Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_007779	3,777,754	A→C	27.0%	T315P (ACC→CCC)	Y75_RS18735 →	PTS transporter subunit EIIC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007779	3,777,754	0	A	C	27.0%	67.7 / 13.8	58	T315P (ACC→CCC)	Y75_RS18735	PTS transporter subunit EIIC
Reads supporting (aligned to +/- strand):  ref base A (29/12);  new base C (2/14);  total (31/27)
Fisher's exact test for biased strand distribution p-value = 8.70e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.67e-01

GACAGTTTATCTTTGGTCCGGCAGCTGTTGAAGGCGGCATTCAGATGTACTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCC‑‑GAGCCGCTGAAA‑TCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTT‑T‑GGTG‑CC‑GTGGGCATTTCTTT‑A‑GCGATGTACTTCACTGCCGCACCGGAAAA‑TCGGGTAAAA‑GTGGCGGGCTTGCT‑GATTCCCGCAACCTT‑AA‑CCGCCATGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGATGTTCAGCAACCACGCGGATATGATGCTGACCCAAATCGCCATTGGGTT  >  NC_007779/3777521‑3777992                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                                 gACAGTTTATCTTTGGTCCGGCAGCTGTTGAAGGCGGCATTCAGATGTACTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCC‑‑GAGCCGCTGAAA‑TCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTT‑T‑GGTG‑CC‑GTGGGCATTTCTTT‑A‑GCGATGTACTTCACTGCCGCACCGGAAAA‑TCGGGTAAAA‑GTGGCGGGCTTGCT‑GGTTCCCCCCACCttt                                                                                                                                                                                                                                             >  1:211381/1‑238 (MQ=255) gACAGTTTATCTTTGGTCCGGCAGCTGTTGAAGGCGGCATTCAGATGTACTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCC‑‑GAGCCGCTGAAA‑TCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTT‑T‑GGTG‑CC‑GTGGGCATTTCTTT‑A‑GCGATGTACTTCACTGCCGCACCGGAAAA‑TCGGGTAAAA‑GTGGCGGGCGCTCT‑GATTTCCCCGACCCT‑a                                                                                                                                                                                                                                            >  1:904547/1‑239 (MQ=255)     gTTTATCTTTGGTCCGGCAGCTGTTGAAGGCGGCATTCAGATGTACTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCC‑‑GAGCCGCTGAAA‑TCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTT‑T‑GGTG‑CC‑GTGGGCATTTCTTT‑A‑GCGATGTACTTCACTGCCGCACCGGAAAA‑TCGGGTAAAA‑GTGGCGGGCTTGCT‑GCTTCGCGCAACCCT‑AA‑ca                                                                                                                                                                                                                                        >  2:1303453/1‑237 (MQ=255)      tttATCTTTGGTCCGGCAGCTGTTGAAGGCGGCATTCAGATGTACTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCC‑‑GAGCCGCTGAAA‑TCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTT‑T‑GGTG‑CC‑GTGGGCATTTCTTT‑A‑GCGATGTACTTCACTGCCGCACCGGAAAA‑TCGGGTAAAA‑GTGGCGGGGTTGGT‑GATTTCCCCAACCTT‑AA‑CCg                                                                                                                                                                                                                                       >  1:1325857/1‑238 (MQ=255)      tttATCTTTGGTCCGGCAGCTGTTGAAGGCGGCATTCAGATGTACTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCC‑‑GAGCCGCTGAAA‑TCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTT‑T‑GGTG‑CC‑GTGGGCATTTCTTT‑A‑GCGATGTACTTCACTGCCGCACCGGAAAA‑TCGGGTAAAA‑GTGGCGGGCTTGCT‑GATTCCCCCCACCCT‑AA‑CCg                                                                                                                                                                                                                                       >  1:1173253/1‑238 (MQ=255)          tttgtGGGCCGGCAGGTGTGGAGGGCGGCAGTCGGATGTGTGGGGCGAGGCCTCGGAAAGTGTTGAGGTTGCGCGCG‑‑GAGCCGCTGAAA‑TCGTTGTTCCGGGAGGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTT‑G‑GGTG‑CG‑GGGGGATTTTTTTT‑A‑GCGATGTACTTCACTGCCGCACCGAAAAA‑TGGGGTAAAG‑GGGGGGGGTTTGCT‑GATCCCCGCACCCTT‑AA‑CCGCCATg                                                                                                                                                                                                                                  <  2:811302/235‑1 (MQ=255)              tGGTCCGGCAGCTGTTGAAGGCGGCATTCAGATGTACTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCC‑‑GAGCCGCTGAAA‑TCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTT‑T‑GGTG‑CC‑GTGGGCATTTCTTT‑A‑GCGATGTACTTCACTGCCGCACCGGAAAA‑TCGGGTAAAA‑GTGGCGGGCTTGCT‑GGTTTCCCCCACCTT‑AA‑CCCCCCTGCtgg                                                                                                                                                                                                                              >  1:246977/1‑239 (MQ=255)              tGGTCCGGCAGCTGTTGAAGGCGGCATTCAGATGTACTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCC‑‑GAGCCGCTGAAA‑TCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTT‑T‑GGTG‑CC‑GTGGGCATTTCTTT‑A‑GCGATGTACTTCACTGCCGCACCGGAAAA‑TCGGGTAAAA‑GTGGCGGGCTTGCT‑GATTTCCCCAACCCT‑TA‑ACGCCCTGCtgg                                                                                                                                                                                                                              >  1:1497640/1‑239 (MQ=255)                gTCCGGCAGCTGTTGAAGGCGGCATTCAGATGTACTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCC‑‑GAGCCGCTGAAA‑TCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTT‑T‑GGTG‑CC‑GTGGGCATTTCTTT‑A‑GCGATGTACTTCACTGCCGCACCGGAAAA‑TCGGGTAAAA‑GTGGCGGGGTTTCT‑GATTTCCGCCAACCT‑CA‑CCGCCCTGCtgggg                                                                                                                                                                                                                            >  1:218398/1‑237 (MQ=255)                gTCCGGCAGCTGTTGAAGGCGGCATTCAGATGTACTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCC‑‑GAGCCGCTGAAA‑TCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTT‑T‑GGTG‑CC‑GTGGGCATTTCTTT‑A‑GCGATGTACTTCACTGCCGCACCGGAAAA‑TCGGGTAAAA‑GTGGCGGGGCTGGT‑GTTTTTCGCCACCTT‑AA‑ACGCCATACtggtg                                                                                                                                                                                                                            >  1:1075778/1‑239 (MQ=255)                gTCCGGCAGCTGTTGAAGGCGGCATTCAGATGTACTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCC‑‑GAGCCGCTGAAA‑TCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTT‑T‑GGTG‑CC‑GTGGGCATTTCTTT‑A‑GCGATGTACTTCACTGCCGCACCGGAAAA‑TCGGGTAAAA‑GTGGCGGGCTTGTT‑GGTTTCCCCCACCTT‑AA‑CCCCCAAGCtgggg                                                                                                                                                                                                                            >  1:218691/1‑237 (MQ=255)                                    ggcATTCAGATGTACTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCC‑‑GAGCCGCTGAAA‑TCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTT‑T‑GGTG‑CC‑GTGGGCATTTCTTT‑A‑GCGATGTACTTCACTGCCGCACCGGAAAA‑TCGGGTAAAA‑GTGGCGGGGTTGCT‑GATTTCCCCCACCCT‑TA‑CCGCCCTGCTGGGGGGGATTACCGAAACGCCggg                                                                                                                                                                                                        >  1:503233/1‑238 (MQ=255)                                      cATTCAGATGTACTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCC‑‑GAGCCGCTGAAA‑TCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTT‑T‑GGTG‑CC‑GTGGGCATTTCTTT‑A‑GCGATGTACTTCACTGCCGCACCGGAAAA‑TCGGGTAAAA‑GTGGCGGGCTTGCT‑GGTTTCCCCAAACCT‑AA‑CCCCCAGACTGGGGGGGATTTTCGAAcccccaggaa                                                                                                                                                                                                      >  1:669329/1‑231 (MQ=255)                                      cATTCAGATGTACTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCC‑‑GAGCCGCTGAAA‑TCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTT‑T‑GGTG‑CC‑GTGGGCATTTCTTT‑A‑GCGATGTACTTCACTGCCGCACCGGAAAA‑TCGGGTAAAA‑GTGGCGGGCTTGCT‑GATTTCCGCCACCCT‑AA‑CCGCCCAGCTGGGGGGGATTTCCGAACCCCTGGGAt                                                                                                                                                                                                      >  1:473083/1‑239 (MQ=255)                                      cATTCAGATGTACTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCC‑‑GAGCCGCTGAAA‑TCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTT‑T‑GGTG‑CC‑GTGGGCATTTCTTT‑A‑GCGATGTACTTCACTGCCGCACCGGAAAA‑TCGGGTAAAA‑GTGGCGGGCGTGCG‑TATTCCCCCCACCCT‑AA‑CCCCCATGCTGGGGGGAAATACCTAACCGcaccgat                                                                                                                                                                                                      >  1:535320/1‑233 (MQ=255)                                                     ggCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCC‑‑GAGCCGCTGAAA‑TCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTT‑T‑GGTG‑CC‑GTGGGCATTTCTTT‑A‑GCGATGTACTTCACTGCCGCACCGGAAAA‑TCGGGTAAAA‑GTGGCGGGCTTGCT‑GTTTTCCCCCACCTT‑AA‑CCCCCCTGCTGGGGGGGATTAACGAACCCCCGGAAATTACATTCCTCtt                                                                                                                                                                                         >  1:771762/1‑237 (MQ=255)                                                       cgcAGCATCTGCAAGAGTTCAGTTTGAGCGCC‑‑GAGCCGCTGAAA‑TCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTT‑T‑GGTG‑CC‑‑‑GGGCATTTCTTT‑A‑GCGATGTACTTCACTGCCGCACCGGAAAA‑TCGGGTAAAA‑GTGGCGGGGTTGCT‑GGTTCCCGCCACCCT‑AA‑CCGCCCTGCTGGGGGGGGATACCGAACCGCCGGGATTTACCCTCCTGTTCttt                                                                                                                                                                                     >  1:91811/1‑237 (MQ=255)                                                          gcagctgtagagagTGCGGTTTGTGCGCCCGGCGCCGTTAAAA‑TCTTTTTTCCCGGAGGGCGT‑TTTTCCCCTCCACGATATGTAAAAAGTCTT‑T‑GGGG‑CC‑GTGGGTTTTTCTTT‑A‑GCGATGTGCTCCCCTGCCGCACCGAAAAA‑TCGGATAAAA‑GGGGCGGGTTTGCT‑GATCCCCGCACTCTT‑AC‑CCGCCATGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCAttt                                                                                                                                                                                    <  2:464109/229‑1 (MQ=255)                                                          agcaTCTGCAAGAGTTCAGTTTGAGCGCC‑‑GAGCCGCTGAAA‑TCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTT‑T‑GGTG‑CC‑GTGGGCATTTCTTT‑A‑GCGATGTACTTCACTGCCGCACCGGAAAA‑TCGGGTAAAA‑GTGGCGGGGTTGCT‑GTGTTCCCCAACCTT‑AA‑CCGCCCCACCGGGGGGGGTTACCGAACCGCTGGGGTTTATCTTCCTGGTCttttt                                                                                                                                                                                   >  1:1358786/1‑237 (MQ=255)                                                            caTCTGCAAGAGTTCAGTTTGAGCGCC‑‑GAGCCGCTGAAA‑TCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTT‑T‑GGTG‑CC‑GTGGGCATTTCTTT‑A‑GCGATGTACTTCACTGCCGCACCGGAAAA‑TCGGGTAAAA‑GTGGCGGGCTTTCT‑GATTTCCCCCCCCCT‑AA‑CCCCCAAGCTGGTGGGGATTACCGGACCCCCGGAATTTAACTTCCCTTTCTTTTCAc                                                                                                                                                                                 >  1:1043691/1‑238 (MQ=255)                                                              tCTGAAAGAGTTCAGTTGGAGCGCC‑‑GAGCCGCTGAAA‑TCGTTGTTCCCGGAGGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTT‑T‑GGTG‑CC‑GTGGGCTTTTCTTT‑A‑GCGATGTACTTCACTGCCGCACCGAAAAA‑TCGGGTAAAA‑GTGGCGGGCTTGCT‑GATCCCCGCAACCTT‑AA‑CCGCCATGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTc                                                                                                                                                                                              <  1:46782/223‑1 (MQ=255)                                                                    agagTTCAGTTTGAGCGCC‑‑GAGCCGCTGAAA‑TCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTT‑T‑GGTG‑CC‑GTGGGCATTTCTTT‑A‑GCGATGTACTTCACTGCCGCACCGGAAAA‑TCGGGTAAAA‑GTGGCGGGCTTGCT‑GATTTCCCCAACCTT‑AA‑CCCCCAATCTGGTGGGGATTATCGAACCGCCGGGATTTACCTTCCTTTTTCTTTTACCGTTGCTGt                                                                                                                                                                        >  1:652518/1‑239 (MQ=255)                                                                        ttCAGTTTGAGCGCC‑‑GAGCCGCTGAAA‑TCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTT‑T‑GGTG‑CC‑GTGGGCATTTCTTT‑A‑GCGATGTACTTCACTGCCGCACCGAAAAA‑TCGGGTAAAA‑GTGGCGGGCTTGCT‑GATTCCCGCAACCTT‑AA‑CCGCCATGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTg                                                                                                                                                                     <  1:111817/238‑1 (MQ=255)                                                                                 ggcgcC‑‑GAGCC‑CTGAAATTTGTTGTCCCGGGAGGGGGT‑TTTTGCCTGGCGCGGTACCTAAAAAAT‑TT‑T‑GGGG‑CCGGGGGGCTTTTCTTT‑A‑GGGGTTTCTTTCCCTCCCCCCCCGAAAAA‑T‑GGGTAAAAGGGGGGGGGTTTGCT‑GTTCCCCGCAACCTA‑AA‑CCGCCATGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACg                                                                                                                                                            <  2:935310/237‑1 (MQ=255)                                                                                 aGCGCC‑‑GAGCCGCTGAAA‑TCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTT‑T‑GGTG‑CC‑GTGGGCATTTCTTT‑A‑GCGATGTACTTCACTGCCGCACCGGAAAA‑TCGGGTAAAA‑GTGGCGGGCTTGCT‑GATTCCCCCCACCCT‑AA‑CCGCCCTGCTGGGGGGGATTACCGAACCGCCGGGAATTTCCTTCCTGTTCTTTTTACCGTTGCTGTTTTCGGTACACg                                                                                                                                                            >  1:935310/1‑238 (MQ=255)                                                                                         gAGCCGCTGAAA‑TCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTT‑T‑GGTG‑CC‑GTGGGCATTTCTTT‑A‑GCGATGTACTTCACTGCCGCACCGGAAAA‑TCGGGTAAAA‑GTGGCGGGCTTGCT‑GATTCCCGCCACCCT‑AA‑CCCCCCTGCTGGGGGGGATTACCGAACCGCCGGAATTTACCTTCCTGTTCATTTCACCCCTGCTGTTTTCGGTACACGcccg                                                                                                                                                        >  1:889994/1‑234 (MQ=255)                                                                                             ggatGAAG‑TCG‑TGTTCCGGGGAGGTTG‑TTTTCTCCTCCGCGGTTAATCAAAAATTTT‑TGGGGG‑CC‑GGGGTATTTTCTTT‑G‑GGGATTTCCTCCCCT‑CCCCCCCGGAAAACGGGGGTAAAG‑GGGGGGGGCTTCCT‑GTTCCCCGCATCTTT‑AC‑CCGCCATGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTggc                                                                                                                                                  <  2:1067531/235‑1 (MQ=255)                                                                                                    attCGTTTTCCCGGGAGGGCGT‑TTTTCCCTTGCCGGTTAACTAAAAATTCTT‑G‑GGGG‑CG‑GTGGGTATTTTTTT‑G‑GCGTTGTCCTTCACTCCCCCCCCGAAAAA‑TCGGGTAAAA‑GTGGGGGGTTTGCT‑GATCCCCGCACCTTT‑AA‑CCGCCATGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCa                                                                                                                                           <  1:987847/237‑1 (MQ=255)                                                                                                        ttgtttCCGGGAGGGCTG‑TTTCGCCCTTCGTGATAAATAAAAATTTTT‑T‑GGTG‑CG‑GGGGGTATTTTTTT‑G‑GCGTTGTCCTCCCCTGCCCCACGGGAAAG‑CGGGGAAAAG‑GGGGGGGGTTTGCT‑GTTTCCCGC‑ACCTT‑AACCCGCCATGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGt                                                                                                                                       <  2:889994/235‑1 (MQ=255)                                                                                                        gttgttCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTT‑T‑GGTG‑CC‑GTGGGCATTTCTTT‑A‑GCGATGTACTTCACTGCCGCACCGGAAAA‑TCGGGTAAAA‑GTGGCGGGGTTGCTGGTTTACCCCACCCTT‑AA‑CTCCCCCCTCGGGGGGAATT‑CACAGCCGCTGGGATTTATCTTCCACTTTCTTTTTCCGTTTTTGTTTGTGGGAGAAGCCGTGCTGGCCGCGTCaacgg                                                                                                                                       >  2:729560/1‑236 (MQ=255)                                                                                                         tgtttCCCGGAGGGTGG‑TTTTGCCTGGCAAGTTATCAC‑AAAATCTTGT‑GGTG‑GC‑GTGGGCATTT‑TTT‑T‑GCGGTTTTATTTCCGTCCGCCACCGAAAA‑CGGGGAAAAAGGTGGGGGTTTGGTT‑GATCCCCGAAACTTT‑CC‑CCGCCATGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTc                                                                                                                                      <  2:693775/236‑1 (MQ=255)                                                                                                            ttCCAGGGAGGGCG‑TTTTGCCCTGGCCGGGAACCAAAAAATTTT‑T‑GGTG‑GC‑GGGGGTTTTTTTTTGG‑GGGTTTTCCTCCCCCGCCCCACCGAAAAG‑TGGGGAAAAG‑GGGGCGGGCTTGGT‑G‑TTCCCCGAACCTTAAA‑CCGCCATGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGa                                                                                                                                    <  2:1293919/239‑1 (MQ=255)                                                                                                               ccGGGAGGGGGTTTTTGCCCGGCCGGTTAACT‑AAAAATTTT‑T‑TGGG‑CC‑GGGGGGTTTTTTTT‑AGGTGATTTCCTCCCCCCCCGCACCGAAAAA‑GCGGAAAAAG‑GGGGGGGGTTTGTT‑GATCCCCAAACCCTT‑AC‑CCGCCATGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCg                                                                                                                                 <  2:246977/239‑1 (MQ=255)                                                                                                                      gCGT‑TTTTCCCTTGCACGGAAACT‑AAAAATTTT‑T‑GGGGTGG‑GTGGTTTTTTTTTT‑A‑GGTATGTTTTTCACGCCCGCCCCGGAAAA‑TCGGATAAAA‑GGGGCGGGCTGGCT‑GATCCCCGCACTCTA‑CA‑CCGCCATGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTa                                                                                                                          <  2:1325857/238‑1 (MQ=255)                                                                                                                        tg‑TTTTTCCCGACACGGTACCTCAAAAAGTGT‑T‑GGGG‑GC‑GTGGGGCTTTCTTT‑G‑GGCGTGTCCTTCCCCGGCAGCCCGGAAAAGTGGGGTAAAG‑GGGGGGGTTTGGCT‑GCTCCCCGACCCCTA‑CA‑CCGCCATGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTAt                                                                                                                         <  2:1173253/237‑1 (MQ=255)                                                                                                                        cgtttttGCCCTGACCGGTAACTAAAAAATTTT‑G‑GGTG‑CC‑GTGGGCTTTTTTTT‑A‑GCGATTTCCTTCCCTGCCGCACGGAAAAA‑TCGGGTAAAG‑GTGGCGGGTTTGCT‑GATCCCCCAACCCTT‑AA‑CCGCCATGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTAt                                                                                                                         <  1:711843/235‑1 (MQ=255)                                                                                                                        cgtttttCCCCTGCACGGAAACTAAAAAATTTT‑T‑GGTG‑CC‑GGGGGATTTTTTTT‑A‑GCGATGTCCTTCACTGCCGCACCGAAAAA‑TGGGGTAAAA‑GGGGCGGGTTGGCT‑GATCCCCGCACCCTT‑AA‑CCGCCATGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTAt                                                                                                                         <  1:161248/235‑1 (MQ=255)                                                                                                                                              taaaaaaTCTT‑G‑GGGG‑CC‑GTGGGCTTTTCTTT‑A‑GCGATTTCCTCCACTGCCGCACCGAAAAA‑TCGGGAAAAA‑GTGGCGGGTTTGCT‑GATCCCCGCACCCTT‑AA‑CCGCCATGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACAt                                                                                                  <  1:729560/237‑1 (MQ=255)                                                                                                                                               cAAAAATCTT‑T‑GGTG‑CC‑GTGGGCATTTCTTT‑A‑GCGATGTACTTCACTGCCGCACCGGAAAA‑TCGGGTAAAA‑GTGGCGGGCTTTCT‑GATTCCCCCAACCTT‑TA‑CCGCCCTGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCATTTCACCCTTGCTGTTTGTGGTACACCCCGTGCTTGCGGCCTCCATCGCGACCGTAATGTATCTCTTTGGTGTGGGGGGCAACATg                                                                                                 >  1:1395879/1‑239 (MQ=255)                                                                                                                                                                               ttt‑A‑GCGATGTACTCCCCTCCCGCACCGGAAAA‑CCGGGAAAAA‑GGGGCGGGCTTGCT‑GATCCCCGCACCCTT‑AA‑CCGCCATGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTg                                                                                                                                                                     <  1:236207/143‑1 (MQ=255)                                                                                                                                                                                 t‑A‑GCGATGTCCTTCCCTGCCGCACCGAAAAA‑TGGGGTAAAA‑GGGGCGGGTTTGCT‑GTTCCCCCCACCCTT‑AA‑CCGCCATGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCg                                                                   <  1:1580796/239‑1 (MQ=255)                                                                                                                                                                                          gtgcttcgcgcccGCAACGGAAAA‑GGGGATAAAG‑GTGGGGGCGTTGCT‑GATCCCCAAAACCTT‑AA‑CCGCCATGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACt                                                            <  1:1672984/228‑1 (MQ=255)                                                                                                                                                                                              ttCACTGCCGCACCGGAAAA‑TCGGGTAAAA‑GTGGCGGGCTTTCT‑GATTTCCGCCACCTT‑AA‑CCGCCATGCTGGTGGGGATTTACGAACCCCTGGAATTTTCCTTCCTGTTTATTTTACCCTTTCTGTTTTCGGTACACGCCGTGCTGGCGGCCTCCATGTCGACCGTAATGTATCTCTTTTGTGTGGGGGGGAAAATGGGGGGGGGGCTGATTGTCTAGGGTTTTCCGCCAAACTggg                                                         >  1:199369/1‑237 (MQ=255)                                                                                                                                                                                                   tcccccccgggAAAA‑GCGGGTAAAG‑GGGGCGGGCTTGCT‑GATCCCCCCAACCTT‑AC‑CCGCCATGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGa                                                   <  1:739797/230‑1 (MQ=255)                                                                                                                                                                                                        cACCGGAAAA‑TCGGGTAAAA‑GTGGCGGGCTTGCT‑GATTCCCCCAACCCT‑AA‑CCGCCATGCTGGGGGGAATTACCGAACCCCCGGGATTTTCCTTCCTCTTCATTTTCCCCTTGCTGTTTTCGGGACACGCCGTGCTGGCGGCCTCAATg                                                                                                                                        >  1:1759817/1‑149 (MQ=255)                                                                                                                                                                                                                  atggggTAAAG‑GTGGCGGGTTTGCT‑GTTTCCCACAACCTT‑AA‑CCGCCATGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCATTTCCCCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGATGTTCAGCAACCAc                                     <  2:211381/236‑1 (MQ=255)                                                                                                                                                                                                                     ggatAAAA‑GGGGCGGGCTTGTT‑TATCCCCGCAACTTC‑AA‑CCGCCATGCTGGTGGGAATTCCCGAACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGATGTTCAGCAACCAcgc                                   <  1:1045764/235‑1 (MQ=255)                                                                                                                                                                                                                          aagggtgtCGGGCTGCCT‑GATCCCGGCACTCTT‑AA‑CCGCCATGCGGGGGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGATGTTCAGCAACCACGCGGata                              <  2:1842915/235‑1 (MQ=255)                                                                                                                                                                                                                                           gttcgtCCCACAACCTT‑AC‑CCGCCATGCTGTTGTGAATTACCGAACCGCTGGAATTTCCCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGATGTTCAGCAACCACGCGGATATGATGCTGACCCAAAt              <  2:1075778/234‑1 (MQ=255)                                                                                                                                                                                                                                               ttCCCGCAACCTT‑AA‑CCGCCATGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGATGTTCAGCAACCACGCGGATATGATGCTGACCCAAATCGcc          >  1:143872/1‑239 (MQ=255)                                                                                                                                                                                                                                               ttCCCGCAACCTT‑AA‑CCGCCATGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGATGTTCAGCAACCACGCGGATATGATGCTGACCCAAATCGcc          >  1:1316972/1‑239 (MQ=255)                                                                                                                                                                                                                                                tgccGCAACCTT‑AA‑CCGCGGTGCTGTTGGGAATTACCGAACCGCGGGTAATTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTCCACGCCGTGCTGGCGGGCTCGATGTCGACGGTGATGGATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTGTGATTGCCTGGGTTTTACCGCACAGTTGGATCGGGTGGTTCGGCAACCACGCGGAGATGATGCTGACCAAAGTCGcct         >  2:1511986/3‑238 (MQ=255)                                                                                                                                                                                                                                                tCCCGCAACCTT‑AA‑CCGCCATGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGATGTTCAGCAACCACGCGGATATGATGCTGACCCAAATCGCCa         >  2:252588/1‑239 (MQ=255)                                                                                                                                                                                                                                                tCCCGCAACCTT‑AA‑CCGCCATGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGATGTTCAGCAACCACGCGGATATGATGCTGACCCAAATCGCCa         >  1:802913/1‑239 (MQ=255)                                                                                                                                                                                                                                                tCCCGCAACCTT‑AA‑CCGCCATGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGATGTTACGCAACCACGTGGGTATGATGCTGACCCAAATCGCCa         >  2:1704833/1‑239 (MQ=255)                                                                                                                                                                                                                                                ccccGCACCTTA‑AA‑CCGCCATGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGATGTTCAGCAACCACGCGGATATGATGCTGACCCAAATCGCCa         <  1:157303/238‑1 (MQ=255)                                                                                                                                                                                                                                                ccccGCACCCTT‑AC‑CCGCCATGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGATGTTCAGCAACCACGCGGATATGATGCTGACCCAAATCGCCa         <  1:16541/238‑1 (MQ=255)                                                                                                                                                                                                                                                ccccGC‑ACCTT‑AACCCGCCATGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGATGTTCAGCAACCACGCGGATATGATGCTGACCCAAATCGCCa         <  1:1745511/238‑1 (MQ=255)                                                                                                                                                                                                                                                      caCCTTAAA‑CCGCCATGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGATGTTCAGCAACCACGCGGATATGATGCTGACCCAAATCGCCATTggg    <  1:238852/238‑1 (MQ=255)                                                                                                                                                                                                                                                       aCCTA‑AA‑CCGCCATGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCAGTTCACCGTTGCTGTTTGCGTTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGATGTTCAGCAACCACGCGGATATGATGCTGACCCAAATCGCCATTGGGtt  <  1:1694031/239‑1 (MQ=255)                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                                 GACAGTTTATCTTTGGTCCGGCAGCTGTTGAAGGCGGCATTCAGATGTACTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCC‑‑GAGCCGCTGAAA‑TCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTT‑T‑GGTG‑CC‑GTGGGCATTTCTTT‑A‑GCGATGTACTTCACTGCCGCACCGGAAAA‑TCGGGTAAAA‑GTGGCGGGCTTGCT‑GATTCCCGCAACCTT‑AA‑CCGCCATGCTGGTGGGAATTACCGAACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGATGTTCAGCAACCACGCGGATATGATGCTGACCCAAATCGCCATTGGGTT  >  NC_007779/3777521‑3777992

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑