Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	KT2440	1,645,364	C→T	7.4%	V1487V (GTG→GTA)	shlA ←	Hemolysin

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	KT2440	1,645,364	0	C	T	7.4%	164.6 / 3.9	54	V1487V (GTG→GTA)	shlA	Hemolysin
Reads supporting (aligned to +/- strand):  ref base C (30/20);  new base T (2/2);  total (32/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.87e-01

CGGGTGTCAGCAGCAGGGCACAAGATTGCTGATATCCCCAAATGGCCAGGGCCGCGATGGCGTCTTAGTGCTTCTTCCCTTGCATGCTCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGATTGCCGTGCCCAGATCCACCGGTGAGTTGGACGCATCCAACGACAGGTCTCGGCGATAGTCATTGCCGCT  >  KT2440/1645234‑1645495                                                                                                                                    |                                                                                                                                    cGGGTGTCAGCATCAGGGCACAAGATTGCTGATATCCCCAAATGGCCAGGGCCGCGATGGCGTCTTAGTGCTTCTTCCCTTGCATGCTCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAACACGc                                                                                                                                 >  8:266718/1‑135 (MQ=255)                 ggCACAAGATTGCTGATATCCCCAAATGGCCAGGGCCGCGATGGCGTCTTAGTGCTTCTTCCCTTGCATGCTCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCAtt                                                                                                                 >  7:53861/1‑135 (MQ=255)                                atatCCCCAAATGGCCAGGGCCGCGATGGCGTCTTAGTGCTTCTTCCCTTGCATGCTCGAAACCCA‑TTGCTCGCTGCGCCTATGCCCACTGGTTCTCAACACCCCCAGGCCCAGCGCATTTTCCCCATccgccg                                                                                                   >  5:189298/1‑134 (MQ=255)                                atatCCCCAAATGGCCAGGGCCGCGATGGCGTCTTAGTGCTTCTTCCCTTGCATGCTCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATccgccg                                                                                                   >  3:18106/1‑134 (MQ=255)                                atatCCCCAAATGGCCAGGGCCGCGATGGCGTCTTAGTGCTTCTTCCCTTGCATGCTCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACGGGTTCTCAACACGCCCAGGTCCAGCGGATTTTCCCCATCcgccgc                                                                                                  >  4:81765/1‑135 (MQ=255)                                       cAAATGGCCAGGGCCGCGATGGCGTCTTAGTGCTTCTTCCCTTGCATGCTCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAATACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTg                                                                                           >  7:287487/1‑135 (MQ=255)                                       cAAATGGCCAGGGCCGCGATGGCGTCTTAGTGCTTCTTCCCTTGCATGCTCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAATACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTg                                                                                           >  7:287482/1‑135 (MQ=255)                                       cAAATGGCCAGGGCCGCGATGGCGTCTTAGTGCTTCTTACCTTGCATGCTCGAAACCCA‑TTGCTCGCTGCGCCTATGCCCCCTGGTTCTCAACACGCCCACGTCCCGCGCATTTTGCCCATCCGCCCCCCttttt                                                                                           >  4:216246/1‑134 (MQ=255)                                          aTGGCCAGGGCCGCGATGGCGTCTTAGTGCTTCTTCCCTTGCATGCTCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCCTCCGCCGCCATTTTGCtt                                                                                        >  7:137167/1‑135 (MQ=255)                                               cAGGGCCGCGATGGCGTCTTAGTGCTTCTTCCCTTGCATGCTCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTgg                                                                                    >  1:241902/1‑134 (MQ=255)                                                  ggCCGCGATGGCGTCTTAGTGCTTCTTCCCTTGCATGCTCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTAt                                                                                >  4:62895/1‑135 (MQ=255)                                                     cgcgATGGCGTCTTAGTGCTTCTTCCCTTGCATGCTCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTAtctc                                                                             >  3:188226/1‑135 (MQ=255)                                                     cgcgATGGCGTCTTAGTGCTTCTTCCCTTGCATGCTCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTAt                                                                                <  5:67350/132‑1 (MQ=255)                                                     cgcgATGGCGTCTTAGTGCTTCTTCCCTTGCATGCTCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTAt                                                                                >  6:67350/1‑132 (MQ=255)                                                          tGGCGTCTTAGTGCTTCTTCCCTTGCATGCTCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCACCACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGa                                                                        >  2:335860/1‑135 (MQ=255)                                                            gCGTGTTAGTGCTTCTGCCGTTGCATGCGCTCAACCCA‑TTCGACCGTGCGAATATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGAtt                                                                      <  6:48402/135‑1 (MQ=255)                                                            gCGTCTTAGTGCTTCTTCCCTTGCATGCTCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGAtt                                                                      <  3:62895/135‑1 (MQ=255)                                                             cggcTTAGGGCTTCTTCCCTTGCATGCTCGAAACCCA‑TTCCTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGATTg                                                                     <  2:75300/132‑1 (MQ=255)                                                             cGTCTTAGTGCTTCTTCCCTTGCATGCTCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGAtt                                                                      <  4:388506/134‑1 (MQ=255)                                                               tCTTAGTGCTTCTTCCCTTGCATGCTCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGATTGcc                                                                   >  6:338597/1‑135 (MQ=255)                                                                   aGTGCTTCTTCCCTTGCATGCTCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGATTGCCGTg                                                                <  5:137481/134‑1 (MQ=255)                                                                    gTGCTTCTTCCCTTGCATGCTCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGATTGCCGt                                                                 <  4:73789/132‑1 (MQ=255)                                                                    gTGCTTCTTCCCTTGCATGCTCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGATTGCCGTg                                                                <  7:309061/133‑1 (MQ=255)                                                                     tggttcttcCATGCCTTGCTC‑AAACCCATTTGGCCGCGGCGACAATGCCCACTGGTCACCACCACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTAACTCGGCGATTGCCGTGcc                                                              <  8:361058/131‑1 (MQ=255)                                                                            tcCCTTGCATGCTCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGATTGCCGTGCCCAGATCCa                                                      >  5:135743/1‑135 (MQ=255)                                                                            tcCCTTGCATGCTCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGATTGCCGTGCCCAGATCCa                                                      <  4:18106/135‑1 (MQ=255)                                                                            tcCCTTGCATGCTCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGATTGCCGTGCCCAGATCCa                                                      <  2:110352/135‑1 (MQ=255)                                                                            tcCCTTGCATGCTCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGATTGCCGTGCCCAGATCCa                                                      >  2:228996/1‑135 (MQ=255)                                                                             cccTTGCATGCGTGAAACCCA‑TTGCTCGCTGCGACTATGCCCTGTGGTTGTCAACACGCCGAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGATTGCCGTGCCCAGATCCa                                                      <  6:189298/134‑1 (MQ=255)                                                                              ccTTGCATGCTCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGATTGCCGTGCCCAGATCCa                                                      <  3:356949/133‑1 (MQ=255)                                                                              ccTTCCATGCTGCAAACGCT‑TTGCGGGGTGCGAGTATGCCCACTGGTTCTCACCACGCCCAGGTCCAGCGCATTTTGCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGATTGCCGTGCCCAGATCCa                                                      <  5:181934/133‑1 (MQ=255)                                                                               cTTGCATGCTCTAACCCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGATTGCCGTGCCCAGATCCAcc                                                    <  8:5724/134‑1 (MQ=255)                                                                                   cATGCTCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGATTGCCGTGCCCAGATCCACCGGTGa                                               >  1:5991/1‑135 (MQ=255)                                                                                   cATGCTCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGATTGCCGTGCCCAGATCCACCGGTGa                                               >  3:384554/1‑135 (MQ=255)                                                                                    aTGCTCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCgccgcc                                                                                                 <  8:61045/84‑1 (MQ=255)                                                                                    aTGCTCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCgccgcc                                                                                                 >  7:61045/1‑84 (MQ=255)                                                                                      gCTCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGATTGCCGTGCCCAGATCCACCGGTGAGtt                                            <  1:11306/135‑1 (MQ=255)                                                                                       ctctAACCCCA‑TTGCTCGCTGCTACTTTGCCCAGTGTTTCTAAACACGCCCAGTTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATATCGGCGATTGCCGTGCCCAGATCCACCGGTGAGtt                                            <  7:278837/134‑1 (MQ=255)                                                                                        tCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGATTGCCGTGCCCAGATCCACCGGTGAGTTgg                                          >  4:376903/1‑135 (MQ=255)                                                                                        tCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGATTGCCGTGCCCAGATCCACCGGTGAGTTgg                                          >  7:248271/1‑135 (MQ=255)                                                                                          gAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTAGGCGATTGCCGTGCCCAGCTCCACCGGTGAGTTGGAc                                        >  4:246935/1‑135 (MQ=255)                                                                                             aCCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAATACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGATTGCCGTGCCCAGATCCACCGGTGAGTTGGACGCa                                     <  8:287482/135‑1 (MQ=255)                                                                                             aCCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAATACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGATTGCCGTGCCCAGATCCACCGGTGAGTTGGACGCa                                     <  8:287487/135‑1 (MQ=255)                                                                                                    tGCTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGATTGCCGTGCCCAGATCCACCGGTGAGTTGGACGCAGCCAAc                               <  8:137749/135‑1 (MQ=255)                                                                                                      cTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGATTGCCGTGCCCAGATCCACCGGTGAGTTGGACGCATCCAACg                              >  1:91202/1‑134 (MQ=255)                                                                                                             cGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGATTGCCGTGCCCAGATCCCCCGGTGAGTTGGACGCATCCAACGACAGGtct                      >  4:208084/1‑135 (MQ=255)                                                                                                              gACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGATTGCCGTGCCCAGATCCCCCGGTGAGTTGGACGCATCCAACGACAGGtctc                     >  2:260456/1‑135 (MQ=255)                                                                                                                cTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGATTGCCGTGCCCAGATCCACCGGTGAGTTGGACGCAGCCAACGACAGGTCTCgg                   >  7:238660/1‑135 (MQ=255)                                                                                                                        aCTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGATTGCCGTGCCCAGATCCACCGGTGAGTTGGACGCATCCAACGCCAGGTCTCGGCGATAGTc           >  8:177190/1‑135 (MQ=255)                                                                                                                        aCTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGATTGACGTGCCCAGATCCACCGGTGAGTTGGACGCATCCAACGACAGGTCTCGGCGATAGTc           >  6:255152/1‑135 (MQ=255)                                                                                                                           ggTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGATTGCCGTGCCCAGATCCa                                                      >  1:391906/1‑89 (MQ=255)                                                                                                                           ggTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGATTGCCGTGCCCAGATCCa                                                      <  2:391906/89‑1 (MQ=255)                                                                                                                                  aaCACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGATTGCCGTGCCCAGATCCACCGGTGAGTTGGACGCATCCAACGACAGGTCTCGGCGATAGTCATTGCCGc   >  4:216896/1‑133 (MQ=255)                                                                                                                                  aaCACGCCCAGGTCCAGCGCATTTTCCCCAACCGCCGCCATTTTGCTTTTCGCTATCTCGGCGATTGCCGTGCCCAGATCCACCGCTGAGTTGGAAGCATCCACCGCCAGGTCTCGCCGATAGTCATTGCCGc   >  6:109500/1‑133 (MQ=255)                                                                                                                                   ccacGCCCAGGTCCAGCGCATTTTCCCCATCCGCAGCCTTTTTGCTTTTGGCTATCTCGGCGATTGCCGTGCCCATATCCACCGGTGAGTTGGACGCATCCAACGACAGGTCTCGGCGATAGTCATTGCCGCt  <  6:233307/132‑1 (MQ=255)                                                                                                                                    |                                                                                                                                    CGGGTGTCAGCAGCAGGGCACAAGATTGCTGATATCCCCAAATGGCCAGGGCCGCGATGGCGTCTTAGTGCTTCTTCCCTTGCATGCTCGAAACCCA‑TTGCTCGCTGCGACTATGCCCACTGGTTCTCAACACGCCCAGGTCCAGCGCATTTTCCCCATCCGCCGCCATTTTGCTTTTGGCTATCTCGGCGATTGCCGTGCCCAGATCCACCGGTGAGTTGGACGCATCCAACGACAGGTCTCGGCGATAGTCATTGCCGCT  >  KT2440/1645234‑1645495

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑