTCTTGAGTCAATGTGTGATGTTTTTCTATGTTTCTTTGTCTTTTGATGCGT  >  USA300TCH1516_ALE/47597‑47872                                                                                                                                            |                                                                                                                                         aaaTAGATTCCTATAAGATTTTTATCTTTCGTAATGTGAATGGTTTCAATATAGGGGTACAATATGTTTAACGTGAAACGTTTTTGAATAATATTTTGAATGATGTGTTGTATTTGATGCCCATTGATAGATGTAGTGCGt                                                                                                                                         >  1:83685/1‑141 (MQ=255)  aaTAAATTCCTATAAGATGTTTATCTTTCGTAATGTGAATGGGTTCAATATAGGGGTATAATATGTTTAACGTGAAACGTTTGTGAATAATATTTTGAATGATGTGTTGTATTTGATGCCCATTGATAGATGTAGTGCGtt                                                                                                                                        <  2:162963/141‑1 (MQ=255)      gATTCCTATAAGATTTTTATCTTTCGTAATGTGAATGGTTTCAATATAGGGGTACAATATGTTTAACGTGAAACGTTTTTGAATAATATTTTGAATGATGTGTTGTATTTGATGCCCATTGATAGATGTAGTGCGTTGCgg                                                                                                                                    <  1:403999/141‑1 (MQ=255)        ttCCTATAAGATTTTTATCTTTCGTAATGTGAATGGTTTCAATATAGGGGTAGAATATGTTTAACGTGAAACGTTTTTGAATAATATTTTGAATGATGTGTTGTGTTTGATGTTGTTTTAGAAATGGAGTGCGTTGCGgtt                                                                                                                                  <  2:130084/141‑1 (MQ=255)            tataAGATTTTTATCTTTCGTAATGTGAATGGTTTCAATATAGGGGTACAATATGTTTAACGTGAAACGTTTTTGAATAATATTTTGAATGATGTGTTGTATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGttgttg                                                                                                                              <  2:62878/141‑1 (MQ=255)            tataAGATTTTTATCTTTCGTAATGTGAATGGTTTCAATATAGGGGTACAATATGTTTAACGTGAAACGTTTTTGAATAATATTTTGAATGATGTGTTGTATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGttgttg                                                                                                                              <  2:290545/141‑1 (MQ=255)                    ttttATCTTTCGTAATGTGAATGGTTTCAATAGAGGGGTACAATATGTTTAACGTGAAACGTGTTTGAATAATATTTTGAATGATGTGTTGTATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTaagg                                                                                                                      <  2:405855/141‑3 (MQ=255)                           tttCGTAATGTGAATGGTTTCAATATAGGGGTACAATATGTTTAACGTGAAACGTTTTTGAATAATATTTTGAATGATGTGTTGTATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTgtgt                                                                                                               <  2:242415/141‑1 (MQ=255)                               gTAATGTGAATGGTTTCAATATAGGGGTACAATATGTTTAACGTGAAACGTTTTTGAATAATATTTTGAATGATGTGTTGTATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGc                                                                                                           <  1:334766/141‑1 (MQ=255)                               gTAATGTGAATGGTTTCAATATAGGGGTACAATATGTTTAACGTGAAACGTTTTTGAATAATATTTTGAATGATGTGTTGTATTTGATGCCCATTGACCAAAGCAGTGCGGTGCGGTTGTTGACGTAATGATTGTGTTTGc                                                                                                           <  1:284046/141‑1 (MQ=255)                                 aaTGTGAATGGTTTCAATATAGGGGTACAATATGTTTAACGTGAAACGTTTTTGAATAATATTTTGAATGATGTGTTGTATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGctc                                                                                                         <  1:135128/141‑1 (MQ=255)                                    gtgAATGGTTTCAATATAGGGGTACAATATGTTTAACGTGAAACGTTTTTGAATAATATTTTGAATGATGTGTTGTATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGctctct                                                                                                      >  1:246677/1‑141 (MQ=255)                                             ttCAATATAGGGGTACAATATGTTTAACGTGAAACGTTTTTGAATAATATTTTGAATGATGTGTTGTATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTc                                                                                             <  2:238032/141‑1 (MQ=255)                                               cAATATAGGGGTACAATATGTTTAACGTGAAACGTTTTTGAATAATATTTTGAATGATGTGTTGTATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGCTTGTGTTTGCTCTCTGAACGTTTCTg                                                                                           >  1:131023/1‑141 (MQ=255)                                                 atatAGGGGTAAAGTGTGTTTAGCGTGAAACGTTTTTGAATAATATTTGTAATGGTGTGTTGTATTTGATGCCCATTGATTGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCa                                                                                         <  2:401352/141‑1 (MQ=255)                                                  tataGGGGTACAATATGTTTAACGTGAAACGTTTTTGAATAATATTTTGAATGATGTGTTGTATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCAt                                                                                        <  1:51412/141‑1 (MQ=255)                                                          tACAATATGTTTAGCGTGAAACGTTTTTGAATAATAGTTTGAATGATGTGTTGTATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAatgatg                                                                                <  2:193749/141‑1 (MQ=255)                                                             aaTATGTTTTACGTGAAACGTTTTTGAATAATATTGTGAATGATGTGTTGTATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGATGCCt                                                                             <  2:203473/141‑1 (MQ=255)                                                              atatGTTTAACGTGAAACGTTTTTGAATAATATTTTGAATGATGTGTTGTATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGATGCCtt                                                                            >  2:254853/1‑141 (MQ=255)                                                               tatGTTTAACGTGAAACGTTTTTGAATAATATTTTGAATGATGTGTTGTATTTGATGCCCATTGATCGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTGTCTGCATCAATGCTCCCttt                                                                           >  2:141705/1‑140 (MQ=255)                                                               tatGTTTAACGTGAAACGTTTTTGAATAATATTTTGAATGATGTGTTGTATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGATGCCTtg                                                                           >  1:61671/1‑141 (MQ=255)                                                               tatGTTTAACGTGAAACGTTTTTGAATAATATTTTGAATGATGTGTTGTATTTGATGCCCATTGATAGATGTAGTGCATTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGATGCCttt                                                                           >  2:65273/1‑140 (MQ=255)                                                               tatGTTTAACGTGAAACGTTTTTGAATAATATTTTGAATGATGTGTTGTATTTGATGCCCATTGATAGATGTAGTGCATTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGATGCCTtg                                                                           >  2:65261/1‑141 (MQ=255)                                                                atGTTTAACGTGAAACGTTTTTGAATAATATTTTGAATGATGTGTTGTATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGATGCCTtgt                                                                          >  1:266854/1‑141 (MQ=255)                                                                  gTTTAACGTGAAACGTTTTTGAATAATATTTTGAATGATGTGTTGTATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGATGCCTTGTGc                                                                        <  2:330945/141‑1 (MQ=255)                                                                       aCGTGAAACGTTTTTGAATAATATTTTGAATGATGTGTTGTATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGATGCCTTGTGCCAACt                                                                   >  1:89780/1‑141 (MQ=255)                                                                        cGTGAAACGTTTTTGAATAATATTTTGAATGATGTGTTGTATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGATGCCTTGTGCCAACtt                                                                  <  1:260575/141‑1 (MQ=255)                                                                          tGAAACGTTTTTGAATAATATTTTGAATGATGTGTTGTATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGATGCCTTGTGCCAACtttt                                                                >  1:279885/1‑141 (MQ=255)                                                                              aCGTTTTTGAATAATATTTTGAATGATGTGTTGTATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGCTGCCTTGTGCCAACTTTTCTAt                                                            >  2:146070/1‑141 (MQ=255)                                                                               ggTTTTTGAATAATATTTTGAATGATGTGTTGTATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGATGCCTTGTGCCAACTTTTCTATc                                                           <  2:134411/140‑1 (MQ=255)                                                                               cGTTTTTGAATAATATTTTGAATGATGTGTTGTATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGATGCCTTGTGCCAACTTTTCTATc                                                           >  1:235184/1‑141 (MQ=255)                                                                                 tttttGAATAATATTTTGAATGATGTGTTGTATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGATGCCTTGTGCCAACTTTTCTATCAg                                                         >  2:95238/1‑141 (MQ=255)                                                                                    ttGAATAATATTTTGAATGATGGGTTGTATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGATGCCTTGTGCCAACTTTTCTATCAgttg                                                      <  2:206716/141‑1 (MQ=255)                                                                                          aataTTTTGAATGATGTGTTGTATTTGATGGCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGATGCCTTGTGCCAACTTTTCTATCAGTTGTTCTTg                                                <  2:217756/141‑1 (MQ=255)                                                                                           attttgtGAATGATGTGTTGTATTTGATGGCCATTGATAGATGTAGTGCGTTGCGGCCGTTGCCGTCATGATTGTGTTTGCTCTCTGACCGTTTCTGCCTCTATGATGCCTTGTGCCCACTTTTCTACCACTCGTTCTTGa                                               <  2:305069/135‑1 (MQ=255)                                                                                                  gAATGATGTGTTGTATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGATGCCTTGTGCCAACTTTTCTATCAGTTGTTCTTGAGTCAAtg                                        <  1:227787/141‑1 (MQ=255)                                                                                                     tgatgTGTTGTATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTCCACCCGGCGGTCCGTTTGCCAACTTTTCTATCAGTTGTTCTTGAGTCAAtgtgt                                     >  2:86980/1‑141 (MQ=255)                                                                                                      gatgTGTTGTATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGATGCCTTGTGCCAACTTTTCTATCAGTTGTTCTTGAGTCAAtgtgtg                                    <  1:172524/141‑1 (MQ=255)                                                                                                        tgtgTTGTATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGATGCCTTGTGCCAACTTTTCTATCAGTTGTTCTTGAGTCAATGTGTGAt                                  <  1:360325/141‑1 (MQ=255)                                                                                                         ttgttgtAGTTGATGCCCATTGATTGATGTAGTTCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGATGCCTTGTGCTAACTTTTCTATCAGTTGTTCTTGAGTCAATGTGTGATg                                 <  2:172450/140‑1 (MQ=255)                                                                                                         gtgtTGTATTTGATGCCAAATGATAGATGTAGTGCGTTGTAGTTGTTAAAGTAATGATAGTGATTGCACTCTGCAAGTTTCTGTATCAATGATGTCTTGTGACAACACTTTTAATATTTATTCTTGAGTCAATGTGTGATg                                 <  2:50156/141‑1 (MQ=255)                                                                                                          tgttgtATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGATGCCTTGTGCCAACTTTTCTATCAGTTGTTCTTGAGTCAATGTGTGATGt                                <  1:312232/141‑1 (MQ=255)                                                                                                          tgttgtATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGATGCCTTGTGCCAACTTTTCTATCAGTTGTTCTTGAGTCAATGTGTGATGt                                >  1:184474/1‑141 (MQ=255)                                                                                                               tATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGATGCCTTGTGCCAACTTTTCTATCAGTTGTTCTTGAGTCAATGTGTGATGTTTTTc                           >  2:136335/1‑141 (MQ=255)                                                                                                                    gATGCCCATTGATAGATGTAGTGCATTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGATGCCTTGTGCCAACTTTTCTATCAGTTGTTCTTGAGTCAATGTGTGATGTTTTTCTATGt                      <  1:65261/141‑1 (MQ=255)                                                                                                                    gATGCCCATTGATAGATGTAGTGCATTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGATGCCTTGTGCCAACTTTTCTATCAGTTGTTCTTGAGTCAATGTGTGATGTTTTTCTATGt                      <  1:65273/141‑1 (MQ=255)                                                                                                                     aTGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGAACTCTGAACGTTTCTGCATCAATGATGCCTTGTGCCAACTTTTCTATCAGTTGTTCTTGAGTCAATGTGTGATGTTTTTCTATGtt                     >  1:260921/1‑141 (MQ=255)                                                                                                                      tGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATTATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGATGCCTTGTGCCAACTTTTCTATCAGTTGTTCTTGAGTCAATGTGTGATGTTTTTCTATGttt                    <  1:159495/141‑1 (MQ=255)                                                                                                                        cccATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGATGCCTTGTGCCAACTTTTCTATCAGTTGTTATTGAGTCAATGTGTGATGTTTTTCTATGTTTCt                  >  1:200034/1‑141 (MQ=255)                                                                                                                              ggtAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGATGCCTTGTGCCAACTTTTCTATCAGTTGTTCTTGAGTCAATGTGTGATGTTTTTCTATGTTTCTTTGTCt            >  2:308283/3‑141 (MQ=255)                                                                                                                                  gATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGATGCCTTGTGCCAACTTTTCTATCAGTTGTTCTTGAGTCAATGTGTGATGTTTTTCTATGTTTCTTTGTCTTTTg        <  1:103249/141‑1 (MQ=255)                                                                                                                                      tAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGATGCCTTGTGCCAACTTTTCTATCAGTTGTTCTTGAGTCAATGTGTGATGTTTTTCTATGTTTATTAATCGTTTTATga    >  2:245378/1‑140 (MQ=255)                                                                                                                                        gTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGATGCCTTGTGCCAACTTTTCTATCAGTTGTTCTTGAGTCAATGTGTGATGTTTTTCTATGTTTCTTTGTCTTTTGCTGCGt  >  1:39460/1‑141 (MQ=255)                                                                                                                                            |                                                                                                                                         AAATAGATTCCTATAAGATTTTTATCTTTCGTAATGTGAATGGTTTCAATATAGGGGTACAATATGTTTAACGTGAAACGTTTTTGAATAATATTTTGAATGATGTGTTGTATTTGATGCCCATTGATAGATGTAGTGCGTTGCGGTTGTTGACGTAATGATTGTGTTTGCTCTCTGAACGTTTCTGCATCAATGATGCCTTGTGCCAACTTTTCTATCAGTTGTTCTTGAGTCAATGTGTGATGTTTTTCTATGTTTCTTTGTCTTTTGATGCGT  >  USA300TCH1516_ALE/47597‑47872

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: ‑