Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	KT2440	1,095,616	T→A	12.2%	S2R (AGT→AGA)	CJ019_01035 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	KT2440	1,095,616	0	T	A	12.2%	68.9 / 5.2	33	S2R (AGT→AGA)	CJ019_01035	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (14/15);  new base A (2/2);  total (16/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.64e-01

TTCCGTGACCAGTTCGCCGATGCCATGCAGCGCAACGGCAATGACCTGGACAAGACCATCGACGGCTGGGCCGGCGAAGTGGCCAAGGCCAAGCAGGCTGCCGACAACTCGCCAGAGAAGAGCGTCAAATGAGTGAGGCCGCTGTAAGCATGGCAGAGCCAGGCGTGCTGCGTCTGACTGGCGTGCTGGACTACCGCAGCGGCCCGGCCTTGCGCAAGCAAGGCAAGGTGCTGATCGATGGCTCGCGCGAGCCGCGACTG  >  KT2440/1095483‑1095742                                                                                                                                      |                                                                                                                               ttCCGTGACCAGTTCGCCGATGCCATGCAGCGCAACGGCAATGACCTGGACAAGACCATCGACGGCTGGGCCGGCGAAGTGGCCAAGGCCAAGCAGGCTGCCGACAACTCGCCAGAGAAGAGCGTCAAAtgagtga                                                                                                                              <  7:208494/136‑1 (MQ=255)  tCCGTGACCAGTTCGCCGATGCCATGCAGCGAAACGGCAATGACCTGGCCAAGACCATCGTCGGCTGGGCCGGCGAAGTGGCAAAGGCCAAGCAGGCTGCCGACAACTCGCCAGAGAAGAGCGTCAAAtgagtga                                                                                                                              <  2:55641/135‑1 (MQ=255)  tCCGCGACCAGTTCGCCGAGGCCATCCCCCCCACCGGAAATCACCTCGACAAGCCCCTCCACGGCGGGGCCGGCGAAGTGGCCAAGGCCAAGCAGGCTGCCGACAACTCGCCAGAGAAGAGCGTCAAAtgagtga                                                                                                                              <  5:271104/135‑1 (MQ=255)         ccAGTTCGCCGATGCCATGCAGCGCAACGGCAATGACCTGGACAAGACCATCGACGGCTGGGCCGGCGAAGTGGCCAAGGCCAAGCAGGCTGCCGACAACTCGCCAGAGAAGAGCGTCAAATGAGTGAGGCCGCt                                                                                                                       >  1:40472/1‑135 (MQ=255)           aGTTCGCCGATGCCATGCAGCGCAACGGCAATGCCCTGGACAAGACCATCGACGGCTGGGCCGGCGAAGTGGCCAAGGCCAAGCAGTCTGCCGACAACTCGCCAGAGAAGAGCGTCAAATGAGTGAGGCCGCTGt                                                                                                                     <  2:53862/135‑1 (MQ=255)                gCCGATGCCATGCAGCGCAACGGCAATGACCTGGACAAGACCATCGACGGCTGGGCCGGCGAAGTGGCCAAGGCCAAGCAGGCTGCCGACAACTCGCCAGAGAAGAGCGTCAAATGAGTGAGGCCGCTGTAAGCa                                                                                                                >  3:158702/1‑135 (MQ=255)                 ccGATGCCATCCACCGCACCGGCAATGACCTGGACAACCCCATCGACGGCTGGGCCGGCGAAGTGGCCAAGGCCAAGCAGGCTGCCGACAACTCGCCAGAGAAGAGCGTCAAATGAGTGAGGCCGCTGTAAGCAt                                                                                                               <  5:64338/135‑1 (MQ=255)                      gCCATGCAGCGCAACGGCAATGACCTGGACAAGACCATCGACGGCTGGGCCGGCGAAGTGGCCAAGGCCAAGCAGGCTGCCGACAACTCGCCAGAGAAGAGCGTCAAATGAGTGAGGCCGCTGTAAGCATGGCag                                                                                                          <  1:8189/135‑1 (MQ=255)                       ccATGCAGCGCAACGGCAATGACCTGGACAAGACCATCGACGGCTGGGCCGGCGAAGTGGCCAAGCCCAAGCAGGCTGCCGACAACTCGCCAGAGAAGAGCGTCAAATAAGTGAGGCCGCTGTAAGCATGGCaga                                                                                                         >  1:63271/1‑135 (MQ=255)                              gcgcAACGGCAATGACCTGGACAAGACCATCGACGGCTGGGCCGGCGAAGTGGCCAAGGCCAAGCAGGCTGCCGACAACTCGCCAGAGAAGAGCGTCAAATGAGTGAGGCCGCTGTAAGCATGGCAGAGCCAGGc                                                                                                  <  4:169817/135‑1 (MQ=255)                                          tGACCTGGACAAGACCATCGACGGCTGGGCCGGCGAAGTGGCCAAGGCCAAGCAGGCTGCCGACAACTCGCCAGAGAAGAGCGTCAAATGAGTGAGGCCGCTGTAAGCATGGCAGAGCCAGGCGTGCTGCGTCTGa                                                                                     <  7:75884/136‑1 (MQ=255)                                           gACCTGTACAAGACCATCGACGGCTGGGCCGGCGAAGTGGCCAAGGCCAAGCAGGCTGCCGACAACTCGCCAGAGAAGAGCGTCAAATGAGTGAGGCCGCTGTAAGCATGGCAGAGCCAGGCGTGCTGCGTCTGa                                                                                     <  8:58000/135‑1 (MQ=255)                                                ggACAAGACCATCGACGGCTGGGCCGGCGAAGTGGCCAAGGCCAAGCAGGCGGCCGACAACTCGCCAGAGAAGAGCGTCAAATGAGTGAGGCCGCTGTAAGCATGGCAGAGCCAGGCGTGCTGCGTCTGACTGGCg                                                                               <  7:226287/136‑1 (MQ=255)                                                      gcccATCGACGGCTGGGCCGGCGAAGTGGCCAAGGCCAAGCAGGCTGCCGACAACTCGCCAGAGAAGAGCGTCAAATGAGTGAGGCCGCTGTAAGCATGGCAGAGCCAGGCGTGCTGCGTCTGACTGGCGTGCTg                                                                          <  5:44139/133‑1 (MQ=255)                                                         cATCGACGGCTGGGCCGGCGAAGTGGCCAAGGCCAAGCAGGCTGCCGACAACTCGCCAGAGAAGAGCGTCAAATGAGTGAGGCCGCTGTAAGCATGGCAGAGCCAGGCGTGCTGCGTCTGACTGGCGTGCTGGa                                                                        >  3:142367/1‑134 (MQ=255)                                                         cATCGACGGCTGGGCCGGCGAAGTGGCCAAGGCCAAGCAGGCTGCCGACAACTCGCCAGAGAAGAGCGTCAAATGAGTGAGGCCGCTGTAAGCATGGCAGAGCCAGGCGTGCTGCGTCTGACTGGCGTGCTGGa                                                                        >  5:91510/1‑134 (MQ=255)                                                         cATCGACGGCTGGGCCGGCGAAGTGGCCAAGGCCAAGCAGGCTGCCGACAACTCGCCAGAGAAGAGCGTCAAATGAGTGAGGCCGCTGTAAGCATGGCAGAGCCAGGCGTGCTGCGTCTGACTGGCGTGCTGGAc                                                                       >  8:203285/1‑135 (MQ=255)                                                              aCGGCTGGGCCGGCGAAGTGGCCAAGGCCAAGCAGGCTGCCGACAACTCGCCAGAGAAGAGCGTCAAATGAGTGAGGCCGCTGTAAGCATGGCAGAGCCAGGCGTGCTGCGTCTGACTGGCGTGCTGGACTACCg                                                                  <  3:95664/135‑1 (MQ=255)                                                              aCGGCTGGGCCGGCGAAGTGGCCAAGGCCAAGCAGGCTGCCGACAACTCGCCAGAGAAGAGCGTCAAATGAGTGAGGCCGCTGTAAGCATGGCAGAGCCAGGCGTGCTGCGTCTGACTGGCGTGCTGGACTACCg                                                                  >  1:8396/1‑135 (MQ=255)                                                                   tGGGCCGGCGAAGTGGCCAAGGCCAAGCAGGCTGCCGACAACTCGCCAGAGAAGAGCGTCAAATGAGTGAGGCCGCTGTAAGCATGGCAGAGCCAGGCGTGCTGCGTCTGACTGGCGTGCTGGACTACCGCAGcg                                                             <  2:39987/135‑1 (MQ=255)                                                                   tGGGCCGGCGAAGTGGCCAAGGCCAAGCAGGCTGCCGACAACTCGCCAGAGAAGAGCGTCAAATGAGTGAGGCCGCTGTAAGCATGGCAGAGCCAGGCGTGCTGCGTCTGACTGGCGTGCTGGACTACCGCAGcg                                                             >  1:236396/1‑135 (MQ=255)                                                                    gggCCGGCGAAGTGGCCAAGGCCAAGCAGGCTGCCGACAACTCGCCAGAGAAGAGCGTCAAATGAGTGAGGCCGCTGTAAGCATGGCAGAGCCAGGCGTGCTGCGTCTGACTGGCGTGCTGGACTACCGCAGcggc                                                           >  7:93881/1‑136 (MQ=255)                                                                      gCCGGCGAAGTGGCCAAGGCCAAGCAGGCTGCCGACAACTCGCCAGAGAAGAGCGTCAAATGAGTGAGGCCGCTGTAAGCATGGCAGAGCCAGGCGTGCTGCGTCTGACTGGCGTGCTGGACTACCGCAGcggccc                                                         <  8:212730/136‑1 (MQ=255)                                                                             aaGTGGCCACGGCCAAGCAGGCTGCCGACAACTCGCCAGAGAAGAGCGGCAAATGAGTGAGGCCGCTGTAAGCATGGCAGAGCCAGGCGTGCTGCGGCTGACTGGCGTGCTGGACTACCGCAGCGGCCCGGCCtt                                                   <  1:260100/135‑1 (MQ=255)                                                                                               aGGCTGCCGACAACTCGCCAGAGAAGAGCGTCAAATGAGTGAGGcc                                                                                                                          <  2:215133/46‑1 (MQ=255)                                                                                               aGGCTGCCGACAACTCGCCAGAGAAGAGCGTCAAATGAGTGAGGcc                                                                                                                          >  1:215133/1‑46 (MQ=255)                                                                                                ggCTGCCGACAACTCGCCAGAGAAGAGCGTCAAATGAGTGAGGCCGCTGTAAGCATGGCAGAGCCAGGCGTGCTGCGTCTGACTGGCGTGCTGGACTACCGCAGCGGCCCGGCCTTGCGCAAGcaaggcaagggg                                >  1:230070/1‑133 (MQ=255)                                                                                                     ccGACAACTCGCCAGAGAAGAGCGTCAAATGAGTGAGGCCGCTGTAAGCAt                                                                                                               >  4:63689/1‑51 (MQ=255)                                                                                                     ccGACAACTCGCCAGAGAAGAGCGTCAAATGAGTGAGGCCGCTGTAAGCAt                                                                                                               <  3:63689/51‑1 (MQ=255)                                                                                                     ccGACAACTCGCCAGAGAAGAGCGTCAAATGAGTGAGGCCGCTGTAAGCATGGCAGAGCCAGGCGTGCTGCGTCTGACTGGCGTGCTGGACTACCGCAGCGGCCCGGCCTTGCGCCAGCCAGGCAAGGGGcgggg                           >  1:266475/1‑131 (MQ=255)                                                                                                      cGACAACTCGCCAGAGAAGAGCGTCAAATGAGTGAGGCCGCTGTAAGCATGGCAGAGCCAGGCGTGCTGCGTCTGACTGGCGTGCTGGACTACCGCAGCGGCCCGGCCTTGCGCAAGCAAGGCAAGGTGCTGa                            <  4:211844/133‑1 (MQ=255)                                                                                                               gCCAGAGAAGAGCGTCAAATGAGAGAGGCCGCTGTAAGCATGGCAGAGCCAGGCGTGCTGCGTCTGACTGGc                                                                                <  7:155043/72‑1 (MQ=255)                                                                                                               gCCAGAGAAGAGCGTCAAATGAGAGAGGCCGCTGTAAGCATGGCAGAGCCAGGCGTGCTGCGTCTGACTGGc                                                                                <  7:151025/72‑1 (MQ=255)                                                                                                               gCCAGAGAAGAGCGTCAAATGAGAGAGGCCGCTGTAAGCATGGCAGAGCCAGGCGTGCTGCGTCTGACTGGc                                                                                >  8:151025/1‑72 (MQ=255)                                                                                                               gCCAGAGAAGAGCGTCAAATGAGAGAGGCCGCTGTAAGCATGGCAGAGCCAGGCGTGCTGCGTCTGACTGGc                                                                                >  8:155043/1‑72 (MQ=255)                                                                                                                              cAAATGAGTGAGGCCGCTGTAAGCATGGCAGAGCCAGGCGTGCTGCGTCTGACTGGCGTGCTGGACTACCGCAGCGGCCCGGCCTTGCGCAAGCAAGGCAAGGTGCTGATCGCTGGCTCGCGCGAGCcgcgccgg  >  5:178651/1‑131 (MQ=255)                                                                                                                                      |                                                                                                                               TTCCGTGACCAGTTCGCCGATGCCATGCAGCGCAACGGCAATGACCTGGACAAGACCATCGACGGCTGGGCCGGCGAAGTGGCCAAGGCCAAGCAGGCTGCCGACAACTCGCCAGAGAAGAGCGTCAAATGAGTGAGGCCGCTGTAAGCATGGCAGAGCCAGGCGTGCTGCGTCTGACTGGCGTGCTGGACTACCGCAGCGGCCCGGCCTTGCGCAAGCAAGGCAAGGTGCTGATCGATGGCTCGCGCGAGCCGCGACTG  >  KT2440/1095483‑1095742

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: ‑