Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	KT2440	4,880,240	T→A	21.8%	M90L (ATG→TTG)	CJ019_04574 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	KT2440	4,880,240	0	T	A	21.8%	78.9 / 2.0	53	M90L (ATG→TTG)	CJ019_04574	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (15/25);  new base A (8/3);  total (23/30)
Fisher's exact test for biased strand distribution p-value = 4.77e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATCGCACTGATCGCACACTGCTCGTCGATATCCGACGTATCGCCGCTGATCCCCACGGCACCCAGCACCTTGCCGTCCTGATCACGAATCAGCACCCCACCCGGCGCCGGCACCACCGGCCGC‑TCACCCATCCCGTTCAACGCGGCAAAAAAAGCCGGCCGCTGCTGCGCATCCAGCGCCAGCAAGCGCGAGCCCTTGCCCAGGGCAATCGCACCCCAGGCTTTGCCAGTGGCCACTTCAGGCCGAATCAGGCTAGCGCCATCC  >  KT2440/4880110‑4880373                                                                                                                                    |                                                                                                                                      aTCGCACTGATCGCACACTGCTCGTCGATATCAGACGTATCGCCGCTTATCCCCACGGCACCCAGCAACTTGCAGTCCTCAACACGAATCAGCACACCACCCGCCGACCGCCAAACACGCCGC‑TCACCCAAcccc                                                                                                                                   >  4:380027/1‑134 (MQ=255)     cACTGATCGCACACTGCTCGTCGATATCCGACGTATCGCCGCTGATCCCCACGGCACCCAGCACCTTGCCGTCCTGATCACGAATCAGCACCCCCCCCCGCGCCCGCCCCCCCCGCCGC‑TCACCCAAcccagtct                                                                                                                               >  8:382876/1‑130 (MQ=255)        tGATCGCACACTGCTCGTCGATATCCGACGTATCGCCGCTGATCCCCACGGCACCCAGCACCTTGCCGTCCTGATCACGAATCAGCACCCCACCCGGCGCCGGCACCACCGGCCGC‑TCACCCATCCCGTTCAAcg                                                                                                                            >  4:42630/1‑135 (MQ=255)             gCACACTGCTCGTCGATATCCGACGTATCGCCGCTGATCCCCACGGCACCCAGCACCTTGCCGTCCTGATCACGAATCAGCACCCCCCCCGGCGCCCGCCCCCCCGGCCGC‑GCCCCCATACCCGTCAAccccgc                                                                                                                        >  3:17103/1‑129 (MQ=255)                   tGCTCGTCGATATCCGACGTATCGCCGCTGATCCCCACGGCACCCAGCACCTTGCCGTCCTGATCACGAATCAGCACCCCACCCGGCGCCCGCACAACCCGCCGC‑TCCCCCAACCACTTCAACCCCGCaaaaaaa                                                                                                                 >  2:350783/1‑135 (MQ=255)                       cgtcgATATCCGACGTATCGCCGCTGATCCCCACGGCCCCCAGCACCTTGCCGTCCTGATAACGAATCAGCACCCCCCCCGCCGCCGGCCACAACGGCCGC‑AGACCCCTCCCGGTCAACGCGGCAAAAAAAcccg                                                                                                             >  7:98138/1‑135 (MQ=255)                       cgtcgATATCCGACGTATCGCCGCTGATCCCCACGGCACCCAGCACCTTGCCGTCCTGATCACGAATCAGCACCCCCCCCGGCGCCGGCCCCACCGGCCGC‑TCACCCATCCCCGTCCACGCGGCCACAAAAgccc                                                                                                             >  7:277320/1‑134 (MQ=255)                       cgtcgATATCCGACGTATCGCCGCTGATCCCCACGGCACCCAGCACCTTGCCGTCCTGATCACGAATCAGCACCCCACCCGGCGCCGGCACCACCGGCCGCGGCCCCCATCCCGGTAAACCCGGCAAAAAAAccc                                                                                                              >  1:320762/1‑135 (MQ=255)                            atatCCGACGTATCGCCGCTGATCCCAACGGCACCCAGCACCTTGCCGTCCTGATCACCAATCAGCACCCCACCCGGCGCCGGCACCAACCGCCGC‑GCCCCCCACACGGTGAACGCGGCGAAAAAAaccggcccc                                                                                                        >  4:320527/1‑133 (MQ=255)                                cctccGTTTCGCCGCTGACCACCACGGCACCCAGCACCTTGCCGGCCTGATCACCAATCACCACCCCACCCGGCGCCGGCACCCCCGGCCGC‑GCACCCATCCCGTTCAACGCGGCAAAAAAAGCCGGCCgctgct                                                                                                    <  6:149822/131‑1 (MQ=255)                                ccGACGTATCGCCGCTGATCCCCACGGCACCCAGCACCTTGCCGTCCTGATCACGAATCAGCCCCCCCCCCGGCGCCGGCCCCCCCGGCCGC‑TCCCCCAAACCCTTCAACGCGGCAAAAAAAgcccgccccagca                                                                                                    >  4:35686/1‑129 (MQ=255)                                ccGACGTATCGCCGCTGATCCCCACGGCACCCAGCACCTTGCCGTCCTGATCACGAATCAGCACCCCACCCCGCGCCCGCACCACCCGCCGC‑GCCCCCAACCCCTTCAACCCCGCAAAAAAAgcccgccccggca                                                                                                    >  2:312533/1‑129 (MQ=255)                                  gACGTATCGCCGCTGATCCCCACGGCACCCAGCACCTTGCCGTCCTGATCACGAATCAGCACCCCCCCCGGCGCCGGCCCCCCCCGCCGC‑GCCCCCATCCCGGTCAACCCGGCAAAAAAAGCCGGCCGCggcggc                                                                                                  >  7:228264/1‑135 (MQ=255)                                               tGATCCCCCCGGCACCCACCACCTTGCCGTCCTGATCACCAATCAGCACCCCACCCGGCGCCGGCACCACCGGCCGC‑TCACCCATCCCGTTCAACGCGGCAAAAAAAGCCGGCCGCTGCTGCGCATCCAGCGCCa                                                                                     <  2:4602/135‑1 (MQ=255)                                                     ccACGGCACCCCGCACCTTGCCGTCCTGAGCACGAATCCGCACCCCACCCGGCGCCGGCACCCCGGGCCGC‑TCACCCATCCCGTTCCCCGCCGCAAAAAACGCCGGCCGCTGCTGCGCATCCAGCGCCAGCATgc                                                                               <  4:291832/135‑1 (MQ=255)                                                         ggCACCCAGCACCTTGCCGTCCTGATCACGAATCAGCACCCCACCCGGCGCCGGCCCCCCCGGCCGC‑TCACCCCTCCCGGTAAACGCGGCAAAAAAAGCCGGCCGCAGCGGCGCCTACACCGCCAGCAAccgcca                                                                           >  4:285047/1‑133 (MQ=255)                                                          gCACCCCGCACCTTGCCGCCCTGATCACGACTCCGCACCCCACCCGGCGCCGGCACCACCGGCCGC‑TCACCCATCCCGTTCAACGCGGCAAAAAACGCCGGCCGCTGCTGCGCATCCAGCGCCAGCAAGCGCGAg                                                                          <  1:16273/135‑1 (MQ=255)                                                          gCACCCAGCACCTTGCCGTCCTGATCACGAATCAGCACCCCACCCGGCGCCGGCACCACGGGCCGC‑TCACCCAACCCGTGCACCGCGCAAAAAAACGCCGGCCGCTGCTGCGCATCCAGCGCCAGCAAGCGCGAg                                                                          <  1:312533/135‑1 (MQ=255)                                                          gCACCCAGCACCTTGCCGTCCTGATCACGAATCAGCACCCCACCCGGCGCCGGCACCACCGGCCGC‑TCACCCATCCCGTTCAACGCGGCAAAAAAAGCCGGCCGCTGCTGCGCATCCAGCGCCAGCAAGCGCGAg                                                                          <  8:356305/135‑1 (MQ=255)                                                          ccacccaccCCCTTGCCGTCCTGACCACGAATCAGCACCCCACCCGCCGCCGGCCCCCCCGGCCGC‑TCCCCCATCCGGTGCAACGCGGCAAAAAAAGCCGGCCGCTGCTGCGCATCCAGCGCCAGCAAGCGCGAg                                                                          <  1:261733/134‑1 (MQ=255)                                                               catcACCTTGCCGTCCTGATCACGAATCAGCCCCCCACCCGGCGCCGGCACCACCGGCCGC‑GCACCCATCCCGTTCAACGCGGCAAAAAATGCCGGCCGCTGCTGCGCATCCAGCGCCAGCAAGCGCGAGCCCtt                                                                     <  4:320582/132‑1 (MQ=255)                                                               cAGCACCTTGCCGTCCTGATCACGAATCAGCACCCCACCCGGCGCCGGCACCACCGGCCGC‑TCACCCATCCCGTTCAACGCGGCAAAAAAAGCCGGCCGCTGCTGCGCATCCAGCGCCAGCAAGCGCGAGCCCtt                                                                     <  7:231545/135‑1 (MQ=255)                                                               cAGCACCTTGCCGTCCTGATCACGAATCAGCACCCCACCCGGCGCCGGCACCACCGGCCGC‑TCACCCATCCCGTTCAACGCGCCAAAAAAAGCCGGCCGCTGCTGCGCATCCAGCGCCAGCAAGCGCGAGCCCtt                                                                     <  1:65162/135‑1 (MQ=255)                                                                aGCACCTTGCCGTCCTGATCACGAATCAGCACCCCACCCGGCGCCGGCACCCCCGGCCGC‑TCCCCCATCCCGTTCAACGCGGCAAAAAAAGCCGGCCGCTGCTGCGCCACCCGCGCCAGCAAGCGCGCGCCCTTg                                                                    >  4:159166/1‑135 (MQ=255)                                                                aGCACCTTGCCGTCCTGATCACGAATCAGCACCCCACCCGGCGCCGGCACCACCGGCCGC‑TCACCCATCCCGGTCAACGCGGCAAAAAAAGCCGGCCGCTGCTGCGCCTCCAGCGCCAGCCAGCGCCCGCCCGTg                                                                    >  3:305413/1‑135 (MQ=255)                                                                aGCACCTTGCCGTCCTGATCACGAATCAGCACCCCACCCGGCCCCGGCCCCCCCGGCCGC‑TCCCCCCAACCCTTCAAAGCGGCAAAAAAAACCCGCCCCGGCAGCGCCTACACCGCCCGCCACCCCGAGCCCATg                                                                    >  1:278788/1‑135 (MQ=255)                                                                   aCCTTGCCGTCCTGATCACGAATCAGCACCCCACCCGGCGCCGGCCCCACCGGCCGC‑GCCCCCCTCCCGTTCCACGCGGGAAAAAAAGCCGGCCGCTGGGGGGCCTCCCGCGCCCGCCAGCGCGCCCCCGTGccc                                                                 >  2:43015/1‑135 (MQ=255)                                                                         ccGTCCTGATCACGAATCAGCACCCCACCCGGCGCCGGCACCACCGGCCGC‑TCACCCATCCCGTTCAACGCGGCAAAAAAAGCCGGCCGCTGCTGCGCATCCAGCGCCAGCAAGCGCGAGCCCTTGCCCAGGGc                                                            <  8:228264/134‑1 (MQ=255)                                                                          cGTCCTGATCACGAATCAGCACCCCACCCGGCGCCGGCACCACCGGCCGC‑GCCCCCAACCCGTTCAACCCGGCAAAAAAACCCCGCCGCGGCGGCGCAACCCGCGCCACCCACCCCGCGCCCATGCCCAggggc                                                           >  2:296840/1‑132 (MQ=255)                                                                          cGTCCTGAGCACTAATCAGCACCCCCCCCGGCGCCGGCACCACCGGCCGC‑TCACCCCCCCCGTGCACCGCGCCAAAAAACGCCGGCCGCTGCTGCGCATCCAGCGCCAGCAAGCGCGAGCCCTTGCCCAGGGCaa                                                          <  5:126250/135‑1 (MQ=255)                                                                               tGATCACGAATCAGCACCCCACCCGGCGCCGGCACCACCGGCCGC‑TCACCCCTCCCGTTCAACGCGGCAAAAAAAGCCGGCCGCTGCTGCGCATCCCGCGCCCGCAAGCCCCCGCCCATTCCCACGGCCATCGCa                                                     >  2:209375/1‑135 (MQ=255)                                                                               tGATCACGAATCAGCACCCCACCCGGCGCCGGCACCACCGGCCGC‑TCACCCATCCCGTTCCACGCCGCAAAAAAAGCCGGCCCCTGCTGCGCCTCCAGCGCCCGCAAGCCCGCGCCCATGCCCACGGCAATCGcc                                                     >  2:215943/1‑134 (MQ=255)                                                                                 aTCACGAATCAGCACCCCACCCCGCCCCCGCACCACCCGCCGC‑TCACCCATCCCCTTCAACCCCGCAAAAAAAGCCCGCCGCTACTTCGCATCCAGCGCCACCAACCGCCCGCCCTATCCCACGGCCATCGcccc                                                   >  4:162535/1‑135 (MQ=255)                                                                                      gAATCAGCACCCCCCCCGGCGCCGGCACCACCGGCCGC‑TCACCCATCCCGTTCAACGCGGCAAAAAAAGCCGGCCGCTGCTGCGCATCCAGCGCCAGCAAGCGCGAGCCCTTGCCCAGGGCAATCGCACCCCAgg                                              <  1:209375/135‑1 (MQ=255)                                                                                      gAATCAGCACCCCACCCGGCGCCGGCACCACCGGCCGC‑TCACCCATCCCGTTCACCGCGGCAAAAAAAGCCGGCCGCTGCTGCGCATCCAGCGCCAGCAAGCGCGAGCCCTTGCCCAGGGCAATCGCACCCCAgg                                              <  1:215943/135‑1 (MQ=255)                                                                                            gCACCCCACCCGGCGCCGGCACCACCGGCCGC‑TCACCCATCCCGTTCAACGCGGCAAAAAAAGCCGGCCGCTGCTGCGCATCCAGCGCCAGCAAGCGCGAGCCCTTGCCCAGGGCAATCGCACCCCAGGCTTTg                                         <  8:332480/134‑1 (MQ=255)                                                                                               ccccacccGGCGCCGGCACCACCGGCCGC‑GCACCCATCCCGTTCAACGCGGCAAAAAAAGCCGGCCGCTGCTGCGCATCCAGCGCCAGCAAGCGCGAGCCCTTGCCCAGGGCAATCGCACCCCAGGCTTTGCCAg                                     <  4:17103/135‑1 (MQ=255)                                                                                                cccccccGGCGCCGGCCCCACCGGCCGC‑TCCCCCAACCCGTTCACCGCGCCAAAAAAAGCCGGCCGCTGCTGCGCATCCAGCGCCAGCAAGCGCGAGCCCTTGCCCAGGGCAATCGCACCCCAGGCTTTGCCAGt                                    <  1:362798/135‑1 (MQ=255)                                                                                                cccacccGGCGCCGGCACCACCGGCCGC‑TCACCCATCCCGGTCAACGCGGCAAAAAAAGCCGGCCGCTGCTGCGCATCCAGCGCCAGCAAGCGCGAGCCCTTGCCCAGGGCAATCGCACCCCAGGCTTTGCCAGt                                    <  2:259129/135‑1 (MQ=255)                                                                                                     ccGGCGCCGCCACCCCCGGCCGC‑GCCCCCATCCGGGTCCCCGCGCCAAAAAACCCCGGCCGCTGCTGCGCATCCAGCGCCAGCAAGCGCGAGCCCTTGCCCAGGGCAATCGCACCCCAGGCTTTGCCAGTGGCCa                               <  7:144595/135‑1 (MQ=255)                                                                                                         cgcCGGCACCACCGGCCGC‑TCACCCATCCCGTTCAACGCGGCAAAAAAAGCCGGCCGCTGCTGCGCATCCAGCGCCAGCAAGCGCGAGCCCTTGCCCAGGGCAATCGCACCCCAGGCTTTGCCAGTGGCCACTTc                           <  6:139395/135‑1 (MQ=255)                                                                                                               caccccCGGCGGC‑TCCCCCTACCGGTCCAACGCGGCAAAAAATGCCGGCCGCTGCTGCGCATCCAGCGCCAGCAAGCGCGAGCCCTTGCCCAGGGCAATCGCACCCCAGGCTTTGCCAGTGGCCACTTCAGGCCg                     <  3:35686/135‑1 (MQ=255)                                                                                                               caccccCGGCCGC‑GCACCCATCCCGTTCAACGCGGCAAAAAAAGCCGGCCGCTGCTGCGCATCCAGCGCCAGCAAGCGCGAGCCCTTGCCCAGGGCAATCGCACCCCAGGCTTTGCCAGTGGCCACTTCAGGCCg                     <  4:75956/135‑1 (MQ=255)                                                                                                               caccccCGCCCGC‑TCCCCCACCCCATACAACCCCCAAAAAAACGCCGGCCGCTGCTGCGCATCCAGCGCCAGCAAGCGCGAGCCCTTGCCCAGGGCAATCGCACCCCAGGCTTTGCCAGTGGCCACTTCAGGCCg                     <  1:185858/135‑1 (MQ=255)                                                                                                               caccacGGGCCGC‑TCACCCATCCCGTTCAACGCGGCAAAAAAAGCCGGCCGCTGCTGCGCATCCAGCGCCAGCAAGCGCGAGCCCTTGCCCAGGGCAATCGCACCCCAGGCTTTGCCAGTGGCCACTTCAGGCCg                     <  2:320762/135‑1 (MQ=255)                                                                                                               caccacCGGCCGC‑TCACCCATCCCGTTCAACGCGGCAAAAAACGCCGGCCGCTGCTGCGCATCCAGCGCCAGCAAGCGCGAGCCCTTGCCCAGGGCAATCGCACCCCAGGCTTTGCCAGTGGCCACTTCAGGCCg                     <  3:285047/135‑1 (MQ=255)                                                                                                               caccacCGGCCGC‑GCACCCCTCCCGTGCAACGCGGCAAAAACAGCCGGCCGCTGCTGCGCATCCAGCGCCAGCAAGCGCGAGCCCTTGCCCAGGGCAATCGCACCCCAGGCTTTGCCAGTGGCCACTTCAGGCCg                     <  2:233085/135‑1 (MQ=255)                                                                                                                 ccaccGGCCGC‑TCACCCATCCCGTTCAACGCGGCAAAAAAAGCCGGCCGCTGCTGCGCATCCAGCGCCAGCAAGCGCGAGCCCTTGCCCAGGGCCATAGCACCCCAGGCATTGCCAGTGGCCACATCAGGccca                    >  3:37405/1‑132 (MQ=255)                                                                                                                   accGGCCGC‑GCACCCATCCCGTTCACCGCGGCAAAAAACGCCGGCCGCTGCTGCGCATCCAGCGCCAGCAAGCGCGAGCCCTTGCCCAGGGCAATCGCACCCCAGGCTTTGCCAGTGGCCACTTCAGGCCGAATc                 <  4:7129/135‑1 (MQ=255)                                                                                                                             tCACCCATCCCGTTCAACGCGGCAAAAAAAGCCGGCCGCTGCTGCGCCTCCAGCGCCCGCAAGCGCGCGCCCTTGCCCAGGGCAATCGCACCCCAGGCTTTGCCAGTGGCCACTTCAGGCCGAATCAGGCTAgcg        >  5:169534/1‑135 (MQ=255)                                                                                                                                   aTCCCGTTCAACGCGGCAAAAACAGCCGGCCGCTGCTGCGCATCCAGCGCCAGCAAGCGCGAGCCCTTGCCCAGGGCAATCGCACCCCAGGCTTTGCCAGTGGCCACTTCAGGCCGAATCAGGCTAGCGCCATcc  <  4:164792/135‑1 (MQ=255)                                                                                                                                   aTCCCGTTCAACGCGGCAAAAAAAGCCGGCCGCTGCTGCGCATCCAGCGCCAGCAAGCGCGAGCCCTTGCCCAGGGCAATCGCACCCCAGGCTTTGCCAGTGGCCACTTCAGGCCGAATCAGGCTAGCGCCATcc  <  7:250198/135‑1 (MQ=255)                                                                                                                                   aTCCCGTTCAACGCGGCAAAAAAAGCCGGCCGCTGCTGCGCATCCAGCGCCAGCAAGCGCGAGCCCTTGCCCAGGGCAATCGCACCCCAGGCTTTGCCAGTGGCCACTTCAGGCCGAATCAGGCTAGCGCCATcc  <  7:177198/135‑1 (MQ=255)                                                                                                                                    |                                                                                                                                      ATCGCACTGATCGCACACTGCTCGTCGATATCCGACGTATCGCCGCTGATCCCCACGGCACCCAGCACCTTGCCGTCCTGATCACGAATCAGCACCCCACCCGGCGCCGGCACCACCGGCCGC‑TCACCCATCCCGTTCAACGCGGCAAAAAAAGCCGGCCGCTGCTGCGCATCCAGCGCCAGCAAGCGCGAGCCCTTGCCCAGGGCAATCGCACCCCAGGCTTTGCCAGTGGCCACTTCAGGCCGAATCAGGCTAGCGCCATCC  >  KT2440/4880110‑4880373

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: ‑