Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	ACB122	1,670,685	A→C	31.2%	intergenic (+22/‑109)	thrC_2 → / → CJ019_01569	Threonine synthase/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	ACB122	1,670,685	0	A	C	31.2%	29.5 / 3.2	50	intergenic (+22/‑109)	thrC_2/CJ019_01569	Threonine synthase/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (28/4);  new base C (9/7);  total (37/13)
Fisher's exact test for biased strand distribution p-value = 2.70e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGCGACCTGTTCAGCCGTGAAGAGCGTTGCACGGTCCTGGCCAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCAT‑GGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCATCAGGAGCGGCTCATGCACCAGCCCTATGTGTTGATTCA  >  ACB122/1670559‑1670819                                                                                                                                 |                                                                                                                                       aGCGACCTGTTCAGCCGTGAAGAGCGTTGCACGGTCCTGGCCAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTGATTGCAT‑GGCGTTT‑GGGGCTGCAGCGCAGcc                                                                                                                                >  2:176413/1‑135 (MQ=255)                    aaGAGCGTTGCACGGTCCTGGCCAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCAT‑GGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCACAGCCGTTTc                                                                                                             >  4:156369/1‑135 (MQ=255)                     agagCGTTGCACGGTCCTGGCCAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCAT‑GGCGTTT‑GGGGGTGCCGCGCCGCCCCCACGTCTCAGCCgtttgc                                                                                                            >  5:248838/1‑133 (MQ=255)                       agCGTTGCACGGTCCTGGCCAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCAT‑GGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCCGCCGTTTCcct                                                                                                          >  2:45401/1‑135 (MQ=255)                       agCGTTGCACGGTCCTGGCCAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCAT‑GGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCcct                                                                                                          >  4:239533/1‑135 (MQ=255)                            tGCACGGTCCTGGCCAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCAT‑GGCGTTT‑TGGGCTGCAGCGCAGCCCCCACGTCGCAGCCGTTTAcctcct                                                                                                       >  3:77573/1‑133 (MQ=255)                               aCGGTCCTGGCCAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCAT‑GGCGTTT‑GGGGCTGCCGCGCAGCCCCCACGTCTCACCCGTTTACCTCCGGTCt                                                                                                   >  6:12111/1‑134 (MQ=255)                               aCGGTCCTGGCCAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCAT‑GGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCt                                                                                                   >  7:160731/1‑134 (MQ=255)                               aCGGTCCTGGCCAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCAT‑GGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTa                                                                                                  >  6:179613/1‑135 (MQ=255)                                  gTCCTGGCCACCTCCCTGATGGGTGTACTGGGTTTTGTCTGCCCGCGCGGAAACGGGGGAAAGCCGGTGTAA‑TGCAT‑TGGGTTTGGGGGGTGAGGGGCTGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCa                                                                                               <  6:99490/135‑1 (MQ=255)                                      tGGCCAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCCAGCCGCTGTAATTGCAT‑GGCGTTT‑TGGGCTGCAGAGCAGCCCCAACGTGTCAGCCTAGTCACTCCTGTCTATAAGaa                                                                                            >  6:86141/1‑134 (MQ=255)                                      tGGCCAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCAT‑GGCGTTT‑GGGGCAGCCGCCCACCCCCCACGAATCCCCCTTTTCCCACCTGTCTATCACaa                                                                                            >  2:392221/1‑134 (MQ=255)                                           aaCTACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCAT‑GGCGTTT‑GGGGCTGCAGCGCAGCCCCCACGGCGCCGCCGTTTGCCGCCTGGCGATGATCAACATc                                                                                       >  3:39456/1‑134 (MQ=255)                                           aaCGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCACGCCGCTGTAATTGCAT‑GGCGTTT‑GGGGCTGCAGCGCCGCCCCCACGTCGCAGCCTTTTCCCTCCGGTCTATCAGAAACCTc                                                                                       >  3:320478/1‑134 (MQ=255)                                           aaCGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCAT‑GGCGTTT‑GGGGCTGCAGCGCCGCCCCCAAGTCTCCGCCGTTTCCCTCCTGTCTATCAGAAACATc                                                                                       >  5:129021/1‑134 (MQ=255)                                                ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCAT‑GGCGTTT‑GGGGCTGGAGCGCCGCCCCCACCGCTCAGCCTTTTGCCTCCAGTCTATGAGGAACATCCGATTc                                                                                 >  1:197760/1‑135 (MQ=255)                                                ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCAT‑GGCGTTT‑GGGGCTGCCGCGCAGCCCCAACGTCTCCCCCGTTTACCTCCTGTCTATCAGCAACCTCCTAtta                                                                                 >  4:464259/1‑134 (MQ=255)                                                ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCAT‑GGCGTTT‑GGGGCTGCCGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCAGTCGATCAGAAACATCCTATTc                                                                                 >  4:159996/1‑135 (MQ=255)                                                ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCAT‑GGCGTTT‑GGGGCTGCCGCGCAGCCCCAACGTCTCAGCCGTTTCCCTCCTGTCTATCAGCAACATCCTAt                                                                                   >  1:79835/1‑133 (MQ=255)                                                ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCAT‑GGCGTTT‑GGGGCTGCAGCGCCGCCCCCACGTCTCAGCCTTTTCCCTCCTGTCTATCAGCAAAATCCTATTc                                                                                 >  1:367192/1‑135 (MQ=255)                                                ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCAT‑GGCGTTT‑GGGGCTGCAGCGCCGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCGATCAGAAACATCCTAt                                                                                   >  2:100947/1‑133 (MQ=255)                                                ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCAT‑GGCGTTT‑GGGGCTGCAGCGCCCCCCCCACCTCTCAGCCTATTCGCTCCTGTCAATCAGAAACATGCGAtta                                                                                 >  6:419643/1‑134 (MQ=255)                                                ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCAT‑GGCGTTT‑GGGGCTGCAGCGCAGCCCCCACGTCTCAGCCATTTCCCTCCTGTCTATCAGAAACATCCTAt                                                                                   >  4:325475/1‑133 (MQ=255)                                                ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCAT‑GGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTAt                                                                                   >  8:214134/1‑133 (MQ=255)                                                ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCAT‑GGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCGATCAGAAACATCCTATTc                                                                                 >  8:51717/1‑135 (MQ=255)                                                ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCAT‑GGCGTTT‑GGGGCTGCAGCGCAGCCCCAACCTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCGAtta                                                                                 >  3:433282/1‑134 (MQ=255)                                                ccTGAAGGCTGTACAGGGCTTTGACAGCCACCCCGCCACCCGCGCCACGCCGCTGTAATTGAAT‑GGCTTTG‑GGGCCTGCCGCGAAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTc                                                                                 <  4:458867/135‑1 (MQ=255)                                                      ggCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCAT‑GGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTg                                                                           >  8:446043/1‑135 (MQ=255)                                                          gtccAGGGCTTGGCCACCCCCCCCGCCAACCGCGCCAAGCCGCTG‑AATACCCTGGGCGTGG‑GGGGCCGCAGCCCCCCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCgg                                                                       <  3:395654/132‑1 (MQ=255)                                                            cccgggCTTTGCCAGCCACCCCTGCACCCGCGCCACCCCGCTTTAATGGCGG‑GGGGTTG‑GGGGCCCCCGCCCCGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGgc                                                                     <  6:6357/132‑1 (MQ=255)                                                                 gCTTTGTCCGCCAGCACGGCAACCGCGGCACGCCGCTGTAATTGCAG‑GGGGTTG‑GGGGCGGCCGCGCCGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCa                                                                 <  4:43932/134‑1 (MQ=255)                                                                 gCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCAT‑GGCGTTT‑GGGGCTGCCCCGCCACCCCAACGTCTCACCCTTTTCCCACCTGGCTATCAGAACCATCCTATTCAGCCTGCCGGGCGCCaa                                                                >  2:389573/1‑135 (MQ=255)                                                                   tttGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCAT‑GGCGTTT‑GGGGCTGCCGCGCCGCCCCCCCGGGGCCGCCGTTTGCCGGCGGTGTTTTAGAAACATCCGATTAAGCCGGCCCGgcggccac                                                               >  6:41450/1‑129 (MQ=255)                                                                   tttGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCAT‑GGCGTTT‑GGGGCTGCCGCGCAGCCCCAACGGCGCCGCCTTGTACCGCCGGGATATCAGAAACACACGATTCAGCCTGCCGGGCGcccac                                                               >  7:242882/1‑131 (MQ=255)                                                                   tttGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCAT‑GGCGTTT‑GGGGCTGCATCGCAGCCCCAACGTCTCAGCCGTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGc                                                              >  5:74662/1‑135 (MQ=255)                                                                   tttGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCAT‑GGCGTTT‑GGGGCTGCAGCGCAGGCCCCACGTCTCAGCCGTTTCCCTCCTGTCTATGAGAAACATGCTATTCAGCCTGCCGGGCGCCAAGc                                                              >  3:409597/1‑135 (MQ=255)                                                                             agcACGGCAACCGCGGCAAGCCGCTGTAATTGCAT‑GGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGc                                                    >  8:342958/1‑135 (MQ=255)                                                                               cACGGCAACCGCGGCAAGCCGCTGAAATTGCTG‑GGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCg                                                  <  3:340477/135‑1 (MQ=255)                                                                               cACGCCCACCGCGGCAAGCCGCTGTATTGGCCT‑GGGGGTG‑GGGGCGGCCGCGCAGCCCCCACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCg                                                  <  1:162351/135‑1 (MQ=255)                                                                                 ccccacccGCGCCACGCCGGTTTATTTGCTG‑GGGGTTG‑GGGGGTGCCGCCCCCCCCCCACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGt                                                <  1:146061/129‑1 (MQ=255)                                                                                      aCCGCGGCAAGCCGCTGTAATTGCAT‑GGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGtcctc                                            >  4:394237/1‑134 (MQ=255)                                                                                             catgCCGCTGTTTTTGCAG‑GTGGTTT‑GGGGCGGCTGCGCTGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCATCAgg                                    <  4:73861/132‑1 (MQ=255)                                                                                                   gCTGTAATTGCAG‑GGGGTTG‑GGGGCTCCAGCGCCCCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCATCAGGAGCGGc                              <  7:238345/135‑1 (MQ=255)                                                                                                        aaTTGCAT‑GGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCGATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCATGAGGAGCGGCTCAt                          >  7:246564/1‑134 (MQ=255)                                                                                                                gggggTTG‑GGGGCTGCCGCGCCGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCATCAGGAGCGGCTCATGCACCAGc                  <  8:327856/131‑1 (MQ=255)                                                                                                                   cGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCCGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCATCAGGAGCGGCTCCTGCACCCGcccg               >  5:212258/1‑134 (MQ=255)                                                                                                                   cGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCATCAGGAGCGGCTCATGCACCAGCCCt               >  4:337760/1‑135 (MQ=255)                                                                                                                     ttt‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCATCAGGAGCGGCTCATGCACCAGCCCTAt             >  3:158247/1‑135 (MQ=255)                                                                                                                          gggCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCATCAGGAGCGGCTCATGCACCAGCCCTATgtgt         <  4:158247/135‑1 (MQ=255)                                                                                                                          gggCGGCCGCCCCGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCATCAGGAGCGGCTCATGCACCAGCCCTATgtgt         <  7:263823/135‑1 (MQ=255)                                                                                                                                 agcgccgcCCCAACGTCTCAGCCTTTTACCTACTGTGTATAATAAACATCATATTAAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCCTCAGGAGCGGCTCATGCACCAGCCCGATGTGTTTATTCa  >  8:28424/1‑135 (MQ=255)                                                                                                                                 agcgcagcCCCAACGTCTCAGCCGTTTACCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCAAAAATTAGCCGGTCCTCCCATCAGGAGCGGCTCATGCACCAGCCCTATGTGTTGCTTCa  >  8:304482/1‑135 (MQ=255)                                                                                                                                 agcccagcccCAACGTCTCAGCCATTTACCAACTGTCTATAAGAAACAAACAATTCAGCCTGCCGGGCGCCCAGCATAAAATATCCGGTCCTCCCATCACGAGCGGCTCATTCACCACCCCAAAGTGTTGATTCa  >  2:27004/1‑135 (MQ=255)                                                                                                                                 |                                                                                                                                       AGCGACCTGTTCAGCCGTGAAGAGCGTTGCACGGTCCTGGCCAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCAT‑GGCGTTT‑GGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCATCAGGAGCGGCTCATGCACCAGCCCTATGTGTTGATTCA  >  ACB122/1670559‑1670819

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑