Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	249,538	T→G	28.9%	pseudogene (533/1713 nt)	lfhA ←	pseudogene, flagellar system protein, promoterless fragment, flagellar biosynthesis

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	249,538	0	T	G	28.9%	43.0 / 2.6	47	pseudogene (533/1713 nt)	lfhA	pseudogene, flagellar system protein, promoterless fragment, flagellar biosynthesis
Reads supporting (aligned to +/- strand):  ref base T (11/18);  new base G (10/7);  total (21/26)
Fisher's exact test for biased strand distribution p-value = 2.25e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TACCCTGTGCTTTGTCCACCAGCGCCACCAGTTTGT‑AACCGAGGCTTAAACTGATAGGCTCGATCAGCGGAATGGTTTCCCAACTGACCTGCTGCTCGCTGGTT‑TCGGTGATGGTGCGGGTCAGCGTTTCGAGGC‑TTTTCTCTTCCGCCTCCGCCGCCAGCGGCTGTTTGCTCAT‑CCGCCAGCCGGTAAAACCAAGCA‑GGGCGCTGAACAGCAAAAACGGCAGGTGC‑GGCATTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGACGCGGGTGACGATAATCGCCGCCGCGGTGGAGAGCAGCAGGGAAGGGATCTGCGCCACCAGGCCGTCGCCGATGGTCATCAGCACATACTGCTGGAA  >  NC_000913/249314‑249752                                                                                                                                                                                                                                      |                                                                                                                                                                                                                        atcccTTTGGTTTTCCCCCCGGCGCCACGGGTTTGT‑AA‑CGAGGCTTAAACTGATAGGCTCGATCAGGGGATTGTTTCCCCAACTGACCGGCTGCTCGCTGGTT‑TCGGTGATGGTTCGGGTCAGCGTTTCGAGGC‑TTTTCTCTTCCGCCTCCGCCGCCAGCGGCTGTTTGCTCAT‑CCGCCAGCCGGTAAAACCAAGCA‑GGGCGCTGAACAGCAAAAACGGCAGGTGC‑gg                                                                                                                                                                                                                    <  2:649949/226‑1 (MQ=255)  aCCCTGTGCTTTGTCCACCAGCGCCACCAGTTTGT‑AACCGAGGCTTAAACTGATAGGCTCGATCAGCGGAATGGTTTCCCAACTGACCTGCTGCTCGCTGGTT‑TCGGTGATGGTGCGGGTCAGCGTTTCGAGGC‑TTTTCTCTTCCGCCTCCGCCGCCAGCGGCTGTTTGCTCAT‑CCGCCAGCCGGTAAAACCAAGCA‑GGGCGCTGAACAGCAAAAACGGCAGGTGC‑gg                                                                                                                                                                                                                    >  1:416069/1‑228 (MQ=255)   cccttggCTTTGGCCCCCAGCGCCCCCAGTTTGT‑AACCGAGGCTTAAACTGATAGGCTCGATCAGCGGAATGGTTTCCCAACTGACCTGCTGCTCGCTGGTT‑TCGGTGATGGTGCGGGTCAGCGTTTCGAGGC‑TTTTCTCTTCCGCCTCCGCCGCCAGCGGCTGTTTGCTCAT‑CCGCCAGCCGGTAAAACCAAGCA‑GGGCGCTGAACAGCAAAAACGGCAGGTGC‑GGc                                                                                                                                                                                                                   <  1:581971/222‑1 (MQ=255)    ccTGTGCTTTGTCCACCAGCGCCACCAGTTTGT‑AACCGAGGCTTAAACTGATAGGCTCGATCAGCGGAATGGTTTCCCAACTGACCTGCTGCTCGCTGGTT‑TCGGTGATGGTGCGGGTCAGCGTTTCGAGGC‑TTTTCTCTTCCGCCTCCGCCGCCAGCGGCTGTTTGCTCAT‑CCGCCAGCCGGTAAAACCAAGCA‑GGGCGCTGAACAGCCAAAACGGCAGGGGC‑ggga                                                                                                                                                                                                                  >  1:235294/1‑226 (MQ=255)     ctgtttttttgcccccggcgcCACCA‑TTTGTGAACCGGGGCTTAACATGATGGGTGCGACACGCGGAACGTGTCCCCTACGGCCCGGCGGTTCCCGGGTT‑TCGTGGATGGTGCGGGTCGGCGTTTCGAGGT‑TTTTCTCTTCCGCCTCCGCCGGCAGCGGCTTTTGGCTCAT‑CCGCCAGCCGGTAAAACCAAGCA‑GGGCGCTGAACAGCAAAAACGGCAGGTGC‑GGCAtt                                                                                                                                                                                                                <  2:448729/212‑1 (MQ=255)        ggCTTTGTCCACCAGCGCCACCAGTTTGT‑AACCGAGGCTTAAACTGATAGGCTCGATCAGCGGAATGGTTTCCCAACTGACCTGCTGCTCGCTGGTT‑TCGGTGATGGTGCGGGTCAGCGTTTCGAGGC‑TTTTCTCTTCCGCCTCCGCCGCCAGCGGCTGTTTGCTCAT‑CCGCCAGCCGGTAAAACCAAGCA‑GGGCGCTGAACAGCAAAAACGGCAGGTGC‑GGCATTcc                                                                                                                                                                                                              <  1:407141/227‑1 (MQ=255)         gCTTTGTCCACCAGCGCCACCAGTTTGT‑AACCGAGGCTTAAACTGATAGGCTCGATCAGCGGAATGGTTTCCCAACTGACCTGCTGCTCGCTGGTT‑TCGGTGATGGTGCGGGTCAGCGTTTCGAGGC‑TTTTCTCTTCCGCCTCCGCCGCCAGCGGCTGTTTGCTCAT‑CCGCCAGCCGGTAAAACCAAGCA‑GGGCGCTGAACTGCAAAAACGGCAGGTGC‑GGCCATccc                                                                                                                                                                                                             >  1:152146/1‑228 (MQ=255)             tGTCCACCAGCGCCACCAGTTTGT‑AACCGAGGCTTAAACTTATAGGCTCGATCAGCGGAATGGTTTCCCAACTGACCTGCTGCTCGCTGGTT‑TCGGTGATGGTGCGGGTCAGCGTTTCGAGGC‑TTTTCTCTTCCGCCTCCGCCGCCAGCGGCTGGTTGCTCAT‑CCGCCAGCCGGTAAAACCAAGCA‑GGGCGCCGAACAGCCACAAAGGCAGGTGC‑GGCCCTCCCgtgt                                                                                                                                                                                                         >  1:375285/1‑225 (MQ=255)             tGTCCACCAGCGCCACCAGTTTGT‑AACCGAGGCTTAAACTGATAGGCTCGATCAGCGGAATGGTTTCCCAACTGACCTGCTGCTCGCTGGTT‑TCGGTGATGGTGCGGGTCAGCGTTTCGAGGC‑TTTTCTCTTCCGCCTCCGCCGCCAGCGGCTGTTTGCTCTT‑CCGCCAGCCGGTCAAACCAACCC‑AGGCCCCGAACAGCAAAAACGGCAGAGGC‑GGGATTccccgaaa                                                                                                                                                                                                        >  2:53990/1‑224 (MQ=255)             tGTCCACCAGCGCCACCAGTTTGT‑AACCGAGGCTTAAACTGATAGGCTCGATCAGCGGAATGGTTTCCCAACTGACCTGCTGCTCGCTGGTT‑TCGGTGATGGTGCGGGTCAGCGTTTCGAGGC‑TTTTCTCTTCCGCCTCCGCCGCCAGCGGCTGTTTGCTCAT‑CCGCCAGCCGGTAAAACCAAGCA‑GGGCGCTGAACAGCAAAAACGGCAGGGGC‑GGCATTCCCggga                                                                                                                                                                                                         >  1:415855/1‑226 (MQ=255)                         ccaccaGTTTGT‑AACCGAGGCTTAAACTGATAGGCTCGATCAGCGGAATGGTTTCCCAACTGACCTGCTGCTCGCTGGTT‑TCGGTGATGGTGCGGGTCAGCGTTTCGAGGC‑TTTTCTCTTCCGCCTCCGCCGCCAGCGGCTGTTTGCTCAT‑CCGCCAGCCGGTAAAACCAAGCA‑GGGCGCTGAACAGCCAAAACGGCAGGGGC‑GGGCTTCCCGGTAACCccgcccgcc                                                                                                                                                                                             >  1:582705/1‑227 (MQ=255)                         ccaccaGTTTGT‑AACCGAGGCTTAAACTGATAGGCTCGATCAGCGGAATGGTTTCCCAACTGACCTGCTGCTCGCTGGTT‑TCGGTGATGGTGCGGGTCAGCGTTTCGAGGC‑TTTTCTCTTCCGCCTCCGCCGCCAGCGGCTGTTTGCTCAT‑CCGCCAGCCGGTAAAACCAAGCA‑GGGCGCTGAACAGCAAAAACGGCAGGGGC‑GGGATTTCCGGTACCACCGCCAGcc                                                                                                                                                                                             >  1:42829/1‑227 (MQ=255)                                    t‑AACCGAGGCTTAAACTGATAGGCTCGATCAGCGGAATGGTTTCCCAACTGACCTGCTGCTCGCTGGTT‑TCGGTGATGGTGCGGGTCAGCGTTTCGAGGC‑TTTTCTCTTCCGCCTCCGCCGCCAGCGGCTGTTTGCTCAT‑CCGCCAGCCGGTAAAACCAAGCA‑GGGCGCTGAACAGCAAAAACGGCAGGTGC‑GGCATTGCCGGTGCCACCGCCGGCACGAACATaaaca                                                                                                                                                                                 >  1:141173/1‑226 (MQ=255)                                           aGGCTTAACCTGAGAGGCCCGATCAGGGGAATGGTTCCCCAACTGACCTGCTGCTCGTTGTTT‑TCGGTGAGGGTGCGGGTCAGCGTTTCGAGGC‑TTTTCTCTCCCGCCTCCGCCGCCAGCGGCTGTTTGCTCAT‑CCGCCAGCCGGTAAAACCAAGCA‑GGGCGCTGAACAGCAAAAACGGCAGGTGC‑GGCATTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTgg                                                                                                                                                                           <  1:526663/229‑1 (MQ=255)                                           aGGCTTAAACTGATAGGCTCGATCAGCGGAATGGTTTCCCAACTGCCCTGCTGCTCGCTGGTT‑TCGGTGATGGTGCGGGGCAGCGTTTCGAGGC‑TTTTCTCTTCCGCCTCCGCCGCCAGCGGCTGTTTGCTCAT‑CCGCCCGCCGGTAAAACCAAGCA‑GGGCGCTGAACAGCAAAAACGGCAGGTAG‑GGAATTCCCCGGACCACCCCCACCACCAAAATAATTCCgtgg                                                                                                                                                                            >  1:657745/1‑225 (MQ=255)                                           aGGCTTAAACTGATAGGCTCGATCAGCGGAATGGTTTCCCAACTGACCTGCTGCTCGCTGGTT‑TCGGTGATGGTGCGGGTCAGCGTTTCGAGGC‑TTTTCTCTTCCGCCTCCGCCGCCAGCGGCTGTTTGCTCAT‑CCGCCAGCCGGTAAAACCAAGCA‑GGGCGCTGAACAGCCAAAACGGCAGGTGC‑GGCAATCCCCGGACCACCGccccgtctcttatacacctctccc                                                                                                                                                                           >  1:619515/1‑207 (MQ=255)                                           aGGCTTAAACTGATAGGCTCGATCAGCGGAATGGTTTCCCAACTGACCTGCTGCTCGCTGGTT‑TCGGTGATGGTGCGGGTCAGCGTTTCGAGGC‑TTTTCTCTTCCGCCTCCGCCGCCAGCGGCTGTTTGCTCAT‑CCGCCAGCCGGTAAAACCAAGCA‑GGGCGCTGAACAGCAAAAACGGCAGGTGC‑GGCATTCCCGGCACAACCGCCCCCCCGAAACTAATCCCGGTg                                                                                                                                                                            >  1:216926/1‑228 (MQ=255)                                           aGGCTTAAACTGATAGGCTCGATCAGCGGAATGGTTTCCCAACTGACCTGCTGCTCGCTGGTT‑TCGGTGATGGTGCGGGTCAGCGTTTCGAGGC‑TTTTCTCTTCCGCCTCCGCCGCCAGCGGCTGTTTGCTCAT‑CCGCCAGCCGGTAAAACCAACCA‑GGGCGCTGAACGGCAAAAAGGGCAGGGGG‑GGGCTTTCCGGGAccccccccccccccaccaaaaaccccgggg                                                                                                                                                                           >  2:627081/1‑207 (MQ=255)                                           aGGCTTAAACTGATAGGCTCGATCAGCGGAATGGTTTCCCAACTGACCTGCTGCTCGCTGGTT‑TCGGTGATGGTGCGGGTCAGCGTTTCGAGGC‑TTTTCTCTTCCGCCCCCGCCGCCAGCGGCTGCTTTCTCAT‑CCGCCACCCGGTAAACCCAAGCA‑GGGCGCTGAACAGCAAAAAAGGCAGGGGCGGGCCTCCCCGGACCCCCCCCCCACACAAACAAAACCCCggg                                                                                                                                                                             >  2:369778/1‑227 (MQ=255)                                                   atggatggcgcgcaTCGGCGTATTGGTCCCCCAGCTGCCCGGCTG‑TCGGTGGTTGTGGGTGTTGGGGCGGGTATGTGTTGGGGGGC‑TTTTCTCTCCCGCCCCCGCCGCGAGGGGCTGTTTGCTCAC‑CCGCCAGCCGGTAAACCCAAGCA‑GGGCGCTGAACAGCAAAAACGGCAGGTGC‑GGCATTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTag                                                                                                                                                                   <  2:548923/216‑1 (MQ=255)                                                       aTAGGCTCGATCAGCGGAATGGTTTCCCAACTGACCTGCTGCTCGCTGGTT‑TCGGTGATGGTGCGGGTCAGCGTTTCGAGGC‑TTTTCTCTTCCGCCTCCGCCGCCAGCGGCTGTTTGCTCAT‑CCGCCAGCCGGTAAAACCAAGCA‑GGGCGCTGAACAGCAAAAACGGCAGGTGC‑GGCATTCCCGGGACCCCCGCCAGCACGAACATAAACCCGGGGGGGGGGTGGATCa                                                                                                                                                               >  1:568757/1‑229 (MQ=255)                                                       aTAGGCTCGATCAGCGGAATGGTTTCCCAACTGACCTGCTGCTCGCTGGTT‑TCGGTGATGGTGCGGGTCAGCGTTTCGAGGC‑TTTTCTCTTCCGCCTCCGCCGCCAGCGGCTGTTTGCTCAT‑CCGCCAGCCGGTAAAACCAAGCA‑GGGCGCTGAACAGCAAAAACGGCAGGGGC‑GGCATTCCCGGTACCCCCGCCAGCACGACCATAATCCCGGGGGCGgggtgaggaa                                                                                                                                                               >  1:556700/1‑223 (MQ=255)                                                                     cGGAATGGTTTCCCAACTGACCTGCTGCTCGCTGGTT‑TCGGTGATGGTGCGGGTCAGCGTTTCGAGGC‑TTTTCTCTTCCGCCTCCGCCGCCAGCGGCTGTTTGCTCAT‑CCGCCAGCCGGTAAAACCAAGCA‑GGGCGCTGAACAGCAAAAACGGCAGGGGC‑GGCATTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTGAGGGACCGCCGGGCTTGcc                                                                                                                                                 >  1:533905/1‑229 (MQ=255)                                                                               tCCCAACTGACCTGCTGCTCGCTGGTT‑TCGGTGATGGTGCGGGTCAGCGTTTCGAGGC‑TTTTCTCTTCCGCCTCCGCCGCCAGCGGCTGTTTGCTCAT‑CCGCCAGCCGGTAAAACCAAGCA‑GGGCGCTGAACAGCAAAAACGGCAGGGGC‑GGCATTCCCGGGACCCCCGCCCGCACGAAACTAAACCCGGTGGCGGGGTAGGGCAACCACGGGCtgtcccggcgccggt                                                                                                                                       >  1:410872/1‑215 (MQ=255)                                                                                        aCCTGCTGCTCGCTGGTT‑TCGGTGATGGTGCGGGTCAGCGTTTCGAGGC‑TTTTCTCTTCCGCCTCCGCCGCCAGCGGCTGTTTGCTCAT‑CCGCCAGCCGGTAAAACCAAGCA‑GGGCGCTGAACAGCAAAAACGGCAGGTGC‑GGCATTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGGGTAGAGGACCGACGGGCTTGCCAGCACCTgggttcggcggt                                                                                                                              >  1:517981/1‑219 (MQ=255)                                                                                              tgctCGTTGGTT‑TCGGTGATGGTGCGGGTCAGCGTTTCGAGGC‑TTTTCTCTTCCGCCTCCGCCGCCAGCGTCTGTTTGCTCAT‑CCGCCAGCCGGTAAACCCAAGCA‑GGGCGCTGAACAGCAAAAACGGCAGGTGC‑GGCATTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATggg                                                                                                                        <  1:279476/229‑1 (MQ=255)                                                                                                           tgggttagggTGCGGGGCAGCGTTCCGGGGC‑TTTTCTCTTCCGCCTGCGCCGCCAGCGGCTGTTTGCTCAC‑CCGCCAGCCGGTAAACCCAAGCA‑GGGCGCTGAACAGCAAAAACGGCAGGTGC‑GGCATTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGt                                                                                                            <  1:627082/221‑1 (MQ=255)                                                                                                                    gggCGGGTCACGGTGTCGGGGGTTTTTCTCTTCCCCCCCCGCCGCCAGCGGCTGGTTGCCCAC‑CCGCCAGCCGGTAAAACAAAGCA‑GGGCGCTGAACAGCAAAAACGGCAGGTGC‑GGCATTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCt                                                                                                     <  1:511914/226‑1 (MQ=255)                                                                                                                                    cGAGGC‑TTTTCTCTTCCGCCTCCGCCGCCAGCGGCTGTTTGCTCAT‑CCGCCAGCCGGTAAAACCAAGCA‑GGGCGCTGAACAGCAAAAACGGCAGGTGC‑GGCATTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGCTTAGAGCACCGCCGGGCTTGCCAGCAGCTGGTTAACCACGCCATGGGCGACATCGCCGGTGTCGCTGACGCGGGGGACGacatt                                                                                   >  1:553237/1‑225 (MQ=255)                                                                                                                                                     cgcctccgccGCCAGCGGTTGTTTGCTCAC‑CCGCCAGCCGGTAAAACCAAGCA‑GGGCGCTGAACAGCAAAAACGGCAGGTGC‑GGCATTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGACGCGGGTGACGATAATCGCCGCCGCGGTGgag                                                                   <  1:53990/229‑1 (MQ=255)                                                                                                                                                       ccaccgccgCCAGCGGGTGTTTCCCCAT‑CCGCCAGCCGGTAAAACCAAGCA‑GGGCGCTGAACAGCAAAAACGGCAGGTGC‑GGCATTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGACGCGGGTGACGATAATCGCCGCCGCGGTGGagag                                                                 <  1:97473/226‑1 (MQ=255)                                                                                                                                                          ccgccgCCAGCGG‑TGGTTGCTCATGCCGCCAGCCGGTAAACCCAGGCA‑GGGCGCTGAACAGCAAAAACGGCAGGTGC‑GGCATTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGACGCGGGTGACGATAATCGCCGCCGCGGTGGAGagcag                                                              <  1:627053/229‑1 (MQ=255)                                                                                                                                                                      ggtttttgtccctgcccgcAGCCGTTAAAACCACGCA‑GGGCGCTGACCAGCAAAACCGGCAGGTGC‑GACTTTCCCGGTCCCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGACGCGGGTGACGATAATCGCCGCCGCGGTGGAGAGCAGCagggaaggga                                                   <  2:568756/211‑1 (MQ=255)                                                                                                                                                                                           cgggTAAAACAAGGCG‑GGGCGGGGAACAACAAAAACGGCAGGAGC‑GCCTATCCGGGTCCCACCGCCAGCACGAACATAAGCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGGTGGTTACGCACGTCATGGGCGATATCGCCGTTGGCGCTGACGCGGGTGACGATAATCGCCGCCGCGGTGGAGAGCAGCAGGGAAGGGATCTGCGCCACCAGGCCGTCGc                              <  2:375285/227‑1 (MQ=255)                                                                                                                                                                                              taaaacCCGAGCG‑GGGCCCGGAACAGAAAAAGCGGCGGGGGG‑GCGATCCCGGGAACCCCGGCCAGGCCGAACATAATCCCGGTGGCGGTGTAGGGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCAGGGGCGATATCGCCGTTGTCGCTGACGCGGGTGACGATAATCGCCGCCGCGGTGGAGAGCAGCAGGGAAGGGATCTGCGCCACCAGGCCGTCGCCGa                           <  2:612390/227‑1 (MQ=255)                                                                                                                                                                                                    ccAGGCG‑GGGCGCGGAACAGAAAAAACGGCGGGGGC‑GGCATCCCCGGTACCACCGCCGGACCGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGGTTGCCAGCAGCGGGTTACGCACGTCATGGGCGATATCGCCGGTGTCGCTGACGCGGGTGACGATAATCGCCGCCGCGGTGGAGAGCAGCAGGGAAGGGATCTGCGCCACCAGGCCGTCGCCGATGGtca                     <  2:582704/229‑1 (MQ=255)                                                                                                                                                                                                    ccAAGCAGGGGCGC‑GAACAGAAAAAGCGGCAGGGGG‑GGCATCCCCGCTCCCCCCGCGCGCCTGAACAAAATGCCGGTGGCCGGGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGACGCGGGTGACGATAATCGCCGCCGCGGTGGAGAGCAGCAGGGAAGGGATCTGCGCCACCAGGCCGTCGCCGATGGtca                     <  2:141173/229‑1 (MQ=255)                                                                                                                                                                                                    ccAAGCA‑GGGCGCTAAACAGCAAACCCGGCAGGTGC‑GGCATTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGACGCGGGTGACGATAATCGCCGCCGCGGTGGAGAGCAGCAGGGAAGGGATCTGCGCCACCAGGCCGTCGCCGATGGtca                     <  1:426482/229‑1 (MQ=255)                                                                                                                                                                                                    ccAAGCA‑GGCCGTTGAACAGCAAAAACGGCAGGTGC‑GGCATCCCCGGTCCCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGACGCGGGTGACGATAATCGCCGCCGCGGTGGAGAGCAGCAGGGAAGGGATCTGCGCCACCAGGCCGTCGCCGATGGtca                     <  1:447389/229‑1 (MQ=255)                                                                                                                                                                                                      caaagagggcgagaaaCAGCAAAAACGGCAGGGGC‑GGCTTTCCAGGTCCCACCGCCAGCACGAACATAATCCCGGTGGCGGTGGAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGACGCGGGTGACGATAATCGCCGCCGCGGTGGAGAGCAGCAGGGAAGGGATCTGCGCCACCAGGCCGTCGCCGATGGtcat                    <  2:42829/215‑1 (MQ=255)                                                                                                                                                                                                      aaGCA‑GGGCGCTGAAGCGCAAAAAGGGCAGGTGC‑GGCATTCCCGGTACCACCGCCAGCACGAACATGATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGACGCGGGTGACGATAATCGCCGCCGCGGTGGAGAGCAGCAGGGAAGGGATCTGCGCCACCAGGCCGTCGCCGATGGtcat                    <  1:509065/228‑1 (MQ=255)                                                                                                                                                                                                           aggggccgaaagaGCAAAAACGGCAGGGGC‑GGCATTCCGGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGACGCGGGTGACGATAATCGCCGCCGCGGTGGAGAGCAGCAGGGAAGGGATCTGCGCCACCAGGCCGTCGCCGATGGTCATCAGc                <  1:120650/216‑1 (MQ=255)                                                                                                                                                                                                             ggCGCTGAACAGCAAAAACGGCAGGTGC‑GGCATTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGACGCGGGTGACGATAATCGCCGCCGCGGGGGCGAGCAGCAGGGAAGGGATCTGCGCCACCAGGCCGTCGCCGATGGGCATAAGcacc             >  1:696550/1‑228 (MQ=255)                                                                                                                                                                                                             ggCCCTGAACAGCAAAACGGGCGGGGGG‑GGCTTCCGCGGTCCCCCCGCCAGCACGAACATAATCCCGGTGGCGGTGGAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGACGCGGGTGACGATAATCGCCGCCGCGGTGGAGAGCAGCAGGGAAGGGATCTGCGCCACCAGGCCGTCGCCGATGGTCATCAGcaca             <  2:701770/229‑1 (MQ=255)                                                                                                                                                                                                                cccgaaaagaaaaAGCGGCGGGTGG‑GGAATGCCCGGTACACCCGCCAGCCCGAACATAATCCCGGTGGCGGTGGAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGACGCGGGTGACGATAATCGCCGCCGCGGTGGAGAGCAGCAGGGAAGGGATCTGCGCCACCAGGCCGTCGCCGATGGTCATCAGCACATAc          <  2:556699/226‑1 (MQ=255)                                                                                                                                                                                                                     caacaaaacccggcggGGGC‑GGCATCCCCGGTACCACCGCCAGCACGAACCAAATCCGGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGACGCGGGTGACGATAATCGCCGCCGCGGTGGAGAGCAGCAGGGAAGGGATCTGCGCCACCAGGCCGTCGCCGATGGTCATCAGCACATActgctg     <  2:533905/219‑1 (MQ=255)                                                                                                                                                                                                                         aaaaaaCGGCAGGTGC‑GGCATCCCCGGTCCCCCCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGGACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGACGCGGGTGACGATAATCGCCGCCGCGGTGGAGAGCAGCAGGGAAGGGATCTGCGCCACCAGGCCGTCGCCGATGGTCATCAGCACATACTGCTGGaa  <  1:369778/227‑1 (MQ=255)                                                                                                                                                                                                                                      |                                                                                                                                                                                                                        TACCCTGTGCTTTGTCCACCAGCGCCACCAGTTTGT‑AACCGAGGCTTAAACTGATAGGCTCGATCAGCGGAATGGTTTCCCAACTGACCTGCTGCTCGCTGGTT‑TCGGTGATGGTGCGGGTCAGCGTTTCGAGGC‑TTTTCTCTTCCGCCTCCGCCGCCAGCGGCTGTTTGCTCAT‑CCGCCAGCCGGTAAAACCAAGCA‑GGGCGCTGAACAGCAAAAACGGCAGGTGC‑GGCATTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGACGCGGGTGACGATAATCGCCGCCGCGGTGGAGAGCAGCAGGGAAGGGATCTGCGCCACCAGGCCGTCGCCGATGGTCATCAGCACATACTGCTGGAA  >  NC_000913/249314‑249752

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑