Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	KT2440	4,292,547	T→G	22.4%	intergenic (+57/+34)	CJ019_04026 → / ← CJ019_04027	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	KT2440	4,292,547	0	T	G	22.4%	103.8 / 4.8	55	intergenic (+57/+34)	CJ019_04026/CJ019_04027	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (6/35);  new base G (10/3);  total (17/38)
Fisher's exact test for biased strand distribution p-value = 6.38e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGGCCCGATGCCGACCCGCGCCTCAGCCCAGGCACTGGCCGAACAGTTGCAACCAGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCTTTTTTTTCTTCGCGGATTGCCCGGGCTGCCCCCCTACGTTTGGCCGCTACTGCCCAGCTTACTGGTCAGCACCATGACCTTGCCTTGCAGCCGGCCTACGGTCATCACCAGTTCGTTTCGTTCCTTGGCGAGCA  >  KT2440/4292418‑4292681                                                                                                                                   |                                                                                                                                       cGGCCCGATGCCGACCCGCGCCTCAGCCCAGGCACTGGCCGAACAGTTGCAACCAGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCCCCAATTTTGCGGGCgttttt                                                                                                                                   >  6:396431/1‑135 (MQ=255)      cGATGCCGACCCGCGCCTCAGCCCAGGCACTGGCCGAACAGTTGCAACCAGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCTTTTTTttcttc                                                                                                                             <  8:186305/136‑1 (MQ=255)           ccGACCCGCGCCTCAGCCCAGGCACTGGCCGAACAGTTGCAACCAGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCTTTTTTTTGTTCGCgg                                                                                                                         >  4:393887/1‑135 (MQ=255)                 cgcgCCTCAGCCCAGGCTCTGGCCGAACAGTTGCAACCAGGCACTTTGGGTGCCTGATCCGAAGTTGTTGTGCGTTGCTCCCTACGCCCTTGTCGGCCCCCCCATTTGGGGGGGTGGTTTTTTTTGGGGGGTTGc                                                                                                                    >  5:61019/1‑135 (MQ=255)                 cgcgCCTCAGCCCAGGCACTGGCCGAACAGTTGCAACCAGGCCCTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGGCAATTTTGCGGGCCGTTTTTTCGTCGCGGAGTggc                                                                                                                   >  1:44422/1‑133 (MQ=255)                 cgcgCCTCAGCCCAGGCACTGGCCGAACAGTTGCAACCAGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCCATTTTGCGGGGGTGTTTTTCGTCGCGGATTggc                                                                                                                   >  2:102848/1‑133 (MQ=255)                 cgcgCCTCAGCCCAGGCACTGGCCGAACAGTTGCAACCAGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCCATTTGGCGGGGGTTTTTTTGTTGGCGGTGTGccc                                                                                                                  >  8:198581/1‑136 (MQ=255)                    gcCTCAGCCCAGGCACTGGCCGAACAGTTGCAACCAGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCTTTTTTTTCTTCGCGGATTGCCCggg                                                                                                               <  7:129011/136‑1 (MQ=255)                     ccTCAGCCCAGGCACTGGCCGAACAGTTGCAACCAGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCTTTTTTTTCTTCGCGGATTGCCCggg                                                                                                               <  5:396431/135‑1 (MQ=255)                      cTCAGCCCAGGCACTGGCCGAACAGTTGCAACCAGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCTTTTTTTTCTTCGCGGATTGCCCGGGc                                                                                                              <  5:393696/135‑1 (MQ=255)                      cTCAGCCCAGGCACTGGACGAACAGTTGCAACCAGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCTTTTTTTTCTTCGCGGATTGCCCGGGc                                                                                                              <  5:44627/135‑1 (MQ=255)                          gCCCAGGCACTGGCCGAACAGTTGCAACCAGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCTTTTTTTTCTTCGCGGATTGCCCGGGCTg                                                                                                            <  2:292751/133‑1 (MQ=255)                          gCCCAGGCACTGGCCGAACAGTTGCAACCAGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCTTTTTTTTCTTCGCGGATTGCCCGGGCTGccc                                                                                                         <  7:144555/136‑1 (MQ=255)                           cccAGGCACTGGCCGAACAGTTGCAACCAGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCTTTTTTTTCTTCGCGGATTGCCCGGGCTGccc                                                                                                         <  4:38209/135‑1 (MQ=255)                            ccAGGCACTGGCCGAACAGTTGCAACCAGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGGGTTTTTTTCTTCGCGGATTGCCCGGGCTGccccc                                                                                                       >  7:100361/1‑136 (MQ=255)                                gCACTGGCCGAACAGTAGCAACCAGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCGTTTTTTTCTTCGCGGATTGCCCGGGCTGCCCCCCTa                                                                                                    <  6:333326/135‑1 (MQ=255)                                       ccGAACAGTTGCAACCAGGCACTTTGGTTGCCTGATCCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCTTTTTTTTCTTCGCGGATTGCCCGGGCTGCCCCCCTACGttt                                                                                               <  4:75000/133‑1 (MQ=255)                                       ccGAACAGTTGCAACCAGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCTTTTTTTTCTTCGCGGATTGCCCGGGCTGCCCCCCTACGttt                                                                                               <  5:170968/133‑1 (MQ=255)                                       ccGAACAGTTGCAACCAGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCTTTTTTTTCTTCGCGGATTGCCCGGGCTGCCCCCCTACGttt                                                                                               <  5:354855/133‑1 (MQ=255)                                        cGAACAGTTGCAACCAGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCCATTTGGGGGGGGTTTTTTTCTTAGCGGCTTGCCCCGGCGGCCCCCCGACCGTTGGcc                                                                                           >  7:66213/1‑136 (MQ=255)                                        cGAACAGTTGCAACCAGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCCATTTGGCGGGGTTTTTTTTCTTGGCGGCTTGCCCCGGGTGCCCCCCCAAGTTTGGcc                                                                                           >  7:217492/1‑136 (MQ=255)                                        cGAACAGTTGCAACCAGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTTGGGGGCGTTTTTTTATTGGCGGGTTGGCCGGGCGGCCCCCCGACCTTTGGc                                                                                            >  1:78359/1‑135 (MQ=255)                                        cGAACAGTTGCAACCAGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTTGCGGGCTTTTTTTTGTTCGCGGATTGCCCGGGCTGGCCCCCTACGTTTTGc                                                                                            >  2:9506/1‑135 (MQ=255)                                        cGAACAGTTGCAACCAGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGGGGGGGTTTTTTTTTTTGCGGATTGCCCCGGCTGCCCCCCGACCTTTGGc                                                                                            >  1:309706/1‑135 (MQ=255)                                        cGAACAGTTGCAACCAGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCCCCAATTTTGCGGGCGTTTTTTTATTAGAGGATTTCCCCGGCTGCCCCCCTACCGTTGGc                                                                                            >  6:366648/1‑135 (MQ=255)                                             aGTTGCAACCAGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGGGGGCGTTTTTTTGTTCGCGGATTTCCCGGGCTGGCCCCCGACGTTTGGGCGCt                                                                                        >  3:107132/1‑134 (MQ=255)                                              gTTGCAACCAGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCTTTTTTTTCTTCGCGGATTGCCCGGGCTGCCCCCCTACGTTTGGCCGCTACt                                                                                     <  7:198581/136‑1 (MQ=255)                                               ttGCAACCATGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCTTTTTTTTCTTCGCGGATTGCCCGGGCTGCCCCCCTACGTTTGGCCGCTACt                                                                                     <  4:88612/135‑1 (MQ=255)                                               ttGCAACCAGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCTTTTTTTTCTTCGCGGATTGCCCGGGCTGCCCCCCTACGTTTGGCCGCTACt                                                                                     <  1:65539/135‑1 (MQ=255)                                               ttGCAACCAGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCTTTTTTTTCTTCGCGGATTGCCCGGGCTGCCCCCCTACGTTTGGCCGCTACt                                                                                     <  6:82630/135‑1 (MQ=255)                                               ttGCAACCAGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCTTTTTTTTCTTCGCGGATTGCCCGGGCTGCCCCCCTACGTTTGGCCGCTACt                                                                                     <  6:150723/135‑1 (MQ=255)                                               ttGCAACCAGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCGTTTTTTTCTTCGCGGATTGCCCGGGCTGCCCCCCTACGTTTGGCCGCTACt                                                                                     <  3:35603/135‑1 (MQ=255)                                               ttGCAACCAGGCACTTTGGTTGCCTGAAACGAATTTGTTGTGCGTTGCTCCCTAAGCCCTTGTC‑GCCCGCCAATTTGGCGGGCTTTTTTTTCTTCGCGGATTGCCCGGGCTGCCCCCCTACGTTTGGCCGCTACt                                                                                     <  5:311630/135‑1 (MQ=255)                                                      cAGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCTTTTTTTTCTTCGCGGATTGCCCGGGCTGCCCCCCTACGTTTGGCCGTTACTGCCCAGc                                                                              <  1:434258/135‑1 (MQ=255)                                                      cAGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCTTTTTTTTCTTCGCGGATTGCCCGGGCTGCCCCCCTACGTTTGGCCGCTACTGCCCAGc                                                                              <  3:383679/135‑1 (MQ=255)                                                       aGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCCATTTTGCGGGGGTTTTTTTGTTGGCGGATTTGCCGGGCGGGCCCCCGACGTTTGGGCGCGACTGcccccctt                                                                            >  8:81073/1‑131 (MQ=255)                                                       aGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAAATTGGGGGGGGTTTTTTTGGTCGCGGATTTCCCCGGCGGCCCCCCGCCGGTTGGCCGCATCTGGCCCGCt                                                                             >  6:234986/1‑135 (MQ=255)                                                            cTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCCCCAATTTGGCGGGGTTTTTTTTGTTGGCGGGTTTCCCGCGCTGGCCCCCCAACTTTTGCCCCGACTGCCCCGCTTACTg                                                                        >  3:414686/1‑135 (MQ=255)                                                               tGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCTTTTTTTTCTTCGCGGATTGCCCGGGCTGCCCCCCTACGTTTGGCCGCTACTGCCCAGCTTACTGGt                                                                      <  8:51557/134‑1 (MQ=255)                                                               tGGTTGCCTGAACCGAATTTGTTGTGCGTGGCTCCCTACGCCCTTGTC‑GCCCGACAATTTGGCGGGCTTTTTTTTCTTCGCGGATTGCCCGGGCTGCCCCCCTACGTTTGGCCGCTACTGCCCAGCTTACTGGt                                                                      <  7:208982/134‑1 (MQ=255)                                                                ggTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCTTTTTTTTCTTCGCGGATTGCCCGGGCTGCCCCCCTACGTTTGGCCGCTACTGCCCAGCTTACTGGt                                                                      <  3:89458/133‑1 (MQ=255)                                                                ggTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCTTTTTTTTCTTCGCGGATTGCCCGGGCTGCCCCCCTACGTTTGGCCGCTACTGCCCAGCTTACTGGt                                                                      <  2:356961/133‑1 (MQ=255)                                                                                   gttgtGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCTTTTTTTTCTTCGCGGATTGCCCGGGCTGCCCCCCTACGTTTGGCCGCTACTGCCCAGCTTACTGGTCAGCACCATGAccttgccttg                                                 <  8:27772/135‑1 (MQ=255)                                                                                    ttgtGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCTTTTTTTTCTTCGCGGATTGCCCGGGCTGCCCCCCTACGTTTGGCCGCTACTGCCCAGCTTACTGGTCAGCACCATGAccttgccttg                                                 <  4:409499/134‑1 (MQ=255)                                                                                    ttgtGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCTTTTTTTTCTTCGCGGATTGCCCGGGCTGCCCCCCTACGTTTGGCCGCTACTGCCCAGCTTACTGGTCAGCACCATGAccttgccttg                                                 <  6:103618/134‑1 (MQ=255)                                                                                    ttgtGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCTTTTTTTTCTTCGCGGATTGCCCGGGCTGCCCCCCTACGTTTGGCCGCTACTGCCCAGCTTACTGGTCAGCACCATGAccttgccttg                                                 <  4:147531/134‑1 (MQ=255)                                                                                      gtgCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGGTTTTTTTTGTTCGCGGCTTTCCCCGGCGGGCCCCCGACGTTTGGCCGCTACAGCCCCGCTTACTGGTCAGCCCCAAGACCGTGCCTTGCAg                                              >  2:148857/1‑135 (MQ=255)                                                                                           ttGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCTTTTTTTTCTTCGCGGATTGCCCGGGCTGCCCCCCTACGTTTGGCCGCTACTGCCCAGCTTACTGGTCAGCACCATGACCTTGCCTTGCAGCCGGc                                         <  4:37608/135‑1 (MQ=255)                                                                                           ttGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCTTTTTTTTCTTCGCGGAGTGCCCGGGCTGCCCCCCTACGTTTGGCCGCTACTGCCCAGCTTACTGGTCAGCACCATGACCTTGCCTTGCAGCCGGc                                         <  5:366648/135‑1 (MQ=255)                                                                                               tCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCTTTTTTTTCTTCGCGGATTGCCCGGGCTGCCCCCCTACGTTTGGCCGCTACTGCCCAGCTTACTGGTCAGCACCATGACCTTGCCTTGCAGCCGGCCTAc                                     <  1:212165/135‑1 (MQ=255)                                                                                                                    gccAATTTGGCGGGCTTTTTTTTCTTCGCGGATTGCCCGGGCTGCCCCCCTACGTTTGGCCGCTACTGCCCAGCTTACTGGTCAGCACCATGACCTTGCCTTGCAGCCGGCCTACGGTCATCACCAGttcgtttc                 <  2:309706/135‑1 (MQ=255)                                                                                                                         tttGGCGGGCTTTTTTTTCTTCGCGGATTGCCCGGGCTGCCCCCCTACGTTTGGCCGCTACTGCCCAGCTTACTGGTCAGCACCATGACCTTGCCTTGCAGCCGGCCTACGGTCATCACCAGTTCGTTTCGTTcc            <  2:78359/135‑1 (MQ=255)                                                                                                                             gCGGGCTTTTTTTTCTTCGCGGATTGCCCGGGCTGCCCCCCTACGTTTGGCCGCTACTGCCCAGCTTACTGGTCAGCACCATGACCTTGCCTTGCAGCCGGCCTACGGTCATCACCAGTTCGTTTCGTTCCTTGGc       <  7:294697/136‑1 (MQ=255)                                                                                                                              cGGGCTTTTTTTTCTTCGCGGATTGCCCGGGCTGCCCCCCTACGTTTGGCCGCTACTGCCCAGCTTACTGGTCAGCACCATGACCTTGCCTTGCAGCCGGCCTACGGTCATCACCAGTTCGTTTCGTTCCTTGGc       <  3:31105/135‑1 (MQ=255)                                                                                                                              cGGGCGTTATTTTCTTCGCGGATTGCCCGGGCTGCCCACCTCCGTTTGGCCGCTACTGCCCAGCTTACTGGTCAGCACCATGACCTTGCCTTGCAGCCGGACTACGGTCATCACCAGTTCGTTTCGTTCCTTGGc       <  6:61019/135‑1 (MQ=255)                                                                                                                               gggCTTTTTTTTCTTCGCGGATTGCCCGGGCTGCCCCCCTACGTTTGGCCGCTACTGCCCAGCTTACTGGTCAGCACCATGACCTTGCCTTGCAGCCGGCCTACGGTCATCACCAGTTCGTTTCGTTCCTTGGCg      <  4:304481/135‑1 (MQ=255)                                                                                                                                   ttttttttCTTCGCGGATTGCCCGGGCTGCCCCCCTACGTTTGGCCGCTACTGCCCAGCTTACTGGTCAGCACCATGACCTTGCCTTGCAGCCGGCCTACGGTCATCACCAGTTCGTTTCGTTCCTTGGCGAGCa  <  6:53955/135‑1 (MQ=255)                                                                                                                                   ttttttttCTTCGCGGATTGCCCGGGCTGCCCCCCTACGTTTGGCCGCTACTGCCCAGCTTACTGGTCAGCACCATGACCTTGCCTTGCAGCCGGCCTACGGTCATCACCAGTTCGTTTCGTTCCTTGGCGAGCa  <  5:383284/135‑1 (MQ=255)                                                                                                                                   |                                                                                                                                       CGGCCCGATGCCGACCCGCGCCTCAGCCCAGGCACTGGCCGAACAGTTGCAACCAGGCACTTTGGTTGCCTGAACCGAATTTGTTGTGCGTTGCTCCCTACGCCCTTGTC‑GCCCGCCAATTTGGCGGGCTTTTTTTTCTTCGCGGATTGCCCGGGCTGCCCCCCTACGTTTGGCCGCTACTGCCCAGCTTACTGGTCAGCACCATGACCTTGCCTTGCAGCCGGCCTACGGTCATCACCAGTTCGTTTCGTTCCTTGGCGAGCA  >  KT2440/4292418‑4292681

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: ‑