Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	KT2440	1,670,696	A→C	21.3%	intergenic (+33/‑98)	thrC_2 → / → CJ019_01569	Threonine synthase/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	KT2440	1,670,696	0	A	C	21.3%	58.4 / 6.6	53	intergenic (+33/‑98)	thrC_2/CJ019_01569	Threonine synthase/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (28/12);  new base C (8/5);  total (36/17)
Fisher's exact test for biased strand distribution p-value = 7.34e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCAGCCGTGAAGAGCGTTGCACGGTCCTGGCCAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCATCAGGAGCGGCTCATGCACCAGCCCTATGTGTTGATTCACCAGGCTC  >  KT2440/1670569‑1670827                                                                                                                                  |                                                                                                                                    tCAGCCGTGAAGAGCGTTGCACGGTCCTGGCCAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑TGGGCTGCAGCGCAGCCCCAACggc                                                                                                                                >  3:390848/1‑131 (MQ=255) tCAGCCGTGAAGAGCGTTGCACGGTCCTGGCCAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑GGGGCTTCCGCGCACCCCCAACGtcgc                                                                                                                              >  2:164997/1‑133 (MQ=255) tCAGCCGTGAAGAGCGTTGCACGGTCCTGGCCAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑GGGGCTGCAGCGCAGCCCCCACGtc                                                                                                                                >  5:152647/1‑133 (MQ=255) tCAGCCGTGAAGAGCGTTGCACGGTCCTGGCCAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGtct                                                                                                                               >  7:361238/1‑134 (MQ=255)        tGAAGAGCGTTGCACGGTCCTGGCCAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCttt                                                                                                                       >  4:442904/1‑135 (MQ=255)           agagCGTTGCACGGTCCTGGCCAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑GGGGCTGCAGCGCCGCCCCAACGTCTCCGCCTTTTcc                                                                                                                    >  1:292288/1‑135 (MQ=255)                  tGCACGGTCCTGGCCAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGAAA‑GCCGCTGTAATTGCATGGCGTTT‑GGGGCTGCAGCGCAGCCCCCACGTCTCAGCCTTTTCCCTCCTGTc                                                                                                            >  8:225563/1‑136 (MQ=255)                            tGGCCAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAA‑GCAGCTGTAATTGCATGGCGTTT‑GGGGCTGCAGCGCCGCCCCAACGTCTCAGCCTTTTCCCTCCAGTCTATCAGaa                                                                                                    >  4:34308/1‑134 (MQ=255)                            tGGCAAACGACCTGATGGCTGTACCGGGCTTTGACACCCCGCACGGAACCCGCGGAAA‑GCGGCTTTAATTGCAGGGGGTTG‑GGGGCGGCCGCGCCGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGaaa                                                                                                   <  6:150841/135‑1 (MQ=255)                               ccAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑GGGGCTTCAGCGCAGCCCCCACGTGTCCGCCGTTTGCCTCCTGGCTATCAGAAAcct                                                                                                >  4:444490/1‑133 (MQ=255)                                cAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATcc                                                                                              >  8:265402/1‑136 (MQ=255)                                     cccTGAAGGCTGCACAGGGGGTTGGCACCCCGCACGGCAACCGCGGCAA‑GCCGCTGTAATTGCAGGGGGTTT‑GGGGCTCCCGCCCCCCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTc                                                                                         <  8:424583/135‑1 (MQ=255)                                      ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑TGGGCTGCCGCGCAGCCCCCCCGTCTCCGCCTTTTCCCTCCGGGCGAGAAGAAACATCCGATTc                                                                                         >  6:353234/1‑135 (MQ=255)                                      ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑TGGGCTGCCGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTAtt                                                                                          >  8:415671/1‑134 (MQ=255)                                      ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑TGGGCTGCATCGCAGCCCCAACCTCTCAGCCTTTTTACACATTTGTATAAGAAAACTCCTAtta                                                                                         >  8:392808/1‑134 (MQ=255)                                      ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑GGGGCTGCAGCGCCGCCCCCACGTCTCCGCCTTTTGCCTCCTGTCTATCAGAAACAACCTATTc                                                                                         >  6:425055/1‑135 (MQ=255)                                      ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑GGGGCTGCAGCGCAGCCCCACCGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTAt                                                                                           >  3:97645/1‑133 (MQ=255)                                      ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCCGCCTTTTCCCTCCTGTCTATCAGAAACATCCTAt                                                                                           >  6:420866/1‑133 (MQ=255)                                      ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGCAACATCCTAtt                                                                                          >  7:336478/1‑134 (MQ=255)                                      ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGCAACATCCTATTc                                                                                         >  2:260376/1‑135 (MQ=255)                                      ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCa                                                                                        >  8:270579/1‑136 (MQ=255)                                      ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATAAGAAACATCCTAtt                                                                                          >  7:44560/1‑134 (MQ=255)                                      ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGGCTATCAGAAACATCCTATTc                                                                                         >  4:214839/1‑135 (MQ=255)                                      ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCAGTCTATCAGAAACATCCTaa                                                                                           >  3:348990/1‑132 (MQ=255)                                                 tACCGGGCTTTGTCCGCCCCCCCGCCAACCGCGGCAA‑GCCGCTTTATTTCCAGGGGGTTT‑GGGGCGGCAGCGCAGCCCCCACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGgc                                                                             <  7:139754/136‑1 (MQ=255)                                                    aGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGgcg                                                                            >  3:413036/1‑134 (MQ=255)                                                    aGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCGATCAGAAACATCCTATTCAGCCTGCCGGgcgc                                                                           >  6:142853/1‑135 (MQ=255)                                                         tttGTCAGCCAGCACGGCAACCGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCa                                                                     >  8:283123/1‑136 (MQ=255)                                                         tttGTCAGCCAGCACGGCAACCGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑GGGGCGGCAGCGCCGCCCCCACGGCTCCGCCGTTTGCCGCCTGTCTATCAGCAACATCCTATTCATCCTGCCGGGCGCCCAg                                                                       >  2:174460/1‑134 (MQ=255)                                                           tGTCAGCCAGCACGGCAACCGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCAt                                                                    >  8:120943/1‑135 (MQ=255)                                                              cagccagcACGGCAACCGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGgc                                                                             >  7:374070/1‑123 (MQ=255)                                                              cagccagcACGGCAACCGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGgc                                                                             <  8:374070/123‑1 (MQ=255)                                                              cagccagcACGGCAACCGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCGTTTCCCTCCTGTCTATAAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATaaa                                                                 >  6:285279/1‑135 (MQ=255)                                                              cagccagcACGGCAACCGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑GGGGCTGCAGCGCAGCCCCAACCTCTCAGCCTTTTCCCACCAGTCTATCAGAAACATCCTATTCACCCTGCCGGGCGCCCAGCATaaa                                                                 >  4:407927/1‑135 (MQ=255)                                                                 cccccccGGCACCCGCCGCAACGCCGGT‑TAATTGACTGGGGTTTGGGGGCGGCCCCGACCCCCCCACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAAtt                                                               <  1:203383/129‑1 (MQ=255)                                                                  ccgcACGCCACCCGCGGCAA‑GCCGCTGTATTTGCTTGGCGTTG‑GGGGGGGCCGCGCAGCCCAAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAg                                                             <  1:1806/133‑1 (MQ=255)                                                                     cACGGAAACCGCGGCAA‑GCGGCTGTAATTGCATGGCGTTG‑GGGGCTGACGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCg                                                          <  2:21651/135‑1 (MQ=255)                                                                       gggaaaCGGCGGCAA‑GCCGGTTAATTTGCAGGGCGTTT‑GGGGCGGCAGCGCTGCCCAAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGt                                                        <  6:189890/131‑1 (MQ=255)                                                                        ggCAACCGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGtct                                                      >  7:144323/1‑135 (MQ=255)                                                                             ccGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCCGCCGTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCGAGCATAAATTAGGCGGTCCTccc                                                  >  5:135239/1‑135 (MQ=255)                                                                                cgGCAA‑GCCGCTGTAATTGCATGGCGTTT‑TGGGCTGCCGCGCAGCGCCCACCGCTCCCCCTTTTCCCACCGGGCGATGAGCGACATCCGAATCCGCCGGACGGGCGCCCAGCAAAAATTAGCCGGTCCGCCCagc                                               >  6:329311/1‑133 (MQ=255)                                                                                   aaa‑GCCGCTGTAATGGCATGGCGTTG‑GGGGCGCCAGCGCCGCCCCAACGTCTCAGCATTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCATCAgg                                            <  2:319228/134‑1 (MQ=255)                                                                                                aTTGCATGGCTTTG‑GGGGCGGATGCCCTGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCATCAGGAGCGGCTCATg                                 <  4:348990/134‑1 (MQ=255)                                                                                                aTTGCATGGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCATCAGGAGCGGCTCATGCa                               <  8:361238/136‑1 (MQ=255)                                                                                                         cGTTT‑GGGGCTGCAGCGCCGCCCCAACGGCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCATCAGGAGCGGCTCATGCCCCCGCCCTa                      >  7:355268/1‑136 (MQ=255)                                                                                                         cGTTT‑GGGGCTGCAGCGCAGCCCCCACGTCTCAGCCGTTTCCCTCCTGTCTATCAGAAACATCCGATTCAGCCTGCCGGGCGCCCAGCATAAATTAGCCGGTCCTCCCATCAGGAGCGGCGCATGCACCAGcccga                      >  7:220257/1‑134 (MQ=255)                                                                                                               ggggCTGCAGCGCTGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCTTCCCATCAGGAGCGGCTCATGCACCAGCCCTATgtgt                 <  8:144323/136‑1 (MQ=255)                                                                                                               ggggCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCATCAGGAGCGGCTCATGCACCAGCCCTATgtgt                 <  7:270579/136‑1 (MQ=255)                                                                                                                     gcagcgcagcCCCCACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCATCAGGAGCGGCTCATGCACCAGCCCTATGTGTTGAtt            <  4:179199/135‑1 (MQ=255)                                                                                                                             gcCCCCACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCATCAGGAGCGGCTCATGCACCAGCCCTATGTGTTGATTCACCAGGc    <  1:145694/135‑1 (MQ=255)                                                                                                                              ccccCACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCATCAGTAGCGGCTCATGCACCAGCCCTATGTGTTGATTCACCAGGCTc  <  7:138633/136‑1 (MQ=255)                                                                                                                              ccccAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTTCCGGGCGCCAACCATAAATTAGCCGGTCCTCCCATCAGGAGCGGCTCATTCACCAGCCATATGTGATGATTCACCATGCt   >  2:213544/1‑135 (MQ=255)                                                                                                                              cccaAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGCTCCTCCCATCAGGAGCGGCTCATGCACCAGCCCTATGTGTTGATTCACCAGGCTc  <  7:138630/136‑1 (MQ=255)                                                                                                                               ccaaaCGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCATCAGGAGCGGCTCATGCACCAGCCCTATGTGTTGATTCACCAGGCTc  <  3:13991/132‑1 (MQ=255)                                                                                                                                  |                                                                                                                                    TCAGCCGTGAAGAGCGTTGCACGGTCCTGGCCAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAA‑GCCGCTGTAATTGCATGGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCATCAGGAGCGGCTCATGCACCAGCCCTATGTGTTGATTCACCAGGCTC  >  KT2440/1670569‑1670827

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: ‑