Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	KT2440	3,421,089	G→C	5.9%	A661P (GCA→CCA)	CJ019_03241 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	KT2440	3,421,089	0	G	C	5.9%	210.5 / 2.7	63	A661P (GCA→CCA)	CJ019_03241	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (19/40);  new base C (2/2);  total (21/42)
Fisher's exact test for biased strand distribution p-value = 5.95e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGCCGTCTCCTGCGAAGCAACCGGTCGTTGAGCACCAACACGATGACGACGATGACCCGGACGACGATCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTGACATGGCATATACCCAGGCACACCTCGCGGCCGTCGAGCGTGCGATTGCGCGTGGCGAACGGGTTGTTCGATACA  >  KT2440/3420955‑3421219                                                                                                                                       |                                                                                                                                   aGCCGTCTCCTGCGAAGCAACCGGTCGTGGAGCACCAACACGATGACGACGATGACCCGGACGACGATCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCgg                                                                                                                                    <  3:407225/135‑1 (MQ=255)       ctcCTGCGAAGCAACCGGTCGTTGCGCACCAACACGATGACGACGATGACCCGGACGACGATCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTc                                                                                                                              <  2:297970/135‑1 (MQ=255)       ctcCTGCGAAGCAACCGGGCGTGGAGACCCAACACGATGACGACGATGACCCGGACGACGATCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTc                                                                                                                              <  2:304319/135‑1 (MQ=255)          cTGCGACGCAACCGGTCGTGGAGCACCAACACGATGACGACGATGACCCGGACGACGATCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCAc                                                                                                                           <  8:363911/135‑1 (MQ=255)             cGAAGCAACCGGTCGTTGAGCACCAACACGATGACGACGATGACCCGGACGACGATCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCa                                                                                                                        <  2:152435/135‑1 (MQ=255)               aaGCAACCGGGCGTTGAGCACCAACACGAGGACGACGATGACCCGGACGACGATCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATg                                                                                                                      <  6:310800/135‑1 (MQ=255)                aGCAACCGGTCGTTGAGCACCAACACGATGACCCCGATGACCCGGACGACGATCCAGTTTCACCCCCAACACCACCGGCTCGGCCCCCTCCACGCTCCACTCCCCCGCCCCCTCCCCCCCCACCTCCCCCCaaa                                                                                                                      >  3:332154/1‑132 (MQ=255)                    aCCGGGCGGTGAGCACCAACACGATGACGACGATGACCCGGACGACGATCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAAcgc                                                                                                                <  8:231206/136‑1 (MQ=255)                     ccGGTCGTCGAGCACCAACACGAGGACGACGATGACCCGGACGACGATCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAAcgc                                                                                                                <  1:251373/135‑1 (MQ=255)                       ggTCGTTGAGCACCAACACGATGACGACGATGACCCGGACGACGATCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAAcgccg                                                                                                              >  4:208890/1‑135 (MQ=255)                               aGCACCAACACGATGACGACGATGACCCGGACGACGATCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTcc                                                                                                       <  3:185245/134‑1 (MQ=255)                                       cacGAGGACGACGATGACCCGGACGACGATCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGc                                                                                              <  2:9115/135‑1 (MQ=255)                                         cGATGACGACGATGACCCGGACGACGATCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTAt                                                                                           >  8:303162/1‑136 (MQ=255)                                              acgacgATGACCCGGACGACGATCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCt                                                                                         >  4:64924/1‑133 (MQ=255)                                              acgacgATGACCCGGACGACGATCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCt                                                                                         >  5:174666/1‑133 (MQ=255)                                                 acgaTGACCCGGACGACGATCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCAc                                                                                                                                 >  8:431974/1‑90 (MQ=255)                                                 acgaTGACCCGGACGACGATCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCAc                                                                                                                                 <  7:431974/90‑1 (MQ=255)                                                 acgaTGACCCGGACGACGATCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGa                                                                                       >  1:429508/1‑132 (MQ=255)                                                  cgaTGACCCGGACGACGATCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAagag                                                                                   <  2:192496/135‑1 (MQ=255)                                                  cgaTGACCCGGACGACGATCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAgaga                                                                                  <  7:303162/136‑1 (MQ=255)                                                        cccGGACGACGATCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCt                                                                              <  2:140319/134‑1 (MQ=255)                                                        cccGGACGACGATCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCt                                                                              <  2:111741/134‑1 (MQ=255)                                                        cccGGACGACGATCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTg                                                                             <  2:291754/135‑1 (MQ=255)                                                        cccGGACGACGATCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTg                                                                             <  4:195291/135‑1 (MQ=255)                                                        cccGGACGACGATCCAGTTGCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCt                                                                              <  2:233384/134‑1 (MQ=255)                                                        cccGCACGACGATCCCGTTTCACCGCCAACACCCCCGGCTCGGCCCGCTCCCCGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTg                                                                             <  1:219809/135‑1 (MQ=255)                                                         ccGGACGACGATCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTGa                                                                            <  3:106886/135‑1 (MQ=255)                                                         ccGGACGACGATCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTGa                                                                            <  6:191357/135‑1 (MQ=255)                                                         ccGGACGACGATCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTGa                                                                            <  4:102613/135‑1 (MQ=255)                                                         ccGGACGACGATCCACTGGCACCGCCCACACCCCCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTGa                                                                            <  4:257251/135‑1 (MQ=255)                                                             acgacgATCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTGACATg                                                                        <  4:377238/135‑1 (MQ=255)                                                              cgacgaTCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTGACATGGc                                                                      <  7:61626/136‑1 (MQ=255)                                                               gacgaTCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTGACATGGc                                                                      <  6:214019/135‑1 (MQ=255)                                                                 cgaTCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTGACATGGCat                                                                    <  4:292375/135‑1 (MQ=255)                                                                   aTCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTGACATGGCatat                                                                  <  4:444639/135‑1 (MQ=255)                                                                    tCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTGACATGGCAtata                                                                 <  3:208890/135‑1 (MQ=255)                                                                      cAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCCCCAGCGGCTATCTGAAGAGACGCTGACCTGGctcttat                                                                >  1:194384/1‑128 (MQ=255)                                                                      cAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGCCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCt                                                                              <  6:64474/120‑1 (MQ=255)                                                                      cAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGCCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCt                                                                              >  5:64474/1‑120 (MQ=255)                                                                        gTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTGACATGGCATATACCCAg                                                            <  8:380288/136‑1 (MQ=255)                                                                                gCCCACCCCACCGGGGCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCTTGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTGACATGGCATATACCCAGGCACAcc                                                     <  1:161002/135‑1 (MQ=255)                                                                                gCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTGACATGGCATATACCCAGGCACAcc                                                     <  3:402451/135‑1 (MQ=255)                                                                                 ccAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTGACATGGCATATACCCAGGCACACCt                                                    >  3:245544/1‑135 (MQ=255)                                                                                        caccGGCTCGGCCCGCGCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTGACATGGCATATACCCAGGCACACCTCGCGGcc                                             <  1:424857/135‑1 (MQ=255)                                                                                          ccGGCTCGGTCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTGACATGGCATATACCCAGGCACACCTCGCGGCCGt                                           <  3:93223/135‑1 (MQ=255)                                                                                                   cccgctccccgctcCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTGACATGGCATATACCCAGGCACACCTCGCGGCCGTCGCGCGTg                                   >  2:234771/1‑134 (MQ=255)                                                                                                     cgctccacgctccaCTCCACCGCCGCCTCGCCCGGCACCTCCCCCCATGCAACGCCGCCGCTCCAGCAGCGGCTATCTGAAGAGACGCTGACATGGCATATACCCAGGCACACCTCGCGGCCGTCGCGCGTGCGa                                >  2:165794/1‑135 (MQ=255)                                                                                                     cgctccacgctccaCTCCACCGCCGCCTCGCCCGGCACCTCCCCCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCGGACATGGCATATACCCAGGCACACCTCGCGGCCGTCGCGCGTGCGAt                               >  8:267500/1‑136 (MQ=255)                                                                                                     cgctccacgctccaCTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAagag                                                                                   <  5:429030/84‑1 (MQ=255)                                                                                                     cgctccacgctccaCTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAagag                                                                                   >  6:429030/1‑84 (MQ=255)                                                                                                          cacgctccacTCCACCGCCGCCTCGCCCGGCCCCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTGACATGGCATATACCCAGGCACACCTCGCGGCCGTCGAGCGTGCCTTTgcg                           >  3:67945/1‑135 (MQ=255)                                                                                                                   ctccacCGCCGCCTCGCCCGGCACCTCCACCCCTGCAACGCCGCAGCTCCAGCAGCGGCTATCTGACGAGACGCTGACATGGCATATACCCAGGCACACCTCGCGGCCGTCGAGCGTGCGATTGCGCGTGGCGAAc                 <  8:113369/136‑1 (MQ=255)                                                                                                                    tccccCGCCGCCGCGCCCGGCACCGCCACCCAGGCAACGCCGCAGCGCCAGCAGCGGCTATCTGAAGAGACGCTGACATGGCATATACCCAGGCACACCTCGCGGCCGTCGAGCGTGCGATTGCGCGTGGCGAAc                 <  6:292338/135‑1 (MQ=255)                                                                                                                    tccacCGCCGCCTCGCCCGGCACCTCCACCCATGCACCGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTGACATGGCATATACCCAGGCACACCTCGCGGCCGTCGAGCGTGCGATTGCGCGTGGCGAAc                 <  1:212923/135‑1 (MQ=255)                                                                                                                    tccacCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTGACATGGCATATACCCAGGCACACCTCGCGGCCGTCGAGCGTGCGATTGCGCGTGGCGAAc                 <  6:292331/135‑1 (MQ=255)                                                                                                                    tccacCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTGACATGGCATATACCCAGGCACACCTCGCGGCCGTCGAGCGTGCGATTGCGCGTGGCGAAc                 <  4:288523/135‑1 (MQ=255)                                                                                                                    tccacCGCCGCCGCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTGACATGGCATATACCCAGGCACACCTCGCGGCCGTCGAGCGTGCGATTGCGCGTGGCGAAc                 <  6:286759/135‑1 (MQ=255)                                                                                                                    tccacCGCCCCCTCGCCCGCCACCTCCACGCATCCAACGCAGCAGCTCCAGCAGCGGCTATCTGAATAGACGCTGACATGGCATATACCCAGGCACACCTCGCTGCCGTCGAGCATGCGATTGCGCGTGGCGAAc                 <  6:123752/135‑1 (MQ=255)                                                                                                                       acCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTGACATGGCATATACCCAGGCACACCTCGCGGCCGTCGAGCGTGCGATTGCGCGTGGCGAACGGgt             >  8:134227/1‑136 (MQ=255)                                                                                                                            cgccTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTGACATGGCATATACCCAGGCACACCTCGCGGCCGTCGAGCGTGCGATTGCGCGTGGCGAACGGGTTGTTc        >  8:16458/1‑136 (MQ=255)                                                                                                                              ccTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTGACATGGCATATACCCCGGCACACCTCGCGGCCGTCGAGCGTGCGATTGCGCGTGGCGAACGGGTTGTTCg       >  6:397837/1‑135 (MQ=255)                                                                                                                              ccTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTGACATGGCATATACCCAGGCACACCTCGCGGCCGTCGAGCGTGCGATTGCGCGTGGCGAACGGGTTGTTCg       >  6:209197/1‑135 (MQ=255)                                                                                                                                   cccGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTGACATGGCATATACCCAGGCACACCTCGCGGCCGTCGAGCGTGCGATTGCGCGTGGCGAACGGGTTGTTCGATACa  >  2:415659/1‑135 (MQ=255)                                                                                                                                   cccGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTGACATGGCATATACCCAGGCACACCTCGCGGCCGTCGAGCGTGCGATTGCGCGTGGCGAACGGGTTGTTCGATACa  >  2:421006/1‑135 (MQ=255)                                                                                                                                       |                                                                                                                                   AGCCGTCTCCTGCGAAGCAACCGGTCGTTGAGCACCAACACGATGACGACGATGACCCGGACGACGATCCAGTTTCACCGCCAACACCACCGGCTCGGCCCGCTCCACGCTCCACTCCACCGCCGCCTCGCCCGGCACCTCCACCCATGCAACGCCGCAGCTCCAGCAGCGGCTATCTGAAGAGACGCTGACATGGCATATACCCAGGCACACCTCGCGGCCGTCGAGCGTGCGATTGCGCGTGGCGAACGGGTTGTTCGATACA  >  KT2440/3420955‑3421219

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: ‑