Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	KT2440	188,028	A→C	24.0%	T963P (ACC→CCC)	CJ019_00185 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	KT2440	188,028	0	A	C	24.0%	52.4 / 3.9	38	T963P (ACC→CCC)	CJ019_00185	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (22/6);  new base C (2/8);  total (24/14)
Fisher's exact test for biased strand distribution p-value = 1.86e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AACGATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGACTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCG‑GTAATTTCGAGCAACTGACCCCGAACCCGACCCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTAATCACCTACACCGTGACCCTGAGCA  >  KT2440/187895‑188151                                                                                                                                       |                                                                                                                            aaCGATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGACTTCCAGACCCCGGCGAATGACGTATACAACAACGGTTCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCG‑GTAATTTCGAGCAACTGAc                                                                                                                            <  4:109096/135‑1 (MQ=37)                 gCCGGCAAAACCCAGGGCCTCGTAGAGTTCCAGACCCCGGCGTAGGAAGGATACAACACCGGTTCGACTCTCAGCGGCCCCATCGAGAACGACACAGGCG‑GTAATTTCGAGCAACTGCCCCCGTCCCCGCCCCCgg                                                                                                           >  8:26945/1‑136 (MQ=2)                 gCCGGCAAAACCCAGGGCAGCGTCGACTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCG‑GTAATTTCGAGCAACTGACCCCGAACCCGACCCCg                                                                                                            >  2:291847/1‑135 (MQ=37)                 gCCGGCAAAACCCAGGGCAGCGTCGACTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCG‑GTAATTTCGAGCAACTGACCCCGAACCCGACCCCg                                                                                                            >  2:307691/1‑135 (MQ=37)                  ccGGCAAAACCCAGGGCAGCGTCGACTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCG‑GTAATTTCGAGCACCTGACCCCGCACCCGACCCCGGc                                                                                                          >  7:239628/1‑136 (MQ=255)                  ccGGCAAAACCCAGGGCAGCGTCGACTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCG‑GTAATTTCGAGCAACTGACCCCGAAGCCGACCCCgg                                                                                                           >  1:269650/1‑135 (MQ=37)                       aaaaCCCAGGGCAGCGTCGACTTCCAGACCCCGGCGAATGCCGTCTACAACTACGGTTCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCG‑GTAATTTCGAGCAACTGCCCCCGACCCCGACCCCGGCTCAg                                                                                                      >  1:284691/1‑135 (MQ=255)                       aaaaCCCAGGGCAGCGTCGACTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCG‑GTAATTTCGAGCAACTGACCCCGAACCCGACCCCGGCTCAg                                                                                                      >  6:124347/1‑135 (MQ=37)                        aaaCCCAGGGCAGCGTCGACTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCG‑GTAATTTCGAGCAACTGACCCCGAACCCGACCCCGGCTCAGa                                                                                                     >  4:74930/1‑135 (MQ=37)                                  cAGCGTCGACTTCCAGACCCCGGCGAATGACGTCTACAACAACCGTTCGACTGTCAGCGTCACCATCCAGAACGCCACAGGCG‑GTAATTTCGCGCAACTGACCCCGAACCCGCCCCCCGCTCAGACCACGATCaa                                                                                           >  2:214691/1‑135 (MQ=11)                                   aGCGTCGACTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCG‑GTAATTTCGAGCAACTGACCCCGAACCCGACCCCGGCTCAGACCACGATCAAc                                                                                          >  3:40477/1‑135 (MQ=37)                                                         cGAATGACGTCTACAACAACGGTTCGACTGTCAGCGTCACCATCGAGAATGCCACAGGCG‑GTAATTTCGAGCAACTGACCCCGAACCCGACCCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACcgc                                                                   >  8:111444/1‑136 (MQ=21)                                                               aCGTCTACAACAACGGTTCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCG‑GTAATTTCGAGCAACTGACCCCGAACCCGACCCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGAccc                                                              >  5:188409/1‑135 (MQ=34)                                                                 gTCTACAACAACGGTTCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCG‑GTAATTTCGAGCAACTGACCCCGAACCCGACCCCGGCTCCGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGa                                                           >  8:192989/1‑136 (MQ=21)                                                                     acaacaACGGTTCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCG‑GTAATTTCGAGCAACTGACCCCGAACCCGACCCCGGCTCAGACCACGATCAACGACTCGCTCGCTGCCCCAACCGCGCCCCAGACgcc                                                       >  8:81269/1‑134 (MQ=11)                                                                            cGGTTCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCG‑GTAATTTCGAGCAACTGACCCCGAACCCGACCCCGGCTCAGACCACGCTCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGccc                                                 >  3:254693/1‑135 (MQ=21)                                                                               ttCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCG‑GTAATTTCGAGCAACTGACCCCGAACCCGACCCCGGCTCAGACCACGATCAACGACTCGGTCGACCCCACCACCGCGACCCTGACGGCGAGCCCGTc                                              >  2:131776/1‑135 (MQ=21)                                                                                            gTCACCATCGAGAACGCCACAGGCG‑GTAATTTCGAGCAACTGACCCCGAACCCGACCCCGGCTCAGACCACGATCAACg                                                                                         >  3:392666/1‑79 (MQ=34)                                                                                            gTCACCATCGAGAACGCCACAGGCG‑GTAATTTCGAGCAACTGACCCCGAACCCGACCCCGGCTCAGACCACGATCAACg                                                                                         <  4:392666/79‑1 (MQ=34)                                                                                            gTCACCATCGAGAACGCCACAGGCG‑GTAATTTCGAGCAACTGACCCCGAACCCGACCCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAggc                                 >  1:336415/1‑135 (MQ=32)                                                                                             tCACCATCGAGAACGCCACTGGCG‑GAAATTTCGACCACCTGACCCCGACCCCGACCCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGTCCCTGACGGCGAGCCCGTCGGTCACCGAAggcg                                <  4:355250/135‑1 (MQ=11)                                                                                              cACCATCGAGACCGCCACAGGCG‑TTAATTTCGCCCAACTGCCCCCGAACCCCCCCCCGGCCCACACCCCGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAggcggc                              <  8:336793/136‑1 (MQ=11)                                                                                              cACCAGCGACACCCCCACCGCCG‑GAAATTCCGACCAACTGCCCCCGAACCCCACCCCGCCGCACCCCCCCACCAACGACTCGGGCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAggcggc                              <  7:156982/136‑1 (MQ=2)                                                                                               gccttCGACACCGCCACTGGCG‑TTAATTTCTCCCAACTCACCCCCACCCCGCCCCCGGCTCAGACAACTATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAggcggc                              <  4:295814/131‑1 (MQ=11)                                                                                               acctgcGAGAACGCCAC‑GGCGTGTAATTGCCCCCACCTCCCCCCGAACCCGACCCCGCGTCACCCCCCGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAggcggc                              <  2:270187/130‑1 (MQ=2)                                                                                                 cATCGAGAACGCCACAGGCG‑GTAATTTCGAGCAACTGACCCCGAACCCGACCCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCCCCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGgcggcg                             >  6:238709/1‑134 (MQ=17)                                                                                                      agaACGCCACAGGCG‑GTAATTTCGAGCAACTGACCCCGAACCCGACCCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTAATCa                       >  4:242247/1‑135 (MQ=32)                                                                                                      agaACGCCACAGGCG‑GTAATTTCGAGCAACTGACCCCGAACCCGACCCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTAATCa                       >  3:70958/1‑135 (MQ=32)                                                                                                       caaCGCCCCCGCCG‑TTAATTCCCACCAACTGCCCCCGAACCCCCCCCCGGCCCACACCCCCAGCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTAATCAc                      <  3:213582/134‑1 (MQ=11)                                                                                                           gCCACGGGTG‑TTAATTTCGAGAACCTCACCCCCAACCGCACCCCGGCGCAGCCAACTATCACCGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACCTaca                 <  8:386784/136‑1 (MQ=11)                                                                                                           ccccccggCG‑TTAATTCCGCCCAACTCCCCCCCACCCCCCCCCCGGCTCACACCCCTATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTAATCACCTaca                 <  7:111444/130‑1 (MQ=11)                                                                                                            ccccgggCG‑GTAATTGCCACCAACTCCCCCCGAACCCGCCCCCGGCGCACACCACCACCCACGACTCGGTCGAGGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTAATCACCTaca                 <  3:95367/130‑1 (MQ=11)                                                                                                            ccACCGGCG‑GTAATTGCCACCACCTCCCCCCGACCCCGCCCCCGGCCCAGCCCCCGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTAATCACCTaca                 <  2:355979/135‑1 (MQ=11)                                                                                                              acaGGCG‑GTAATTTCGAGCAACTGACCCCGAACCCGACCCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTAATCACCTAcccc               >  3:295814/1‑135 (MQ=17)                                                                                                                      gTATTTTCCACCAACTGACCCCCAACCCGCCCCCGGCCCACCCCCCGTTCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTAATCACCTACACCGTGACCCt       <  8:19477/136‑1 (MQ=11)                                                                                                                         aTTTCGAGCAACTGACCCCGAACCCGACCCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTGATCACCTACCCCGTGCCCCTGa     >  1:154903/1‑135 (MQ=12)                                                                                                                         aTTTCGAGCAACTGACCCCGAACCCGACCCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTAATCACCTACACCGTGACCCTGa     >  1:250847/1‑135 (MQ=32)                                                                                                                             cGAGCAACTCCCCCCCACCCCCCCCCGGGCTCAGCCCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTAATCACCTACACCGTGACCCTGAGCa  <  3:270000/134‑1 (MQ=11)                                                                                                                                       |                                                                                                                            AACGATTACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGACTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCG‑GTAATTTCGAGCAACTGACCCCGAACCCGACCCCGGCTCAGACCACGATCAACGACTCGGTCGATGCCACCACCGCGACCCTGACGGCGAGCCCGTCGGTCACCGAAGGCGGCGTAATCACCTACACCGTGACCCTGAGCA  >  KT2440/187895‑188151

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: ‑