Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_007779	2,372,048	T→C	20.8%	L103P (CTC→CCC)	arnC →	undecaprenyl‑phosphate 4‑deoxy‑4‑formamido‑L‑arabinose transferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007779	2,372,048	0	T	C	20.8%	128.6 / 10.9	70	L103P (CTC→CCC)	arnC	undecaprenyl‑phosphate 4‑deoxy‑4‑formamido‑L‑arabinose transferase
Reads supporting (aligned to +/- strand):  ref base T (25/29);  new base C (2/13);  total (27/43)
Fisher's exact test for biased strand distribution p-value = 3.41e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAGGCGCACCACCACAGCCTGTGAATCGTTGGGGAAAGAGTATGAGATCCTGCTGATTGATGACGGCAGTAGCG‑ATAATTCCGCGCATATGCTGGTC‑GAAGCCTCACAAGCGGAGAACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGATTCAGTCACGTTACTGGCGACTTAATTA‑TTACCCTTGATGCCGATCTCCAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGATGGGTGATTACGGTTGTATGCTGCGCGCCTATCGCCGTCATATTGTCGATGCGATGTTGCACTGCCATGAACGCAG  >  NC_007779/2371821‑2372282                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                              cAGGCGCACCACCACAGCCTGTGAATCGTTGGGGAAAGAGTATGAGATCCTGCTGATTGATGACGGCAGTAGCG‑ATAATTCCGCGCATATGCTGGTC‑GAAGCCTCACAAGCGGAGAACAGCCGTATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGATTCAGTCACGTTACTGGCGACTTAATTA‑TTACCCTTGATGCCGATCTCCAG‑AATCCGc                                                                                                                                                                                                                                   <  1:618747/239‑1 (MQ=255) cAGGCACACCACAACGGCCTGTGTATCGTTGAGAAAAGAGTATGAGATCCTGCTGATGGATGACGGCAGTAGCG‑AGAATTCCGCGCATATGGTGGTC‑GAAGCCTTACAAGCGGAGAACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGATTCAGTCACGTTACTGGCGACTTAATTA‑TTACCCTTGATGCCGATCTCCAG‑AATCCGc                                                                                                                                                                                                                                   <  2:1384580/239‑1 (MQ=255)  aGGCACCCCACCCCAGCCTGGGAATCGTTGGGAAACGAGGAGGAGATCCGGGTGATAGATGACGAAGGTAGCG‑CTAATGCGCCGCTTATGCTGGTC‑GTGCCCTCACAAGGGTGGCACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGATTCAGTCCCGTTACTGGCGACTTAATTA‑TTACCCTTGAGGCCGATCTCCAG‑AATCCGc                                                                                                                                                                                                                                   <  2:1006308/238‑1 (MQ=255)    gcgcACCACCACAGCCTGTGAATCGTTGGGGAAAGAGTATGAGATCCTGCTGATTGATGACGGCAGTAGCG‑ATAATTCCGCGCATATGCTGGTC‑GAAGCCTCACAAGCGGAGAACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGGGTCAGTCACGTTATTGGCGGCTTTATTA‑TTAACCTTGTTTACGATATCCAG‑AATCCGcccg                                                                                                                                                                                                                                >  1:932050/1‑237 (MQ=255)                    tgtgAATCGTTGGGGAAAGAGTATGAGATCCTGCTGATTGATGACGGCAGTAGCG‑ATAATTCCGCGCATATGCTGGTC‑GAAGCCTCACAAGCGGAGAACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGGTTTAGTCACGTTACTGGCGCCTTTTTTT‑TTACCCTTTATGCCCATTTCCCG‑AATCCCCCCAAA‑AAAAA‑cccccccc                                                                                                                                                                                                               >  1:261275/1‑238 (MQ=255)                      tgAATCGTTGGGGAAAGAGTATGAGATCCTGCTGATTGATGACGGCAGTAGCG‑ATAATTCCGCGCATATGCTGGTC‑GAAGCCTCACAAGCGGAGAACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGGTTTATTCCCCTTTCTGGCGCACTACTTA‑TTATCCCTGTTTGCGACCCCCCG‑AAACCCCCACAA‑CAAAA‑cccccccccg                                                                                                                                                                                                             >  2:1783775/1‑236 (MQ=255)                              tGGGGAAAGAGTATGAGATCCTGCTGATTGATGACGGCAGTAGCG‑ATAATTCCGCGCATATGCTGGTC‑GAAGCCTCACAAGCGGAGAACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGATTCAGTCACGTTACTGGCGACTTAATTA‑TTACCCTTGATGCCGATCTCCAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCaaa                                                                                                                                                                                                     <  1:130612/238‑1 (MQ=255)                              tGGGGAAAGAGTATGAGATCCTGCTGATTGATGACGGCAGTAGCG‑ATAATTCCGCGCATATGCTGGTC‑GAAGCCTCACAAGCGGAGAACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGATTCAGTCACGTTACTGGCGACTTAATTA‑TTACCCTTGATGCCGATCTCCAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCaaa                                                                                                                                                                                                     <  1:1117903/238‑1 (MQ=255)                              tGGGGAAAGAGTATGAGATCCTGCTGATTGATGACGGCAGTAGCG‑ATAATTCCGCGAATAGGCTGGTC‑GAAGCCTCACAAGCGGAAAACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGATTCAGTCACGTTACTGGCGACTTAATTA‑TTACCCTTGATGCCGATCTCCAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCaaaa                                                                                                                                                                                                    <  1:1422562/239‑1 (MQ=255)                                gggAAAGAGTATGAGATCCTGCTGATTGATGACGGCAGTAGCG‑ATAATTCCGCGCATATGCTGGTC‑GAAGCCTCACAAGCGGAGAACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGGTTTAGTCACGTTACTGGCGACTTAATTA‑TTTTCCCTTATTCCGATCTCCCG‑AAACCCCCCGAA‑AAAAA‑ACCCCCCCCGGGGGCcaaaa                                                                                                                                                                                                   >  1:63748/1‑237 (MQ=255)                                    aaGAGTATGAGATCCTGCTGATTGATGACGGCAGTAGCG‑ATAATTCCGCGCATATGCTGGTC‑GAAGCCTCACAAGCGGAGAACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGGATTAGTCCCTCTACTTGCGGCCTAATTATTTATCCTT‑CTGCCGGTCTCCAG‑AAACCGCCCTAA‑CAAAA‑ACCCCCCCCCGTGGCCAAAACCggt                                                                                                                                                                                              >  1:1595176/1‑237 (MQ=255)                                        gattGAGATCCCGTTTATTTATGGGGGGAGTGGCG‑AAAATTCCGCGCATATGCTGGTC‑GAAGCCTCACAAGCGGAGAACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGATTCAGTCACGTTACTGGCGACTTAATTA‑TTACCCTTGATGCCGATCTCCAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGa                                                                                                                                                                                            <  1:64834/234‑1 (MQ=255)                                          aTGAGATCCTGCTGATTGATGACGGCAGTAGCG‑ATAATTCCGCGCATATGCTGGTC‑GAAGCCTCACAAGCGGAGAACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGGTTTAGTCACCTTTCTTGCGGCTTTATTA‑TTTCCCTTGTTTCCGATATCCAG‑AAACCCCCCGAA‑AAAAA‑ACCCCCCCTCGTGGCCAAAACCGAGGAAggg                                                                                                                                                                                        >  1:715738/1‑238 (MQ=255)                                                tccgtcttattgatGAGGGAGGTGGGG‑ATAATTCCGCGAATATGGTGGTG‑GAAGCCCCAAAGGCGGAAACCAGCCATTTTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGATTCAGTCACGTTACTGGCGACTTAATTA‑TTCCCCTTGATGCCGATCTCCAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTacg                                                                                                                                                                                    <  2:1694596/229‑1 (MQ=255)                                                tCCTGTTGATTGATGACGGCAGTAGCG‑ATAATTCCGCGCATATGCTGGTC‑GAGGCCTCACAAGCGGAGAACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGATTCAGTCACGTTACTGGCGACTTAATTA‑TTACCCTTGATGCCGATCTCCAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTacgac                                                                                                                                                                                  <  1:1422129/239‑1 (MQ=255)                                                tCCTGCTGTTTGAGGACGGCAGT‑GCGTATAATTCCGCGGATATGCTGGTC‑GAAGCCTCACAAGGGGAGACCAGCCATATTGTGTCTATTTTGCTTACCCGCAATTACGGGCAACATTCAGCGATTATGGCGGGATTCAGTCACGTTACTGGCGACTTAATTA‑TTCCCCTTGATGCCGATCTCCAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTacgac                                                                                                                                                                                  <  2:63748/239‑1 (MQ=255)                                                tCCTGCTGATTGATGACGGCAGTAGCG‑ATAATTCCGCGCATATGCTGGTC‑GAAGCCTCACAAGCGGAGAACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGATTCAGTCACGTTACTGGCGACTTAATTA‑TTACCCTTGATGCCGATCTCCAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTacgac                                                                                                                                                                                  <  1:1859649/239‑1 (MQ=255)                                                tCCTGCTGATTGATGACGGAAGTAGCG‑ATAATTCCGCGCATATGCTGGTC‑GAAGCCTCACAAGCGGAGAACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGATTCAGTCACGTTACTGGCGACTTAATTA‑TTACCCTTGATGCCGATCTCCAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTacg                                                                                                                                                                                    <  1:863910/237‑1 (MQ=255)                                                tCCGGCTGGTTGATGCCGGAGGTGGCA‑TAAATTCCGCGAATATGCTGGTC‑GAAGCCTCAAAGGGGGAGACCAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGATTCAGTCACGTTACTGGCGACTTAATTA‑TTACCCTTGATGCCGATCTCCAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTacgac                                                                                                                                                                                  <  2:490287/239‑1 (MQ=255)                                                ccgtggtgattaatGCCGGCAGTACCG‑ATAATGCCCCTATTATG‑TGGTCAGAACCCTCACAAGCGGAAACCAGCCATTTTGTGTCTATTTTGCTTAACCGCAATTACGAGCAACATTCACCGATTATGGCGGGATTCAGTCACGTTACTGGCGACTTAATTA‑TTACCCTTGATGCCGATCTCCAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTacgac                                                                                                                                                                                  <  2:1028889/233‑1 (MQ=255)                                                cccTGGTGATTGATGAGGGCAGTAGCG‑ATATTCCCGCGCATATGCTGGTC‑GAGGCCTCACAAGCGGAGAACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGATTCAGTCACGTTACTGGCGACTTAATTA‑TTACCCTTGATGCCGATCTCCAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTacgac                                                                                                                                                                                  <  2:1595176/238‑1 (MQ=255)                                                 ccTGCTGATTGATGACGGCAGTAGCG‑ATAATTCCGCGCATATGCTGGTC‑GAAGCCTCACAAGCGGAGAACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGGTTTTGTCCCGTTACTGGGGACTTAAATT‑TTATCCTTTTTGTCGACCCCCCC‑AAACCCCCCACA‑GAAAA‑CACCCCCCCGGCGGCGAAAACCGCTGAAGGGTatgagg                                                                                                                                                                                 >  1:295008/1‑237 (MQ=255)                                                 ccTGCTGATTGATGACGGCAGTAGCG‑ATAATTCCGCGCATATGCTGGTC‑GAAGCCTCACAAGCGGAGAACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGATTCAGTCACGTTACTGGCGGCTTAATTA‑TTATCCTTTATGCCGAGCTCCCG‑AATCCCCCCGAA‑GAAAA‑ACCCCCCCCGGGGGGGAAAGCCGATGAAGGGTacgacg                                                                                                                                                                                 >  1:954352/1‑239 (MQ=255)                                                      gtgttgatGACGGCGTGAGCA‑ATATTCCCGCTCATAGGTGGTTC‑GACCCCTCAAACGCGGAGAACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGATCCAGTCACGTTACTGGCGACTTAATTA‑TTCCCCTTGATGCCGATCTCCAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGt                                                                                                                                                                             <  2:932050/235‑1 (MQ=255)                                                        attgatGACGGAAGTAGCG‑ATAATTCCCCGCATATGCTGGTC‑GAAGCCTCACAAGCGAACAACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGATTCAGTCACGTTACTGGCGACTTAATTA‑TTACCCTTGATGCCGATCTCCAG‑AATCCGCCAGAA‑GAAAG‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAgg                                                                                                                                                                          <  1:657237/239‑1 (MQ=255)                                                         ttgatGACGGCAGTAGCG‑ATAATTCCGCGCATATGCTGGTC‑GAAGCCTCACAAGCGGAGAACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGATTCAGTCACGTTACTGGCGACTTAATTA‑TTACCCTTGATGCCGATCTCCAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAgg                                                                                                                                                                          <  1:1510558/238‑1 (MQ=255)                                                             tgaCGGCAGTAGCG‑ATAATTCCGCGCATATGCTGGTC‑GAAGCCTCACAAGCGGAGAACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGATTCAGTCACGTTACTGGCGACTTAATTA‑TTACCCTTGATGCCGATCTCCAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTg                                                                                                                                                                     <  1:257245/239‑1 (MQ=255)                                                              caCGGAAGCAGCT‑ATACATCCGCGCTTTTACGGGTT‑GAAGCCTCAACAGCTGTGAACATCATTTTTGTGCTTATTTTGCTTACCCGCAATTCCGGGCACAATTCAGCGATTATGGCGGGATTCAGTCACGTTACTGGCGACTTAATTA‑TTGCCCTTGATGCCGATCTCCAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTg                                                                                                                                                                     <  2:1410864/237‑1 (MQ=255)                                                                  gCAGTAGCG‑ATAATTCCGCGCATATGCTGGTC‑GAAGCCTCACAAGCGGAGAACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGATTTAGTCACGTTACTGGCGACTTAATTA‑TTACCCTTTATGCCCATCTCCAC‑AAACCCCCCGAA‑GAAAA‑ACCCCCCCCGGTGGCGAAAAACGATGAAGGGTACGACGGGGTGGGGGCTGTACg                                                                                                                                                                 >  1:291731/1‑238 (MQ=255)                                                                            aTAATTCCGCGCATATGCTGGTC‑GAAGCCTCACAAGCGGAGAACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGATTCAGTCACGTTACTGGCGGCTTAATTA‑TTAACCTTGTTGCCGATCTCCAG‑AAACCGCCAGAA‑GAAAA‑CCCCCCCCCGGGGGCAAAAGCCGCAGAAGGGGACGACGTGGTAGGGACTGTAAGCCAGAACCg                                                                                                                                                        >  1:256742/1‑238 (MQ=255)                                                                                     cgcATATGCTGGTC‑GAAGCCTCACAAGCGGAGAACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGATTTCGGCCCCTTTCTGGCGGATTAATTT‑TTTCCCTTCGTGCCCATCTCCAG‑AATCCCCCCGAA‑GAAAA‑ACCCCGCCCCGTGGTCAAAGCCGCAGAAGGGTACGACGTGGGAGGGGGTGTACGTCAGAAAAGCCCGGACa                                                                                                                                                >  1:271370/1‑237 (MQ=255)                                                                                     cgcATATGCTGGTC‑GAAGCCTCACAAGCGGAGAACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGATTCAGTCACGTTACTGGCGACTTTATTA‑TTACCCTTTATGCCGATCTCCAG‑AATCCCCCAGAA‑GAAAT‑ACCCCCCCCGGTGGCAAAAACCGATGAAGGGTACGAAGGGGTAGGGGCTGGACGCCCGAAACCCCAGGACaa                                                                                                                                               >  1:123789/1‑237 (MQ=255)                                                                                      gcATATGCTGGTC‑GAAGCCTCACAAGCGGAGAACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGATTCAGTCACGTTACTGGCGACTTAATTA‑TTACCCTTGATGCCGATCTCCAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTacg                                                                                                                                                                                    <  1:286893/200‑1 (MQ=255)                                                                                                gTC‑GAAGCCTCACAAGCGGAGAACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGGGTTCGTCACGATTCCTGCGGCCTCATTA‑TTATTCTTTTTTCCGATCTCCCC‑AAACCCCCCCAA‑AAAAA‑AACCCCCCCCGCGGGGAAACACGACGAAGGGTACGACGTGGTAGGGGGGGCACCCCCAAACCACCCAGACAGCAGGGTTCGtgc                                                                                                                                   >  2:175246/1‑237 (MQ=255)                                                                                                                           ccATTTTGTGTCTATTTTGCTTACCCGCAATTACGGGCAACATTCAGCGATTATGGCGGGATTCAGTCACGTTACTGGCGACTTAATTA‑TTCCCCTTGATGCCGATCTCCAG‑AACCCGCCAGAA‑GAAAC‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGc                                                                                                         <  1:1829158/239‑1 (MQ=255)                                                                                                                                     tCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGGTTCTGTTACGTTCCTTGCGACCTTATTT‑TTATCCTTTTTGCCCACCTCCAG‑AAACCGCCCGAA‑GAAAA‑CACCCCCCCGGTGGCGAAAGCCGAAGAAGGGGACGACGCGGGCGGGGCGCTACCCCCAAACCCCCCCGACAGCCGGGTTCGTGAAAACGCCCCGAAGATGCTAAAACGGGCTATTCcgcg                                                                                               >  2:1034106/1‑239 (MQ=255)                                                                                                                                     tCTATTTGGTTAACCCGAAATTCGGGGAAACATTCAGCGTTTAGGGGGGATTTCAGTCCCGTTACGGGGGATTTAATTA‑TTCCCCTTGATGCCGATCCCAAG‑AACCCGCAAGAA‑GAAAC‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGACGATTAACCGGCTTATTCAgcg                                                                                               <  1:1783775/239‑1 (MQ=255)                                                                                                                                      cTATTTTGCTTAACCGCATTTACGGGCAACATTCAGCGATTATGGCGGGATTCAGTCCCTTTACTGGCGACTTAATTA‑TTCCCCTTGATGCCGATCCCCAG‑AACCCGCCAGAA‑AAAAC‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAgcgc                                                                                              <  1:46037/239‑1 (MQ=255)                                                                                                                                               ttAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGATTCAGTCACTTTACTGGCGACTTAATTA‑TTCCCCTTGATGCCGATCTCAAA‑AACCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGc                                                                                     <  1:371301/239‑1 (MQ=255)                                                                                                                                                      cAATTACGGGCAACATTCAGCGATTATGGCGGGATTCAGTCACGTTACTGGCGATTTAATTA‑TTCCCCTTGATGCGGATCTCAAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGa                                                                              <  1:163844/239‑1 (MQ=255)                                                                                                                                                       aaTTACGGGCAACATTCAGCGATTATGGCGGGATTCAGTCCCGTTCCTGGCGATTTAATTA‑TTCCCCTTGAGGCCGATCCCCAA‑AACCCGCCAGAA‑AAAAC‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGa                                                                              <  1:248628/238‑1 (MQ=255)                                                                                                                                                               gCAACATTCAGCGATTATGGCGGGATTCAGTCACGTTACGGGCGACTTAATTA‑TGCCCCTTGATGCCGATCCCCAG‑AACCCGCCAAAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGATGGGTGAt                                                                      <  1:714677/238‑1 (MQ=255)                                                                                                                                                                 aaCATTCAGCGTTTATGGCGGGATTCAGTCACGTTACTGGCGACTTAATTA‑TTCCCCTTGATGCCGATCCCCAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGATGGGTGATTa                                                                    <  1:433966/238‑1 (MQ=255)                                                                                                                                                                 aaCATTCAGCGTTTATGGCGGAATTCAGTCCCGTTACTGGCGCCTTAATTA‑TTCCCCTGGATGCCGACCTCCAG‑AATCCGCCAAAA‑AAAAC‑CCCCCGCCGGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTCCGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGATGGGTGATTa                                                                    <  1:241010/238‑1 (MQ=255)                                                                                                                                                                              tATGGCGGAATTCAGTCCCGTTCCTGGCGCCTTAATTA‑TTCCCCTTAATGCCGATCTCCAG‑AACCCGCCAGAA‑GAAAC‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGATGGGTGATTACGGTTGTAtgctgc                                                      <  1:1219640/239‑1 (MQ=255)                                                                                                                                                                                 ggCGGGATTCAGTCACGTTACTGGCGACTTAATTA‑TTCCCCTTGATGCCGATCCCCAG‑AATCCGCCAGAA‑GAAAC‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGATGGGTGATTACGGTTGTATGCTgcg                                                     <  1:334737/237‑1 (MQ=255)                                                                                                                                                                                   cGGGATTCAGTCCCGTTACTGGCGATTTAATTA‑TTCCCCTGGATGCCGATCCCCAA‑AACCCGCCAGAA‑GAAAC‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGATGGGTGATTACGGTTGTATGCTgcgcgc                                                  <  1:513903/238‑1 (MQ=255)                                                                                                                                                                                      taTTAAGTCCCTTTAGTGGCGCTTTAATTA‑TTCCCCGTGATGCCGATCTCCAG‑AATCCCCCAGAA‑GAAAC‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGCCTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGATGGGTGATTACGGTTGTATGCTGCGCGCCTa                                               <  1:796134/237‑1 (MQ=255)                                                                                                                                                                                       aTTAAGTCCCGTTCCTGGCGGTTTAATTT‑TTCCCTTTGATGCCGA‑CCCCAGAAACCCGCCAGAA‑AAAAC‑CCCCCGCCGGGGGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTAGGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGATGGGTGATTACGGTTGTATGCTGCGCGCCTAt                                              <  1:1538101/238‑1 (MQ=255)                                                                                                                                                                                           agcccggTTACGGGGGACTTATTTT‑TTCCCCTGGAGCCCAACCACAAG‑TACCCGCCGAAA‑AAACC‑CCCCCGCCTGGTGGCAAAAGCGGATGAAGTTTACGAGGTGGAAGGGACTGTACGCCAGACCCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGATGGGTGATTACGGTTGTATGCTGCGCGCCTATCGCCg                                         <  2:1087547/233‑1 (MQ=255)                                                                                                                                                                                           aGTCACGTTACTGGGGGCTTAATTA‑TTACCCTTGATGCCGATCTCCAG‑AATCCGCCAGAA‑GAAAT‑ACCCCGCCTGGGGGCCAAAGCCGATGAAGGGTACGACGTGGGAGGGACTGTACGCCCGAACCGCCCGGACAGCTGGGTTCGTAAAACCGCTTCGAAGATGATTAACCGGCCTATTCAGCGCACCACTGGCCAAACGATGGGGGATTACGGGTGTATGCTGCGCGCCTATCGcc                                          >  2:334737/1‑238 (MQ=255)                                                                                                                                                                                             caaCGTTAGTGG‑GTCTTTATTA‑TTCCCCTTGGCGGCGGTCCCCAG‑GAACCCCCCGAAGGAAAC‑CCCCCGCCTGGTGGAAAAGGCCGTGAAAGGTTCCGACGTGTTAGGGACTGTCCGCCAGACCCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGATGGGTGATTACGGTTGTATGCTGCGCGCCTATCGCCg                                         <  2:1516537/235‑1 (MQ=255)                                                                                                                                                                                                  ttACTGGCGACTTAATTA‑TTACCCTTGATGCCGATCTCCAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGATGGGTGATTACGGTTGTAtg                                                          >  1:477677/1‑215 (MQ=255)                                                                                                                                                                                                     cTGGCGACTTAATTA‑TTACCCTTGATGCCGATCTCCAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGATGGGTGATTACGGTTGTATGCTGCGCGCCTATCGCCGTCATATTGTc                               >  1:582162/1‑239 (MQ=255)                                                                                                                                                                                                       ggCGACTTAATTA‑TTACCCTTGATGCCGATCTCCAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGATGGGTGATTACGGTTGTATGCTGCGCGCCTATCGCCGTCATATTGTcga                             >  2:1818189/1‑239 (MQ=255)                                                                                                                                                                                                           aCTTAATTA‑TTACCCTTGATGCCGATCTCCAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGATGGGTGATTACGGTTGTATGCTGCGCTCCGATCGCCGCCATATTGTcgatgcg                         >  2:534661/1‑239 (MQ=255)                                                                                                                                                                                                               aaTTA‑TTACCCTTGATGCCGATCTCCAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGATGGGTGATTACGGTTGTATGCTGCGCGCCTATCGCCGTCATATTGTCGATGCGATGt                     >  1:834304/1‑239 (MQ=255)                                                                                                                                                                                                                   a‑ttcCCCTTGATGCCGACCTCAAG‑AATCCGCCAGAA‑AAACC‑CCCCCGCCTGGTGGCAAAAGCCGATGAGGGTTACGACGTGGTAGGGACTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGATGGGTGATTACGGTTGTATGCTGCGCGCCTATCGCCGTCATATTGTCGATGCGATGTTGCa                 <  1:1298021/239‑1 (MQ=255)                                                                                                                                                                                                                       aCCCTTGATGCCGATCTCCAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGATGGGTGATTa                                                                    >  2:1443516/1‑185 (MQ=255)                                                                                                                                                                                                                       aCCCTTGATGCCGATCTCCAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGATGGGTGATTa                                                                    <  1:1443516/185‑1 (MQ=255)                                                                                                                                                                                                                       aCCCTTGATGCCGATCTCCAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGATGGGTGATTACGGTTGTATGCTGCGCGCCTATCGCCGTCATATTGTCGATGCGATGTTGCACt               >  1:1782241/1‑238 (MQ=255)                                                                                                                                                                                                                           ttGATGCCGATCTCCAG‑AATCCGCCAGAA‑GAAAT‑CTCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGATGGGTGATTACGGTTGTATGCTGCGCGCCTATCGCCGTCATATTGTCGATGCGATGTTGCACTCCCAt          >  2:298564/1‑239 (MQ=255)                                                                                                                                                                                                                            tGATGCCGATCTCCAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGATGGGTGATTACGGTTGTATGCTGCGCGCCTATCGCCGTCATATTGTCGATGCGATGTTGCACTGCCATg         >  2:171094/1‑239 (MQ=255)                                                                                                                                                                                                                                 ccGATCCCCAA‑AACCCGCAAGAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGATGGGTGATTACGGTTGTATGCTGCGCGCCTATCGCCGTCATATTGTCGATGCGATGTTGCACTGCCATGAACg     <  1:603785/238‑1 (MQ=255)                                                                                                                                                                                                                                  cGATCCCCAA‑GAACCGGCAAAA‑GAAATCCCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGATGGGTGATTACGGTTGTATGCTGCGCGCCTATCGCCGTCATATTGTCGATGCGATGTTGCACTGCCATGAACg     <  1:1034106/238‑1 (MQ=255)                                                                                                                                                                                                                                   gATCTCCAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGATGGGTGATTACGGTTGTAtg                                                          >  1:1195432/1‑183 (MQ=255)                                                                                                                                                                                                                                   gATCTCCAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGATGGGTGATTACGGTTGTATGCTGCGCGCCTATCGCCGTCATATTGTCGATGCGATGTTGCACTGCCATGAACgca   >  1:9053/1‑238 (MQ=255)                                                                                                                                                                                                                                   gATCCCCAG‑AACCCGCCAGAA‑GAAAT‑CCCCCGCCTGGGGGCAAAAGCCGATGAAGGTTACGACGTGTTAGGGACTGTCCGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGATGGGTGATTACGGTTGTATGCTGCGCGCCTATCGCCGTCATATTGTCGATGCGATGTTGCACTGCCATGAACgcag  <  1:361732/239‑1 (MQ=255)                                                                                                                                                                                                                                   gATCCCCAG‑AACCCGCCAGAA‑GAAAC‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGATGGGTGATTACGGTTGTATGCTGCGCGCCTATCGCCGTCATATTGTCGATGCGATGTTGCACTGCCATGAACgcag  <  1:154359/239‑1 (MQ=255)                                                                                                                                                                                                                                    aTCTCCAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTACGCCGGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGATGGGTGATTACGGTTGTATGCTGCGCGCCTATCGCCGTCATATTGTCGATGCGATGTTGCACTGCCATGAACgcag  >  2:134221/1‑238 (MQ=255)                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                              CAGGCGCACCACCACAGCCTGTGAATCGTTGGGGAAAGAGTATGAGATCCTGCTGATTGATGACGGCAGTAGCG‑ATAATTCCGCGCATATGCTGGTC‑GAAGCCTCACAAGCGGAGAACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGATTCAGTCACGTTACTGGCGACTTAATTA‑TTACCCTTGATGCCGATCTCCAG‑AATCCGCCAGAA‑GAAAT‑CCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGATGGGTGATTACGGTTGTATGCTGCGCGCCTATCGCCGTCATATTGTCGATGCGATGTTGCACTGCCATGAACGCAG  >  NC_007779/2371821‑2372282

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: ‑