Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	KT2440	1,670,690	A→C	33.2%	intergenic (+27/‑104)	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	1,670,690	0	A	C	33.2%	29.1 / 5.0	45	intergenic (+27/‑104)	thrC_2/CJ019_01569	Threonine synthase/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (26/3);  new base C (11/5);  total (37/8)
Fisher's exact test for biased strand distribution p-value = 1.11e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTTCAGCCGTGAAGAGCGTTGCACGGTCCTGGCCAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCATCAGGAGCGGCTCATGCACCAGCCCTATGTGTTGATTCA  >  KT2440/1670567‑1670819                                                                                                                            |                                                                                                                                  gTTCAGCCGTGAAGAGCGTTGCACGGTCCTGGCCAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCAGCGCAGCCCCAACGtc                                                                                                                        >  6:128192/1‑135 (MQ=255)                       aCGGTCCTGGCCAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCt                                                                                                   >  5:191206/1‑134 (MQ=255)                            ccTGGCCAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAg                                                                                              >  6:325822/1‑134 (MQ=255)                              tGGCCAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCCGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGaa                                                                                            >  5:97144/1‑134 (MQ=255)                              tGGCCAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCCGCGCAGCCCCAACGTCTCAGCCATTTACCTCCTGTCTTTCAGaa                                                                                            >  2:112860/1‑134 (MQ=255)                                gCCAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACa                                                                                         >  8:93638/1‑135 (MQ=255)                                   aaCGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTTGGGCTGCAGCGCAGCCCCAACGGCGCAGCCTTTTCCCTCCTGTCTATCAGAAACCTc                                                                                       >  8:336978/1‑134 (MQ=255)                                   aaCGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCCGCGCCGCCCCCACGTCTCAGCCGTTTCCCTCCTGTCTATCAGAAACATc                                                                                       >  1:216091/1‑134 (MQ=255)                                        ccTGAAGGCTGTACCGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCCGCGGCCCCCCCACGGCGCCGCCTTTTCCCGGCTGTCTATCAGCAACATCCTAttgc                                                                                >  3:149324/1‑134 (MQ=255)                                        ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTTGGGCTGCAGCGCCGCCCCAACGTCTCAGGCGTTTACCTCCGGTCTATCAGAAACATCCTATTc                                                                                 >  2:329965/1‑135 (MQ=255)                                        ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCCGCGCCGCCCCAACGTCTCAGCCGTTTCCCTCCTGTGTATCAGAAACATCCTATTc                                                                                 >  8:10420/1‑135 (MQ=255)                                        ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCCGCGCAGCCCCCACGTCTCCGCCGTTTCCCTCCGGTCTATCAGAAACATCCTAt                                                                                   >  5:78640/1‑133 (MQ=255)                                        ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCCGCGCAGCCCCAACGTCTCAGCCGTTTCCCGCCTGTCTATCAGAAACATCCGAtt                                                                                  >  3:30158/1‑134 (MQ=255)                                        ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCAGCGCCGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTAt                                                                                   >  8:188300/1‑133 (MQ=255)                                        ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCAGCGCCGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTAt                                                                                   >  1:212898/1‑133 (MQ=255)                                        ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCAGCGCAGCCCCCACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTAt                                                                                   >  5:186245/1‑133 (MQ=255)                                        ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCAGCGCAGCCCCCACGTCTCAGCCGTTTCCCTCCTGTCTATAAGAAACATCCTAATc                                                                                 >  1:272683/1‑135 (MQ=255)                                        ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTAtt                                                                                  >  3:277410/1‑134 (MQ=255)                                        ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTAt                                                                                   >  2:7867/1‑133 (MQ=255)                                        ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTAt                                                                                   >  2:66449/1‑133 (MQ=255)                                        ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTAt                                                                                   >  8:102233/1‑133 (MQ=255)                                        ccTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTAt                                                                                   >  7:198890/1‑133 (MQ=255)                                        ccTGAAGGCTGTACACGGCTTTGTCAGCCAGCACGCCAACAGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTACCTCCTGTCTATCAGAAACATCCTAt                                                                                   >  1:32921/1‑133 (MQ=255)                                                     ctgggCTTTGCCACCCAGCACGGCAACCGCGGCAAGCCGCTTAAATTGCTGGGCGTTTGGGGCTGCCGCGCCCCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGgc                                                                     <  7:192287/132‑1 (MQ=255)                                                      aGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGGAGCGCCGGCCCCACCTGTCAGGCGGTTTCCGCCGGGGGATAAAAAACAACCTATTAAGCCAGCCCGgcgc                                                                   >  2:156285/1‑135 (MQ=255)                                                      aGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCGGCCGCGCCGCCCCAACGTCTCCTCCGTTTACCACCTGTCTATAACAAAAATACTATTAAGCCTGCCCGGCGcc                                                                  >  3:32168/1‑136 (MQ=255)                                                       gggCTTTGTCCGCCACCACGGCACCCGCGGCAACCCGCTGAAATTGCATGGCGTTGGGGGCGGCCGCGCCGCCCCCACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCa                                                                 <  3:29401/136‑1 (MQ=255)                                                           tttGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCAGCGCCGCCCCACCGGCTCAGCCTTTTACCTCCGGGCGATCAGAACCCTCCAAATCAGCCTGCCGGGCGCCAAGc                                                              >  4:266690/1‑135 (MQ=255)                                                             tGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCAGCGCCGCCCCAACCGCTCAGCCGTTTAAAACCTGGCTATCAGAAACATCCTATTAAGCCTGCCGGGCGCCAAGCa                                                             >  8:28601/1‑134 (MQ=255)                                                             tGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCAt                                                            >  4:333687/1‑135 (MQ=255)                                                              gTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCAGCGCACCCCCAACGGCTCAGCCGTTTCCCTCCAGTCTATCAGAAACAACCTATTCAGCCTGCCGGGCGCCCAGCaa                                                            >  2:343904/1‑133 (MQ=255)                                                                cagccagcACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCCGCGCAGCCCCCACCGCGGAGCCGTTTGCCGCCTGGGGATGAGGAACATCCTATTCCGCCTGCCGGGCGCCCCGCATaaa                                                         >  5:78300/1‑135 (MQ=255)                                                                cagccagcACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCAGCGCAGCCCCCACGTCTCAGCCTTTTACCGCCTGTCTATCAGAAACATCCTATTCAGCCAGCCGGGCGCCAAGCATaaa                                                         >  7:156626/1‑135 (MQ=255)                                                                cagccagcACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATaaa                                                         >  1:106088/1‑135 (MQ=255)                                                                cagccagcACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCAGCGCAGCCCCAACGTCTAAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAATCATaaa                                                         >  1:101050/1‑135 (MQ=255)                                                                     agcACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCGATCAGCAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGcc                                                   >  4:160310/1‑136 (MQ=255)                                                                        ccgcaaaCCGCGGAACGCCGGTGTATTTGATTGGGGTTTGGGGCTGCAGCGCAGCCCAAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGt                                                <  4:277410/131‑1 (MQ=255)                                                                                     cacgCCGCTTTATTTGCTTGGGGTTGGGGGCTGCAGCGCCCCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCATCAgg                                    <  5:128192/132‑1 (MQ=255)                                                                                     cAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCATCa                                      >  2:74975/1‑133 (MQ=255)                                                                                                aaTTGCATGGCGTTTGGGGCTGCAGCGGAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACCTCCTATTCAGCCTGCCGGGCGCCAAGCATTAATTAGCCGGTGCTCCCATCAGGAGCGGCTCATGc                        >  3:236212/1‑136 (MQ=255)                                                                                                 aTTGCTGGGGGTTGGGGGCGGCCGCCCCCCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCATCAGGAGCGGCTCATg                         <  8:156626/134‑1 (MQ=255)                                                                                                  ttGCTTGGCGTTGGGGGCGGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCATCAGGAGCGGCTCATGc                        <  7:264805/134‑1 (MQ=255)                                                                                                    gcttGGCGTTTGGGGCGGCCGCGCAGCCCAAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCATCAGGAGCGGCTCATGCAc                      <  6:78640/131‑1 (MQ=255)                                                                                                       tGGCGTTTGGGGGTGCAGCGCCGCCCCCACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCATCAGGAGCGGCTCATGCACCAGc                  <  8:198890/135‑1 (MQ=255)                                                                                                          cGTTTGGGGCGGCCGCGCCGCCCCAACGTCGCAGCCTTTTCCCTCCTGTCGATAAGAAACATCCTATTCAGCCTGCCCGGCGCCCAGCCTAAAATAGCCGGGCCGCCCCGCAGGAGCGGCTCCTGCACCAGccc                >  6:342709/1‑134 (MQ=255)                                                                                                                      cagcgcagcCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCATCAGGCGCGGCTCATGCACCAGCCCTATGTGTTGATTCa  >  3:88818/1‑136 (MQ=255)                                                                                                                        gcgcagcCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCATCAGGAGCGGCTCATGCACCAGCCCTATGTGTTGATTCa  >  8:275916/1‑134 (MQ=255)                                                                                                                            |                                                                                                                                  GTTCAGCCGTGAAGAGCGTTGCACGGTCCTGGCCAACGACCTGAAGGCTGTACAGGGCTTTGTCAGCCAGCACGGCAACCGCGGCAAGCCGCTGTAATTGCATGGCGTTTGGGGCTGCAGCGCAGCCCCAACGTCTCAGCCTTTTCCCTCCTGTCTATCAGAAACATCCTATTCAGCCTGCCGGGCGCCAAGCATAAATTAGCCGGTCCTCCCATCAGGAGCGGCTCATGCACCAGCCCTATGTGTTGATTCA  >  KT2440/1670567‑1670819

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: ‑