Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	KT2440	4,145,586	A→C	24.1%	intergenic (+131/+20)	CJ019_03903 → / ← nicP_9	hypothetical protein/Porin‑like protein NicP

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	KT2440	4,145,586	0	A	C	24.1%	59.7 / 3.5	48	intergenic (+131/+20)	CJ019_03903/nicP_9	hypothetical protein/Porin‑like protein NicP
Reads supporting (aligned to +/- strand):  ref base A (24/11);  new base C (3/9);  total (27/21)
Fisher's exact test for biased strand distribution p-value = 1.61e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGGCCTTTCGTTGCAAAAGATGAAACGGCTGGGTGCAGGCGTCCGAACGCCTGGTGCAATTCAGGCGGAAAACAGCGAACCCTTCGATTGGG‑AATAAATGGCGAAAAATGGGCCGGCTTCAGAAGGCCGGC‑CCGTTTCGCTATTTAGAAGTTGAAGGTGTAGCGCATGATCAGGCGATTTTCATTAGCGCTGTCAGCGTAGGTCGAGCGGTTCGTGGAGTTACGCCACTGAAACGAAACACCCTTCGCCGGACC  >  KT2440/4145463‑4145716                                                                                                                             |                                                                                                                                    tGGCCTTTCGTTGCAAAAGATGAAACGGCTGGGTGCAGGCGTCCGAACGCCTGGTGCAATTCAGGCGGAAAACAGCGAACCCTTCGATTGGG‑AATAAATGGCGAAAAATGGGGCGGGGTGAGAAGGGCGGc‑cccg                                                                                                                         >  5:82519/1‑133 (MQ=255) tGGCCTTTCGTTGCAAAAGATGAAACGGCTGGGTGCAGGCGTCCGAACGCCTGGTGCAATTCAGGCGGAAAACAGCGAACCCTTCGATTGGG‑AATAAATGGCGAAAAATGGGCCGGCTTCAGAAGGCCGGC‑CCGt                                                                                                                         >  3:99898/1‑135 (MQ=255) tGGCCTTTCGTTGCAAAAGATGAAACGGCTGGGTGCAGGCGTCCGAACGCCTGGTGCAATTCAGGCGGAAAACAGCGAACCCTTCGATTGGG‑AATAAATGGCGAAAAATGGGCCGGCGTCAGAAGGCCGGC‑CCGt                                                                                                                         >  8:136810/1‑135 (MQ=255) tGGCCTTTCGTTGCAAAAGATGAAACGGCTGGGTGCAGGCGTCCGAACGCCTGGTGCAATTCAGGCGGAAAACAGCGAACCCTTCGATTGGG‑AATAAATGGCGAAAAATGGGCCCGCGTCAGAAGGCCGGC‑CCgg                                                                                                                         >  7:68434/1‑134 (MQ=255)      tttCGTTGCAAAAGATGAAACGGCTGGGTGCAGGCGTCCGAACGCCTGGTGCAATTCAGGCGGAAAACAGCGAACCCTTCGATTGGG‑AATAAATGGCGAAAAATGGGCCGGCTTCAGAAGGCCGGC‑CCGTTTCg                                                                                                                     >  8:83737/1‑134 (MQ=255)      tttCGTTGCAAAAGATGAAACGGCTGGGTGCAGGCGTCCGAACGCCTGGTGCAATTCAGGCGGAAAACAGCGAACCCTTCGATTGGG‑AATAAATGGCGAAAAATGGGCCGGCTTCAGAAGGCCGGC‑CCGTTTCg                                                                                                                     >  2:30843/1‑134 (MQ=255)      tttCGTTGCAAAAGATGAAACGGCTGGGTGCAGGCGTCCGAACGCCTGGTGCAATTCAGGCGGAAAACAGCGAACCCTTCGATTGGG‑AATAAATGGCGAAAAATGGGCCGGCTTCAGAAGGCCGGC‑CCGTTTCg                                                                                                                     >  3:146777/1‑134 (MQ=255)      tttCGTTGCAAAAGATGAAACGGCTGGGTGCAGGCGTCCGAACGCCTGGTGCAATTCAGGCGGAAAACAGCGAACCCTTCGATTGGG‑AATAAATGGCGAAAAATGGGCCCGCGTGAGCACGCCGGCGCCGttagc                                                                                                                     >  8:261201/1‑132 (MQ=255)      tttCGTTGCAAAAGATGAAACGGCTGGGTGCAGGCGTCCGAACGCCTGGTGCAATTCAGGCGGAAAACAGCGAACCCTTCGATTGGG‑AATAAATGGCGAAAAATGGGCCCGCGTCAGAAGGCCGGG‑CCGgttgg                                                                                                                     >  7:261944/1‑132 (MQ=255)          tttGAAAAAGAGCAACGGGCTGGGGGCAGGGGCCCGACCGCCGGGTGAAATTCAGGCGAAAACCAGCCAACCCTTCGATTGGC‑AAAAAATGGCCAAAAATGGGCCGGCTTCATACGCCCGGC‑CCGTTTCGCTAtt                                                                                                                <  4:149259/134‑1 (MQ=255)          gTTGCAAAAGATGAAACGGCTGGGTGCAGGCGTCCGAACGCCTGGTGCAATTCAGGCGGAAAACAGCGAACCCTTCGATTGGG‑AATAAATGGCGAAAAATGGGCCGGCTTCCGCAGGCCGGC‑CCGTGTCGcgtgt                                                                                                                >  7:151313/1‑131 (MQ=255)           ttGCAAAAGATGAAACGGCTGGGTGCAGGCGTCCGAACGCCTGGTGCAATTCAGGCGGAAAACAGCGAACCCTTCGATTGGG‑AATAAATGGCGAAAAATGGGCCGGCTTCCGAAAGCCCGC‑CCCTTTCGCTAttt                                                                                                               >  2:157100/1‑135 (MQ=255)           ttGCAAAAGATGAAACGGCTGGGTGCAGGCGTCCGAACGCCTGGTGCAATTCAGGCGGAAAACAGCGAACCCTTCGATTGGG‑AATAAATGGCGAAAAATGGGCCGGCTTCAGACGGCCGGC‑CCGGTTCGCGAttt                                                                                                               >  4:84197/1‑135 (MQ=255)           ttGCAAAAGATGAAACGGCTGGGTGCAGGCGTCCGAACGCCTGGTGCAATTCAGGCGGAAAACAGCGAACCCTTCGATTGGG‑AATAAATGGCGAAAAATGGGCCGGCTTCAGAATGCCGGC‑CCGTTTCGCtttt                                                                                                                >  4:73196/1‑134 (MQ=255)           ttGCAAAAGATGAAACGGCTGGGTGCAGGCGTCCGAACGCCTGGTGCAATTCAGGCGGAAAACAGCGAACCCTTCGATTGGG‑AATAAATGGCGAAAAATGGGCCGGCGTCAGAAGGGCGGC‑CCCGTTCgggaatt                                                                                                               >  4:287912/1‑129 (MQ=255)           ttGCAAAAGATGAAACGGCTGGGTGCAGGCGTCAGAACGCCTGGTGCAATTCAGGCGGAAAAAAGCGAACCCTTCGATTGGG‑AATAAATGGCGAAAAATGGGCCGGCTGAAGACTGCCGGC‑CCGTGTCGcaagtt                                                                                                               >  7:155527/1‑130 (MQ=255)                aaaGATGAAACGGCTCGGAGCAGGCGTCAGAACGCCTGTTGCAATTCAGGCGGAAAACAGCGAACCCATCGATTGGG‑AATAAATGGCGAAAAATTCGCCCGCATCAGACAGCCCGC‑CCCGTTGGCTATTTAGaaa                                                                                                          >  2:159018/1‑134 (MQ=255)                      aaacgggCTGGGTGCTGGGGTCGCAACGCTGGGTGCATTTCAGGGTTAAAACACCCACCCCTTCTTTGGGG‑AATAAATGGCGAAAATTGGGCCGGCTTCATAAGGCGGGC‑CCGTTTCGCTATTTAGAAGTTGAAg                                                                                                    <  6:82519/130‑1 (MQ=255)                       aacgggCTGGGGGCCGGCGTCCCACGGCCGGGGCCAATACCGGCGAAAACCCGC‑CCCCCATCGCTTGGGAAAAAAAGGGCAAAAAAGGGCCCGGCTCACCAGGGCGGGC‑CCGTTTCGCTATTTAGAAGTTGAAg                                                                                                    <  6:243492/130‑1 (MQ=255)                       aaaCGGCTGGGTGCAGGCGTCCGAACGCCTGGTGCAATTCAGGCGGAAAACAGCGAACCCTTCGATTGGG‑AATAAATGGCGAAAAATGGGCCGGCTTCAGAAGGCCGGC‑CCGTTTCGCTATTTAGAAGTTGAAgg                                                                                                   >  2:14534/1‑135 (MQ=255)                            gaggggTGCAGGCGGCCGAACGCCGGTTGAAATTCCGGCGTAAAACAGCGAACCCTTCGATTGGG‑AATAAATGGCGAAAAATGGGCCGGGTGCTGACGGCCGGC‑CCGTTTCGCTATTTAGAAGTTGAAGGTGTAg                                                                                              <  8:167878/132‑1 (MQ=255)                                            cGAACGCCTGGTGCAATTCAGGCGGAAAACAGCGAACCCTTCGATTGGG‑AATAAATGGCGAAAAATGGGCCGGCTTCAGAAGGCCGGC‑CCGTTTCGCTATTTAGAAGTTGAAGGTGTAGCGCATGATCAGGCGAt                                                                              <  4:146777/135‑1 (MQ=255)                                              aaCGCCTGGTGCAATTCAGGCGGAAAACAGCGAACCCTTCGATTGGG‑AATAAATGGCGAAAAATGGGCCGGCGTCAGCAGGCCGGC‑CCGGTTCGCGATTTAGAAGTTGAAGGTGTAGCGCATGATCAGGCGAtt                                                                             >  4:72757/1‑134 (MQ=255)                                               aCGCCTGGTGCAATTCAGGCGGAAAACAGCGAACCCTTCGATTGGG‑AATAAATGGCGAAAAATGGGCCGGCTTCATAAGGCCGGC‑CCGGTTAGCAATTTATAAGTTGAAGGTGTAGCGCATGATCAGGCGAttt                                                                            >  6:215295/1‑134 (MQ=255)                                               aCGCCTGGTGCAATTCAGGCGGAAAACAGCGAACCCTTCGATTGGG‑AATAAATGGCGAAAAATGGGCCGGCGTACGCACGCCGGC‑CCCGTTCGCGATTTAGAAGTTGAAGGTGTAGCGCATGTACAGGCGAatt                                                                            >  7:199566/1‑134 (MQ=255)                                               aCGCCTGGTGCAATTCAGGCGGAAAACAGCGAACCCTTCGATTGGG‑AATAAATGGCGAAAAATGGGCCGGCATCAGCACGCCGGC‑CCGTTTCGGTATTTAGAAGTTGAAGGTGTAACGCATGAAGAGGCGAtgt                                                                            >  4:165466/1‑132 (MQ=255)                                                    tGGTGCAATTCAGGCGGAAAACAGCGAACCCTTCGATTGGG‑AATAAATGGCGAAAAATTGGCCGGCTTCAGAACGCCGGC‑CCGGTTCGCTATTTAGAACTTGAAGGTGTATCGCATGAACAGGCGAATTTAATTa                                                                      >  4:113519/1‑135 (MQ=255)                                                       tGCAATTCCGGCGCAAAACCGCAACCCCTGCGTTGGGC‑AAAAAAGGGCCAAAACGGGGCCGGCTTCAGAAGCCCGGC‑CCGTTTCGCTATTTAGAAGTTGAAGGTGTAGCGCATGATCAGGCGATTTTCATTAgcg                                                                   <  1:162813/135‑1 (MQ=255)                                                       ggCAATTCCGGCGCAAAACCGCGAACCCTTCGATTGGC‑AAAAAATGGCTAAAAATGGGCGGGCTTCAGACGGCCGGC‑CCGTTTCGCTATTTAGAAGTTGAAGGTGTAGCGCATGATCAGGCGATTTTCATTAgcg                                                                   <  5:126888/134‑1 (MQ=255)                                                       ggCAATGCAGGCGGAAACCAGCCAACCCTTCGATTGGG‑AATAAATGGCGAAAAAGGGGCCGGCTTCACAAGGCCGGC‑CCGTTTCGCTATTTAGAAGTTGAAGGTGTAGCGCATGATCAGGCGATTTTCATTAg                                                                     <  4:206098/132‑1 (MQ=255)                                                        gCAATTCAGGCGGAAAACAGCGAACCCTTCGATTGGG‑AATAAATGGCGAAAAATGGGCCGGCTTCAGAAGGCCGGC‑CCGTTTCGCTATTTAGAAGTTGAAGGTGTAGCGCATGATCAGGCGATTTTCATTAgcgc                                                                  <  4:99898/135‑1 (MQ=255)                                                        gCAATTCAGGCGGAAAACAGCGAACCCTTCGATTGGG‑AATAAATGGCGAAAAATGGGCCGGCCTCAGAAGGCCGGC‑CCGTTTCGCTATTTATAAGTTGAACGTGTAGCGCCTGCTCAGGCGAGTTTCATTAgcgc                                                                  >  6:77481/1‑135 (MQ=255)                                                               aGGCGGAAAACAGCGAACCCTTCGATTGGG‑AATAAATGGCGAAAAATGGGCCGGCTTAAGAAGGCCGGC‑CCGGTTCGCTATTTTGAATTTGAAGGTGTAGCGCATGATAACGCGAATTTCATTAGCGCTGTCAGc                                                           >  2:204875/1‑135 (MQ=255)                                                                       aaCAGAGAACCCTACGATTGTG‑AATAAATGGCTAAAATTGTCCCGGCTTCATACGGCGGGC‑CCGTTTCGCTATTTAGAAGTTGAAGGTGTAGCGCATGATCAGGCGATTTTCATTAGCGCTGTCAGCGTAGGTCg                                                   <  8:53294/135‑1 (MQ=255)                                                                        accgCGACCCCTTGGATTGGT‑AAAAAATGGCTAAAAATGGGCCGGCTTCAGACGGCCGGC‑CCGTTTCGCTATTTAGAAGTTGAAGGTGTAGCGCATGATCAGGCGATTTTCATTAGCGCTGTCAGCGTAGGTCGa                                                  <  8:261944/132‑1 (MQ=255)                                                                             caccccGTCGATTGGG‑AATAAATGTCGAAAAATGGCCCGGCTGAAGAAGGCCGGC‑CCGTTTCGCTATTTAGAAGTTGAAGGTGTAGCGCATGATCAGGCGATTTTCATTAGCGCTGTCAGCGTAGGTCGAGCGGt                                             <  5:43855/132‑1 (MQ=255)                                                                              aaCCCTTCGATTGGG‑AATAAATGGCGAAAAATGGGCCGGCGTCAGAAGGCCGGC‑CCGGTTGGCGTTTTAGAAGTTGAAGGTGTTGCGCATGATCAGGCGCTTTTAATTATCGCTGTGAGCGTTGGTCGAGCGGtt                                            >  3:52468/1‑135 (MQ=255)                                                                                      gATTGGG‑AATAAATGGCGAAAAAGGGGCGGGCTTCAGAAGGCCGGC‑CCGTTTCGCTATTTAGAAGTTGAAGGTGTAGCGCATGATCAGGCGATTTTCATTAGCGCTGTCAGCGTAGGTCGAGCGGTTCGTGGAg                                     <  3:266421/134‑1 (MQ=255)                                                                                            g‑AATAAATGGCGAAACATGGGCCGGCTTCAGAAGGCCGGC‑CCGTTTCGCTATTTAGAAGTTGAAGGTGTAGCGCATGATCAGGCGATTTTCATTAGCGCTGTCAGCGTAGGTCGAGCGGTTCGTGGAGTTACGc                               <  4:202901/134‑1 (MQ=255)                                                                                                 aaaTGGCGAAAAATGGGGCGGCTTCAGCAGGCCGGC‑CCGTTTGGCGATTTAGAAGTTGAAGGTGTTGCGCATGATCAGGCGATTTTGATTAGGGCTGTGAGCGTTGGTCGCGCGGTTCGTGGTGTTACGCCCCt                           >  6:154184/1‑134 (MQ=255)                                                                                                 aaaTGGCGAAAAATGGGCCGGCTTGAGAAGGCCGGC‑CCGGTTCGGTATTTATAAGTTGTATGTGTAGCGCATGTGCCGGCGATTTTAATTTTCGCTGTCCGCGTAGGTCGCGCGGTTCGTGGCGTTTCGCCCCt                           >  7:235659/1‑134 (MQ=255)                                                                                                      ggcaaaaaTGGGCGGCCTTCTGACCGCCGGC‑GCGTTTCGCTTTTTAGAAGTTGAAGGTGTAGCGCATGATCTGCAGATTTTCAATAGCGCTGTCAGCGTAGGTCGAGCGGTTCGTGGAGTTACGCCACTgaaacg                     <  3:240701/132‑1 (MQ=255)                                                                                                        caaaaaGGGGCCGGCTGCACACGGCGGGC‑CCGGTTCGCTATTTAGAAGTTGAAGGTGTAGCGCATGATCAGGCGATTTTCATTAGCGCTGTCAGCGTAGGTCGAGCGGTTCGTGGAGTTACGCCACTgaaacgaa                   <  1:247176/134‑1 (MQ=255)                                                                                                          aaatTGGGCGGGCTGCAGACGGCCGGC‑CCGTTTCGCTATTTAGAAGTTGAAGGTGTAGCGCATGATCAGGCGATTTTCATTAGCGCTGTCAGCGTAGGGCGAGCGGTTCGTGGAGTTACGCCACTgaaacgaaac                 <  3:176961/135‑1 (MQ=255)                                                                                                                    ggattCAGACGGCCGGC‑CCGTTTCGCTATTTAGAAGTTGAAGGTGTAGCGCATGATCAGGCGATTTTCATTAGCGCTGTCAGCGTAGGTCGAGCGGTTCGTGGAGTTACGCCACTGAAACGAAACACCCTTCGcc       <  7:66125/132‑1 (MQ=255)                                                                                                                    ggCTTCAGAAGGCCGGC‑CCGTTTCGCTATTTAGAAGTTGAAGGTGTAGCGCATGATCAGGCGATTTTCATTAGCGCTGTCAGCGTAGGTCGAGCGGTTCGTGGAGTTACGCCACTGAAACGAAACACCCTTCGcc       <  4:54196/135‑1 (MQ=255)                                                                                                                          aGAAGGCCGGC‑CCGTTTCGCTATTTAGAAGTTGAAGGTGTAGCGCATGATCAGGCGATTTTCATTAGCGCTGTCAGCGTAGGTCGAGCGGTTCGTGGAGTTACGCCACTGAAACGAAACACCCTTCGCCGGAcc  <  7:166421/134‑1 (MQ=255)                                                                                                                          aGAAGGCCGGC‑CCGTTTCGCTATTTAGAAGTTGAAGGTGTAGCGCATGATCAGGCGATTTTCATTAGCGCTGTCAGCGTAGGTCGAGCGGTTCGTGGAGTTACGCCACTGAAACGAAACACCCTTCGCCGGAcc  <  1:30843/134‑1 (MQ=255)                                                                                                                             |                                                                                                                                    TGGCCTTTCGTTGCAAAAGATGAAACGGCTGGGTGCAGGCGTCCGAACGCCTGGTGCAATTCAGGCGGAAAACAGCGAACCCTTCGATTGGG‑AATAAATGGCGAAAAATGGGCCGGCTTCAGAAGGCCGGC‑CCGTTTCGCTATTTAGAAGTTGAAGGTGTAGCGCATGATCAGGCGATTTTCATTAGCGCTGTCAGCGTAGGTCGAGCGGTTCGTGGAGTTACGCCACTGAAACGAAACACCCTTCGCCGGACC  >  KT2440/4145463‑4145716

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: ‑