Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_007779	3,878,107	T→C	26.2%	G42G (GGA→GGG)	Y75_RS19225 ←	RHS element protein RhsA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007779	3,878,107	0	T	C	26.2%	127.5 / 7.7	72	G42G (GGA→GGG)	Y75_RS19225	RHS element protein RhsA
Reads supporting (aligned to +/- strand):  ref base T (34/16);  new base C (2/18);  total (36/36)
Fisher's exact test for biased strand distribution p-value = 1.08e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAGCTGTAAGCGGATATCCGCAGGCATTT‑TCCAGCCGGGGCCGAGGCTCCCCACCGGCGCGGGCGTTTTTGTCCGGTAACTGCTGTAGGTGCGGGAGAGGATGAACGGCAGCGGGCCGGGCAGGGCGAT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGAAACCCTACAGATTTATAAGAAAGCCTGAAGTGAGATATCCATCAGAGTGAAATAATTAGGAAAATAT  >  NC_007779/3877915‑3878343                                                                                                                                                                                                     |                                                                                                                                                                                                                                             cggcgtgaggCGGAGACCGGCGGGCTTTT‑TCCAGCCGGCGCCGCGGCTCCCCGCCGGCGCGGGGGTTTTTGTCCGGTAACTGCTGTAGGTGCGGGAGAGGATGAACGGCAGCGGGCCGGGCAGGGCGAT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCGGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATg                                                                                                                                                                                                 <  2:1343324/229‑1 (MQ=11) cAGCTGTAAGCGGATATCCGCAGGCATTT‑TCCAGCTGGGGCCGAGGCTCCCCACCGGCGCGGGCGTTTTTGTCCGGTAACTGCTGTAGGTGCGGGAGAGGATGAACGGCAGCGGGCCGGGCAGGGCGAT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GTTTGACCGGATGGCCGGCC‑GGCACCCCGCCGGGGCACACCGAACAGGCCCCGCCGGTGGGGGcaacaagac                                                                                                                                                                                                >  2:421225/1‑236 (MQ=1)             ggtttCCGAAGGCATTT‑TCCAGCCGGGGCCGAGGCTTCCAACCGGCGCGGGCGTGTTTGCCCGGTAACTGCTGTAGGTGCGGGAGAGGATGAACGGCAGCGGGCCGGGCAGGGCGCT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCCCACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCt                                                                                                                                                                                     <  2:1605946/234‑1 (MQ=11)             ggtgtCCGCAGGAGTTT‑GCCGGCCGGGGCGGGGGCTCCCCACCGGCGCGGGCGTTTTTGTCCGGTAACTGCTGTAGGTGCGGGAGAGGATGATCGGCAGGGGGCCGGGCAGGGCGAT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCCCTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCGCCAATGCGCACCCCGGCt                                                                                                                                                                                     <  2:2109128/234‑1 (MQ=11)              atatCCGCAGGCATTT‑TCCAGCCGGGGCCGAGGCTCCCCACCGGCGCGGGCGTTTTTGTCCGGTAACTGCTGTAGGTGCGGGAGAGGATGAACGGCAGCGGGCCGGGCAGGGCGAT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCCCGCCGGTGGGGGCACCAATGCGCCCCCCGGCTGa                                                                                                                                                                                   >  2:227212/1‑239 (MQ=17)                   cGCAGGCATTT‑TCCAGCCGGGGCCGAGGCTCCCCACCGGCGCGGGCGTTTTTGTCCGGTAACTGCTGTAGGTGCGGGAGCGGATGAACGGCAGCGGGCCGGGCAGGGCGAT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGGTGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATgcg                                                                                                                                                                                               >  1:1807898/1‑222 (MQ=14)                       ggCATTTGTCCGGCCGGGGGCGGGGTTCCCAACGGGCGGGGGCGTTGTTGTCCGGTAGCTGCTGTGGGTGCGGGAGAGGATGAACGGCAGCGGGCCGGGCAGGGCGAT‑GTCGGTTTCGCCGGGAGGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCTCTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGaa                                                                                                                                                                           <  2:1165058/239‑1 (MQ=11)                         cATTT‑TCCAGCCGGGGCCGAGGCTCCCCACCGGCGCGGGCGTTTTTGTCCGGTAACTGCTGTAGGTGCGGGAGAGGATGAACGGCAGCGGGCCGGGCAGGGCGAT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGaa                                                                                                                                                                           <  1:77050/236‑1 (MQ=32)                                                  ccccACCGGCGCGGGCGTTTTTGTCCGGTAACTGCTGTAGGTGCGGGAGAGGATGAACGGCAGCGGGCCGGGCAGGGCGAT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATg                                                                                                                                                 >  1:528908/1‑238 (MQ=32)                                                    ccACCGGCGCGGGCGTTTTTGTCCGGTAACTGCTGTAGGTGCGGGAGAGGATGAACGGCAGCGGGCCGGGCAGGGCGAT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATGTc                                                                                                                                               >  1:417666/1‑238 (MQ=32)                                                          gggcgGGCGTTTTTGTCCGGTAACTGCTGTAGGTGGGGGAGAGGATGAACGGCAGGGGGCCGGGCGGGGCGAT‑GTCGGTTTCCCCGGGAAGGCCCTTGGCACCGAGCAGGG‑GATTGACCGGAGGGCCGGAC‑GTCCCTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTg                                                                                                                                         <  1:1008726/236‑1 (MQ=11)                                                          gcgcGGGCGTTTTTGTCCGGTAACTGCTGTAGGTGCGGGAGAGGATGAACGGCAGCGGGCCGGGCAGGGCGAT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGCCACACCGAACAGGCCACGCCGGGGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATCCCACCGCCATACTGCGCCCTGCCCCCCTg                                                                                                                                         >  2:317801/1‑238 (MQ=11)                                                               ggCGTTTTTGTCCGGTAACTGCTGTAGGTGCGGGAGAGGATGAACGGCAGCGGGCCGGGCAGGGCGAT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCg                                                                                                                                                      >  1:1656577/1‑220 (MQ=32)                                                               ggCGTTTTTGTCCGGTAACTGCTGTAGGTGCGGGAGAGGATGAACGGCAGCGGGCCGGGCAGGGCGAT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGAcgc                                                                                                                                     >  1:1365734/1‑237 (MQ=33)                                                                          ccGGTACCTGCTGTAGGTGGGGGAGAGGATGAACGGCAGCGGGCGGGGCAGGGCGAT‑GTCGGTTTCCCCGGGAAGGACCTTTGCCCCGAGCAGGG‑GATTGACCGGAGGGCCGGAC‑GTCCCCCCGCCGGGCCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTc                                                                                                                        <  1:317801/239‑1 (MQ=11)                                                                            ggTAACTGCTGTAGGTGCGGGAGAGGATGAACGGCAGCGGGCCGGGCAGGGCGAT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGaa                                                                                                                                                                           >  1:1067044/1‑186 (MQ=33)                                                                              tAACTGCTGTAGGTGCGGGAGAGGATGAACGGCAGCGGGCCGGTCAGGGCGAT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGGGGGGGCACCAATGCGCACCCCGGCTGAACCCGGAACAATGCCACCGCCAGACTGCGTCATGCCGACCTGACGCGCCGCCGGCTTTCCGc                                                                                                                     >  2:770726/1‑238 (MQ=11)                                                                                       tAGGTGCGGGAGAGGATGAACGGCAGCGGGCCGGGCAGGGCGAT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCCCTGCCGGTTTTCCCCTCATTtccc                                                                                                            >  2:1600130/1‑236 (MQ=37)                                                                                          ggggggggggtgATGCAGGGCGGGGGGCCGGGCGGGGCGAT‑GGCGGTCTCCGCGGGAGGGACCGTCGCCCCGGGCGGGG‑GTTTGACCGG‑GGGCCGGGCGGTCACCCCCCGGGGACACCCCGAACAGGCCACGCGGGTGGGGGCCCAAATGCGCCCCCCGCCTGACCCCTAAACATTTCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATc                                                                                                         <  2:1097441/227‑1 (MQ=9)                                                                                            gCGGGAGAGGATGAACGGCAGCGGGCCGGGCAGGGCGAT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGGGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACCGCGCCGGGGCACACAGAGCAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCGCTACCGCGGCATGTCCCCCTGACGCGATGCCGGTTTACCGCGCATTTCCCATCCtt                                                                                                      >  2:842351/1‑239 (MQ=11)                                                                                            gCGGGAGAGGATGAACGGCAGCGGGCCGGGCAGGGCGAT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCAccc                                                                                                                                                                                          >  1:1139202/1‑155 (MQ=33)                                                                                            gCGGGAGAGGATGAACGGCAGCGGGCCGGGCAGGGCGAT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCAccc                                                                                                                                                                                          <  2:1139202/155‑1 (MQ=33)                                                                                            gCGGGAGAGGATGAACGGCAGCGGGCCGGGCAGGGCGAT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGAc                                                                                                                                       >  1:1569459/1‑206 (MQ=34)                                                                                            gCGGGAGAGGATGAACGGCAGCGGGCCGGGCAGGGCGAT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCtt                                                                                                      >  1:1484192/1‑239 (MQ=40)                                                                                              gggAGAGGATGAACGGCAGCGGGCCGGGCAGGGCGAT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCt                                                                                                                                                                                     >  1:1371505/1‑158 (MQ=33)                                                                                              gggAGAGGATGAACGGCAGCGGGCCGGGCAGGGCGAT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCt                                                                                                                                                                                     <  2:1371505/158‑1 (MQ=33)                                                                                              gggAGAGGATGAACGGCAGCGGGCCGGGCAGGGCGAT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATa                                                                                                                                                           >  1:875811/1‑184 (MQ=33)                                                                                              gggAGAGGATGAACGGCAGCGGGCCGGGCAGGGCGAT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATg                                                                                                                                                 >  1:1154662/1‑194 (MQ=33)                                                                                              gggAGAGGATGAACGGCAGCGGGCCGGGCAGGGCGAT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGt                                                                                                    >  1:451729/1‑239 (MQ=255)                                                                                                 agagGATGAACGGCAGCGGGCCGGGCAGGGCGAT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCt                                                                                                                                                                                     <  2:1389250/155‑1 (MQ=33)                                                                                                 agagGATGAACGGCAGCGGGCCGGGCAGGGCGAT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCt                                                                                                                                                                                     >  1:1389250/1‑155 (MQ=33)                                                                                                          aCGGCAGCGGGCCGGGCAGGGCGAT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATCGGGTTa                                                                                        >  1:732299/1‑239 (MQ=255)                                                                                                              gaGCGGGGCGGGGAGGGGGGTGGTCGGTTTAACAGGGAGGGACC‑CTGCACCGGGCCGGGTGAGCAACGGGAGGGGCGGAG‑GCACCTCCGCCGGGGCACACCCAACAGGCCGCGCCGGTGGGGCCACGAATGCCCCCCCCGGCTGACCCCTGAACATTTTTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATCGGGTTAtt                                                                                      <  2:996814/237‑1 (MQ=9)                                                                                                               aGCGGGCCGGGCGAGACGAT‑GTCGGTTTCACCGGGAAGCACCTTTCCACTGAGCCGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTAGGGGCAGCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCTCCATACTGCGTCATGTCGCACTGACGCGCTGACGGCTTTCCGCTCATCTCTCATCCTTGTTTTATCGGGTTATTTGt                                                                                   >  2:1650105/1‑239 (MQ=14)                                                                                                               aGCGGGCCGGGCAGGGCGAT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATCGGGTTATTTg                                                                                    >  1:1544920/1‑238 (MQ=255)                                                                                                                        ggcGGGGGGAT‑GTCGGTTTCCCCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGCCCGGATGGCCGGAC‑GTCCCTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCCCCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGAc                                                                           <  1:494183/238‑1 (MQ=255)                                                                                                                             ggCGAT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGcc                                                                                                                                                              >  1:1152935/1‑150 (MQ=34)                                                                                                                             ggCGAT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGa                                                                     >  1:1225462/1‑239 (MQ=255)                                                                                                                              gggAT‑GGCGGTTCCCCCGGGAAGGCCCTTTGCCCCGAGCAGGG‑GATTGACCGGAGGGCCGGAC‑GTCACCCCGCCGGGGCACCCCGAACAGGCCCCGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGa                                                                     <  1:672692/236‑1 (MQ=14)                                                                                                                               cGAT‑GTCGGTTTCCCCGGGAAGGCCCTTTGCACCGAGCAGGG‑GATTGCCCGGATGGCGGGCC‑GTCACCCCGCCGGGGCCCACCGAACAGGCCACGCCGGGGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGaa                                                                    <  1:227212/238‑1 (MQ=14)                                                                                                                                  t‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGAAAc                                                                  >  1:452614/1‑237 (MQ=255)                                                                                                                                    gTCGCTTTCACCGGGAAGGACCATTGAACCGAGCAGGG‑CAATGACCGGGTGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCGCCAGCGGTGGGGGCACAAATCCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCATAATGTCTCCCTCACGCGCCGCCGGTGTTCCGCGCATTTCACATCCTTCTTTTATCGGGTTATTTGCTTGTTGACAGGCGAAACCCt                                                               >  2:1196908/1‑239 (MQ=14)                                                                                                                                      gggttccgcggggagggaCCGTGGCCACGCGCAGGG‑GCTGGCCGGGATGGGCGACC‑GCCCCCCCGCCGGGCCCCACCGAACAGCCCACGCCGGTGGGGGCACCAGTGCGCCCCCCGGCTGACCCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGAAACCCTa                                                              <  2:1318486/228‑1 (MQ=14)                                                                                                                                        gTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATc                                                                                              >  1:102636/1‑204 (MQ=255)                                                                                                                                                  aaaGGCCCTTTGCACCGAGCAGGG‑GATTGCCCGGAGGGCCGGAC‑GTCCCTCCGCCGGGCCACCCCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGAAACCCTACAGATTTATAAg                                                  <  1:22736/237‑1 (MQ=255)                                                                                                                                                         gttcgcccgaggCAGGG‑TATTGACGGGCGGGCGCGAC‑TCCACCCCGCGGGGGCACTCCGAACAGGCCAGGCGGGGGGGGGCCCAATTGCGCACCCCGGCTGAACCCTGAGCGATGCTCCCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGAAACCCTACAGATTTATAAGAAAGCCTg                                          <  2:147077/228‑1 (MQ=14)                                                                                                                                                         cTTTGCACCGAGCAGGG‑GATTGCCCGGATGGCCGGAC‑GTCCCCCCGCGGGGGCACCCCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGAAACCCTACAGATTTATAAGAAAGCCTg                                          <  1:1600130/239‑1 (MQ=255)                                                                                                                                                           ttGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGAAACCCTACAGATTTATAAGAAAGCCTGaa                                        >  2:1793227/1‑239 (MQ=255)                                                                                                                                                           tggccccGGGCGGGG‑GATTGACCGGAGGGCCGGAC‑GCCACGCCGCCGGGCCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCCCCCCGGCTGAACCCTGAACAATGCTTCCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGAAACCCTACAGATTTATAAGAAAGCCTGaa                                        <  1:171753/234‑1 (MQ=14)                                                                                                                                                                cggggcgggg‑gATTGCCCGGATGGCCGGCC‑GTCTCTCCCCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCCCCCCGGCATACCCCTGACCAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGAAACCCTACAGATTTATAAGAAAGCCTGAAGTgag                                   <  1:1039541/232‑1 (MQ=14)                                                                                                                                                                ccggcggggg‑gAGTGACCGGATGGGCGGGC‑TTCACACCCCGGGGGCTCACCGAAAAGGCCTGGCGGGGGGGGGCACCAATGCGCACCCCGGCTGACCCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCAAAACCCTACAGATTTATAAGAAAGCCTGAAGTgag                                   <  2:417666/232‑1 (MQ=14)                                                                                                                                                                ccGAGGGGGG‑GATTACCCGGGTGGCCGGAC‑GGCCCCCCCCCGGGCCACCCCAAACGGCCCACGCCGGTGGGGCCACAACTGCCCCCCCCGGCTGAACCCTCAACAATGTTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGAAACCCTACAGATTTATAAGAAAGCCTGAAGTgag                                   <  2:1544920/239‑1 (MQ=14)                                                                                                                                                                ccGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGCGGGGGCACCAAAGCGCACCCCGGCTGAACCCTGAACAATGCTCCCGCCAGACTGCGTCATGTCGCCCTGACGCGCTGCCGGGTTTCCGCTCATTTCTCATCCTTGTTTTAACGGGTTATTTGTCTGCTGACATGCGAAACCCTACAGCTTTATAAGATAGCCTGCAGTgg                                    >  2:171753/1‑237 (MQ=14)                                                                                                                                                                 ctggCAGGG‑TATGGCCCGGAGGCGCGGAC‑GCCCCCCCGCCGGCGCACACCAAACAGGCCACGCCGGGGGGGGCACCAGTGCGCCCCCCGGCTGACCCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGAAACCCTACAGATTTATAAGAAAGCCTGAAGTgag                                   <  2:1365734/235‑1 (MQ=14)                                                                                                                                                                  gAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGAAACCCTACAGATTTATAAGAAAGCCTGAAGTGAGat                                 >  1:805885/1‑239 (MQ=255)                                                                                                                                                                   aGCGGGG‑GATTGCCCGGATGGCCGGAC‑GTCACCCCGCGGGGGCACACCGAACGGGCCACGCCGGTGGGGGCACCAATGCGCCCCCCGGCTGACCCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGAAACCCTACAGATTTATAAGAAAGCCTGAAGTGAGat                                 <  1:1317287/238‑1 (MQ=255)                                                                                                                                                                   aGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGAAACCCTACAg                                                           >  2:1161101/1‑212 (MQ=255)                                                                                                                                                                   aGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGAAACCCTACAg                                                           <  1:1161101/212‑1 (MQ=255)                                                                                                                                                                        gg‑gATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATc                                                                                                         >  1:1750510/1‑161 (MQ=255)                                                                                                                                                                            aTTGCCCGGGTGGCGGGCC‑GTCACCCCGCGGGGGCACACCAAACAGGCCACGCCGGTGGGGGCACCAATGCGCCCCCCGGCTGAACCCGGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGAAACCCTACAGATTTATAAGAAAGCCTGAAGTGAGATATCCATCa                         <  1:842351/238‑1 (MQ=14)                                                                                                                                                                              tGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTg                                                                                                                                         >  1:69716/1‑124 (MQ=38)                                                                                                                                                                                     aTGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACt                                                                                                                                                         >  2:1504063/1‑101 (MQ=35)                                                                                                                                                                                     aTGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACt                                                                                                                                                         <  1:1504063/101‑1 (MQ=35)                                                                                                                                                                                        gCCGGAC‑GTCCCCCCGCCGGGGCACCCCGAACAGGCCACGCCGGGGGGGGCACCAATGCGCACCCCGGCGGAACCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGAAACCCTACAGATTTATAAGAAAGCCTGAAGTGAGATATCCATCAGAGTGAaataat             <  1:1329493/238‑1 (MQ=255)                                                                                                                                                                                            gAC‑GTCACCCCGCCGGGGCCCCCCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGAAACCCTACAGATTTATAAGAAAGCCTGAAGTGAGATATCCATCAGAGTGAAATAATTAgg         <  1:770726/238‑1 (MQ=255)                                                                                                                                                                                             cc‑GTCACCCCGCCGGGGCACCCCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTAAACATTGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGAAACCCTACAGATTTATAAGAAAGCCTGAAGTGAGATATCCATCAGAGTGAAATAATTAGGa        <  1:1271402/237‑1 (MQ=255)                                                                                                                                                                                             aC‑GTCCCCCCGCCGGGGCACACCGAACAGGCCACGCGGGTGGGGGCACCAATGCGCCCCCCGGCTGACCCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGAAACCCTACAGATTTATAAGAAAGCCTGAAGTGAGATATCCATCAGAGTGAAATAATTAGGa        <  1:914233/238‑1 (MQ=255)                                                                                                                                                                                              c‑GTCCCCCCGCGGGTGCACCCCAAACAGGCCACGCCGGTGGGGGCCCCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTACGCTCATTTCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGAAACCCTACAGATTTATAAGAAAGCCTGAAGTGAGATATCCATCAGAGTGAAATAATTAGGaaa      <  1:1581466/239‑1 (MQ=17)                                                                                                                                                                                              c‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGAAACCCTACAGATTTATAAGAAAGCCTGAAGTGAGATATCCATCAGAGTGAAATAATTAGGaaa      <  1:1793227/239‑1 (MQ=255)                                                                                                                                                                                              c‑GTCACCCCGCCGGGGCACCCCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCCCCCCGGCTGACCCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGAAACCCTACAGATTTATAAGAAAGCCTGAAGTGAGATATCCATCAGAGTGAAATAATTAGGaa       <  1:1828586/238‑1 (MQ=255)                                                                                                                                                                                              c‑GTCACCCCGCCGGGGCACACCGAACAGCCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGAAACCCTACAGATTTATAAGAAAGCCTGAAGTGAGATATCCATCAGAGTGAAATAATTAGGaa       <  1:289039/238‑1 (MQ=255)                                                                                                                                                                                                   aCTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCCCATTTCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGAAACCCTACAGATTTATAAGAAAGCCTGAAGTGAGATATCCATCAGAGTGAACTAATTCGGACAatat  >  2:1581466/1‑239 (MQ=255)                                                                                                                                                                                                     |                                                                                                                                                                                                                                             CAGCTGTAAGCGGATATCCGCAGGCATTT‑TCCAGCCGGGGCCGAGGCTCCCCACCGGCGCGGGCGTTTTTGTCCGGTAACTGCTGTAGGTGCGGGAGAGGATGAACGGCAGCGGGCCGGGCAGGGCGAT‑GTCGGTTTCACCGGGAAGGACCTTTGCACCGAGCAGGG‑GATTGACCGGATGGCCGGAC‑GTCACTCCGCCGGGGCACACCGAACAGGCCACGCCGGTGGGGGCACCAATGCGCACCCCGGCTGAACCCTGAACAATGCTACCGCCATACTGCGTCATGTCGCCCTGACGCGCTGCCGGTTTTCCGCTCATTTCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGAAACCCTACAGATTTATAAGAAAGCCTGAAGTGAGATATCCATCAGAGTGAAATAATTAGGAAAATAT  >  NC_007779/3877915‑3878343

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑