Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	3,289,076	C→A	23.9%	Q89K (CAG→AAG)	yraJ →	putative outer membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,289,076	0	C	A	23.9%	141.7 / 9.1	70	Q89K (CAG→AAG)	yraJ	putative outer membrane protein
Reads supporting (aligned to +/- strand):  ref base C (40/12);  new base A (2/15);  total (42/28)
Fisher's exact test for biased strand distribution p-value = 2.60e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGAAACAGTTGGCGCTCATCATCAAACGTTGTTTGCCGATGGTGCTCACTGGCAGCGGCATGCTTTGCACTACCGCTAACGCCGAAGAGTATTATTTCGACCCCATTATGCTGGAAACCACAAAAA‑GTGGTATGC‑AAACAACCGATCTGTCGCGTTTTTC‑AAAAAAATATGCAC‑AACTACCAGGAACTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTGATCAACTCGCTTGAACAAATCATTCCCGGTACAGCTGCTGAATTTGATTTCAATCATCAGCAACTTAATTTGAGCATTCCCCAAATTGCACTGTACCGTGATGCAA  >  NC_000913/3288849‑3289313                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                                  cGAAACAGTTGGCGCTCATCATCAAACGTTGTTTGCCGATGGTGCTCACTGGCAGCGGCATGCTTTGCACTACCGCTAACGCCGAAGAGTATTATTTCGACCCCATTATGCTGGAAACCACAAAAA‑GTGGTATGC‑AAACAACCGATCTGTCGCGTTTTTC‑AAAAAAAAATGCAC‑AACTACCAGGAACTATTCAGGTTGC‑TATCTGGCTGAATAAAAAAAAGGTTTCAAAAAAAAAAA‑t‑t                                                                                                                                                                                                                                      >  1:52819/1‑239 (MQ=255)           ggCGCTCATCATCAAACGTTGTTTGCCGATGGTGCTCACTGGCAGCGGCATGCTTTGCACTACCGCTAACGCCGAAGAGTATTATTTCGACCCCATTATGCTGGAAACCACAAAAA‑GTGGTATGC‑AAACAACCGATCTGTCGCGTTTTTC‑AAAAAAATATGCAC‑AACTACCAGGAACTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑Acc                                                                                                                                                                                                                           >  2:777798/1‑238 (MQ=255)           ggCGCTCATCATCAAACGTTGTTTGCCGATGGTGCTCACTGGCAGCGGCATGCTTTGCACTACCGCTAACGCCGAAGAGTATTATTTCGACCCCATTATGCTGGAAACCACAAAAA‑GGGGTATGC‑AAACAACCGATCTGTCGCGTTTTTC‑AAAAAAATATGCAC‑AACTACCAGGAACTTATCAGGTTGT‑TATCTGGCTGAATAAAAAAAAGGGTTCACAGAAAAAAA‑T‑TAAA‑ATT‑ACCg                                                                                                                                                                                                                          >  1:944467/1‑239 (MQ=255)                 catcatcaAACGTTGTTTGCCGATGGTGCTCACTGGCAGCGGCATGCTTTGCACTACCGCTAACGCCGAAGAGCATTATTTCGACCCCATTATGCTGGAAACCACAAAAA‑GTGGTATGC‑AAACAACCGATCTGTCGCG‑TTTTC‑AAAAAAATATGCAC‑AACTACCAGGAACTTATCAGGCTGA‑TATCTGGCTGAATAAAAAAAAGGTTTACCAGAAAAAAA‑T‑TAAC‑TTT‑ACTGCCAATga                                                                                                                                                                                                                   >  2:365813/1‑238 (MQ=255)                                  tGCCGATGGTGCTCACTGGCAGCGGCATGCTTTGCACTACCGCTAACGCCGAAGAGTATTATTTCGACCCCATTATGCTGGAAACCACAAAAA‑GTGGTATGC‑AAACAACCGATCTGTCGCGTTTTTC‑AAAAAAATATGCAC‑AACTACCAGGAACTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCa                                                                                                                                                                                                    >  2:337395/1‑238 (MQ=255)                                  tGCCGATGGTGCTCACTGGCAGCGGCATGCTTTGCACTACCGCTAACGCCGAAGAGTATTATTTCGACCCCATTATGCTGGAAACCACAAAAA‑GTGGTATGC‑AAACAACCGATCTGTCGCGTTTTTC‑AAAAAAATATGCAC‑AACTACCAGGAACTTATCAGGCTGA‑TATCCGGCTGAATAAAACGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCAAATGCCGAGCAACTTTTGCa                                                                                                                                                                                                    >  1:523858/1‑238 (MQ=255)                                          gTGCTCACTGGCAGCGGCATTGTTTGCACTCCCGGAAACGCCGAAGGGTATTATTTCGACCCCATTATGCTGGAAACCAAAAAAA‑GTGGTATGA‑AAACAACGGATCTGTCGCGTTTTTC‑AAAAAAATATGCCA‑AACTACCAGGAATTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTACAAAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGtt                                                                                                                                                                                           <  2:429841/239‑1 (MQ=255)                                                  tGGCAGCGGCATGCTTTGCACTACCGCTAACGCCGCAGAGTATTATTTCGACCCCATTATGCTGGAAACCACCAAAA‑GTGGTATGC‑AAACAACCGATCTGTCGCGTTTTTC‑AAAAAAATATGCAC‑AACTACCAGGAACTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAg                                                                                                                                                                                   >  2:97708/1‑239 (MQ=255)                                                     cAGCGGCATGCTTTGCACTACCGCTAACGCCGAAGAGTATTATTTCGACCCCATTATGCTGGAAACCACAAAAA‑GTGGTATGC‑AAACAACCGATCTGTCGCGTTTTTC‑AAAAAAATATGCAC‑AACTACCAGGAACTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCCATGCAGATCAACTTCTGCAGCCCCAATTTACgggaaaaa                                                                                                                                                                                >  1:962291/1‑233 (MQ=255)                                                          gCATGCTTTGCACTACCGCTAACGCCGAAGAGTATTATTTCGACCCCATTATGCTGGAAACCACAAAAA‑GTGGTATGC‑AAACAACCGATCTGTCGCGTTTTTC‑AAAAAAATATGCAC‑AACTACCAGGAACTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGAAACTTCTGCAGCCCAAGCTTACGGTAGAAAAACt                                                                                                                                                                            >  2:338782/1‑238 (MQ=255)                                                            ttttttggccctcccGCTAAGCCCGAAGGGTTTTATTCCCCCCCCTTTTGTCTGAAAACCACAAAAA‑GTGGAATCC‑AACCAACCGATCTGCCGCGGTTTTA‑AAAAAAATATGCAA‑AACTCCCAGGAACTTATCAGGTTTA‑TATCTGGTTAAATAAAAAGAAGTTTGCAAAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTAc                                                                                                                                                                          <  1:97708/225‑1 (MQ=255)                                                                 ttGCACTACCTCTAACGACGAAAAGTATTATTTCGCCCCCATTATGCTGGAACCCAAAAAAA‑GTGGTATGC‑AAACAACCGTTCTGGCGCGTTTTTC‑AAAAAAAAATGCAC‑AACTACAAGGACTTTATCAGGTTGA‑TATCTGGCTGAAAAAAAAGAAGTTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAg                                                                                                                                                                     <  2:375817/238‑1 (MQ=255)                                                                  tccACTCCCGCTAACGCAGAAGAGTTTTATTTCGCCCCAATTATGCTGAAACCCAAAAAAA‑GGGGTATGC‑AAACAACCGATCTGTCGGGTTTTTC‑AAAAAAATAGGCAC‑AACTACCAGGAACTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCt                                                                                                                                                                   <  2:48949/237‑1 (MQ=255)                                                                  tGCCCTCCCGCAAACGCCAAAGAGTTTTATTCCGCCCCAATTAGGCTGAAACCCAAAAAAA‑GTGGAATGC‑AAACAACCGATCTGTCGCGTTTTTC‑AAAAGAATATGCAA‑ACCTACCAGAAACTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCt                                                                                                                                                                   <  2:155895/239‑1 (MQ=255)                                                                            cTAACGCCGAAGAGTATTATTTCGACCCCATTATGCTGGAAACCACAAAAA‑GTGGTATGC‑AAACAACCGATCTGTCGCGTTTTTC‑AAAAAAATATGCAC‑AACTACCAGGAACTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAg                                                                                                                                                         >  2:992353/1‑239 (MQ=255)                                                                            cTAACGCCGAAGAGTATTATTTCGACCCCATTATGCTGGAAACCACAAAAA‑GTGGTATGC‑AAACAACCGATCTGTCGCGTTTTTC‑AAAAAAATATGCAC‑AACTACCAGGAACTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGAAACTTCTGAAGCCACAGTTTACGGTAGAACAAATACGGCAGCTGGGATTTAAg                                                                                                                                                         >  2:44795/1‑239 (MQ=255)                                                                               aaagagAAGGGTATTATTCCCACCCCATTATGCT‑GAAAACACAAAAAGGTGGTAGGC‑AAACAACCGATTTGTCGCGTTTTAA‑AAAAAAATAGGAAC‑AACTACAAGGAATTTAGCAGTTGGA‑TATTTGGCTGAAAAAAAAGAATGTTCAAAAAAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGt                                                                                                                                                       <  2:293802/233‑1 (MQ=255)                                                                                 gCCGAAGAGTATTATTTCGACCCCATTATGCTGGAAACCACAAAAA‑GTGGTATGC‑AAACAACCGATCTGTCGCGTTTTTA‑AAAAAAATATGCAC‑AACTACCAGGAACTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGACCACCTTCTGCAGCCACAGTTTACGGTAAAAAAACAACGTGAACTGGGAATAAAGGGGGa                                                                                                                                                    >  1:490410/1‑239 (MQ=255)                                                                                            ttattTCGACCCCATTATGCTGGAAACCACAAAAA‑GTGGTATGC‑AAACAACCGATCTGTCGCGTTTTTC‑AAAAAAATATGCAC‑AACTACCAGGAACTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTCCGTGAGCTGGGAATTAAGGTGGTTGAAATCCCgg                                                                                                                                         >  2:370585/1‑239 (MQ=255)                                                                                              agtcgcaCCCAATTACGCTGAAAACCAAAAAAA‑GGGGTATGA‑AAACAACCGTTCTGGCGGGTTTTTA‑AAAAAAATAGGCAA‑ACCTACCAGGAACTTATCAGGTTGA‑TATCTGGCTAAATAAAAAGAAGGTTT‑ACAAAAAAAAATT‑TACT‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGgcg                                                                                                                                       <  2:797066/233‑1 (MQ=255)                                                                                                 tCGACCCCATTATGCTGGAAACCACAAAAA‑GTGGTATGC‑AAACAACCGATCTGTCGCGTTTTTC‑AAAAAAATATGCAC‑AACTACCAGGAACTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGACAAACAACGTGAGCTGGGTATTAAGGGGGATGAAAACCCGGCgctg                                                                                                                                    >  1:467896/1‑239 (MQ=255)                                                                                                  cGACCCCATTATGCTGGAAACCACAAAAA‑GTGGTATGC‑AAACAACCGATCTGTCGCGTTTTTC‑AAAAAAATATGCAC‑AACTACCAGGAACTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAAAAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCgctg                                                                                                                                    >  2:418738/1‑238 (MQ=255)                                                                                                    aCCCCATTATGCTGGAAACCACAAAAA‑GTGGTATGC‑AAACAACCGATCTTTCGCGTTTTTC‑AAAAAAATATGCAC‑AACTACCAGGAACTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTAACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGTTCAAACAAACACGTGAGCTGGGGCTTAAGGCGGATGAAATccctgtcccttaa                                                                                                                                 >  1:293802/1‑229 (MQ=255)                                                                                                    aCCCCATTATGCTGGAAACCACAAAAA‑GTGGTATGC‑AAACAACCGATCTGTCGCGTTTTTC‑AAAAAAATATGCAC‑AACTACCAGGAACTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCgctg                                                                                                                                    >  2:713532/1‑236 (MQ=255)                                                                                                    aCCCCATTATGCTGGAAACCACAAAAA‑GTGGTATGC‑AAACAACCGATCTGTCGCGTTTTTC‑AAAAAAATATGCAC‑AACTACCAGGAACTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCcctggct                                                                                                                                 >  2:646135/1‑239 (MQ=255)                                                                                                    aCCCCATTATGCTGGAAACCACAAAAA‑GTGGTATGC‑AAACAACCGATCTGTCGCGTTTTTC‑AAAAAAATATGCAC‑AACTACCAGGAACTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGAGAGCTGGGGATTAAGGGGGAGGAAAACCGGGCgcgggcg                                                                                                                                 >  1:997828/1‑238 (MQ=255)                                                                                                    aCCCCATTATGCTGGAAACCACAAAAA‑GTGGTATGC‑AAACAACCGATCTGTCGCGTTTTTC‑AAAAAAATATGCAC‑AACTACCAGGAACTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTAACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCCCAGTTTACGGTGGAACAACTACGTGAGTTGGGTATTAAGGGGGAGGAAAACCCgagacgggcg                                                                                                                                 >  1:682070/1‑230 (MQ=255)                                                                                                       ccATTATGCTGGAAACCACAAAAA‑GTGGTATGC‑AAACAACCGATCTGTCGCGTTTTTC‑AAAAAAATATGCAC‑AACTACCAGGAACTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGACTTAAGGGGGATGAAATCCCGGGGCTGGCTGaa                                                                                                                              >  1:509067/1‑239 (MQ=255)                                                                                                        cATTATGCTGGAAACCAAAAAAA‑GTGTTATGC‑AAACAACCGATCGGTCGCTTTTTTA‑AAAAAAATATGCAC‑AACTACCAGGAATTTACAAGGTTGA‑TATCTGGCTGAAAAAAAAGAAGGTTTCACAAAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGaaa                                                                                                                             <  2:509067/239‑1 (MQ=255)                                                                                                             ttgcggAAACCCAAAAAA‑GGGGGAAGGAAAACAACCGATCGTTCGGTTTTTTC‑AAAAAAATATGACA‑AACTCCCAGGAACTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGTTTTCAAAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGa                                                                                                                         <  2:52819/235‑1 (MQ=255)                                                                                                                 ggAAACCAAAAAAA‑GGGGAAACA‑AAAAAACCGATCTGTCGCTTTTTTA‑AAAAAAAATGGCAA‑AACTACAAGAAACTTAAAGGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCAAAAAAAAAAA‑T‑TAAA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACg                                                                                                                    <  2:944467/239‑1 (MQ=255)                                                                                                                  gAAACCACAAAAA‑GTGGTATGC‑AAACAACCGATCTGTCGCGTTTTTC‑AAAAAAATATGCAC‑AACTACCAGGAACTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGGAATCCCGGCGCTGGCTGAAAAAGATGACGa                                                                                                                   >  2:72452/1‑239 (MQ=255)                                                                                                                  gAAACCACAAAAA‑GTGGTATGC‑AAACAACCGATCTGTCGCGTTTTTC‑AAAAAAATATGCAC‑AACTACCAGGAACTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGa                                                                                                                   >  2:758648/1‑239 (MQ=255)                                                                                                                       cacaAAAA‑GTGGTATGC‑AAACAACCGATCTGTCGCGTTTTTC‑AAAAAAATATGCAC‑AACTACCAGGAACTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGAATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCg                                                                                                              >  2:627871/1‑239 (MQ=255)                                                                                                                         aaaaat‑GTGGTAGGA‑AAACAACCGATTTGTCGCTTTTTTC‑AAAAAAATATGCCC‑AACTACCAGGAACTTATCAGGTGTA‑TATCTGGATAAAAAAAAAAAAGGTTTCAAAGAAAAAAA‑T‑TACT‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTg                                                                                                            <  2:523858/238‑1 (MQ=255)                                                                                                                              a‑GTTGTATGC‑AAACCCCCTGTCTTGCGCTTTTTTA‑AAAAAAAGAGTCCA‑AACCACCAGCAAATTAACAGGTTAA‑TTTCTGGCTAAATAAAAAGAAGGTTTCAAAGAAAAAAT‑T‑TACA‑TTG‑ACCGCCAATGCAGAGCAGCTTCTGCAGCCACAGGTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTGATCaa                                                                                                       <  1:264411/239‑1 (MQ=255)                                                                                                                                          aaaCAACCGATCTGTCGCGTTTTTC‑AAAAAAATATGCAC‑AACTACCAGGAACTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTGATCAACTCCCTTGac                                                                                             >  2:399379/1‑238 (MQ=255)                                                                                                                                           aacaccCGATCTGCCGCGTTTTAC‑AAAAAAATATGCAC‑AACTACCAGAAACTTATCAGGTTGA‑TATCTGGCTAAATAAAAAGAAGGTTTCAAAAAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTGATCAACTCGCTTGAAc                                                                                            <  2:467896/239‑1 (MQ=255)                                                                                                                                               caccgtatctgccctttttCAAAAAAAATACGCCA‑ACCTCCAAGGAACTTATATGGTGTA‑TATTTGGCTGAAAAAAAAAAAGTTTCCACAAAAAAAAA‑T‑TACT‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTGATCAACTCGCTTGAACaaa                                                                                         <  2:609345/225‑1 (MQ=255)                                                                                                                                                   gtttttttgctttttt‑AAAAAAATTAATACAAACTTCCAGAAAGTTAACAGGTTGT‑TATGTGGCTAAAAAAAAAGAAGCTTCAACAGAAAATAA‑T‑TACT‑TTT‑CCCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTGATCAACTCGCTTGAACAAATCAt                                                                                     <  1:362950/229‑1 (MQ=255)                                                                                                                                                   aTCTGTCGCGTTTTTC‑AAAAAAATATGCAC‑AACTACCAGGAACTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAAt                                                                                                                                              >  2:459428/1‑181 (MQ=255)                                                                                                                                                   aTCTGTCGCGTTTTTC‑AAAAAAATATGCAC‑AACTACCAGGAACTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTGATCAACTCGCTTGAACAAATCAt                                                                                     >  2:274088/1‑238 (MQ=255)                                                                                                                                                      tGTCGCGTTTTTA‑AAAAAAATGGGCAA‑AACTTCCAGGACCTTATCAGGTTGA‑TTTTAGGCTGAAAAAAAGGAAGGTTTCAAAAAAAAAAA‑T‑TACA‑TTA‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTGATCAACTCGCTTGAACAAATCATTccc                                                                                 <  2:899336/239‑1 (MQ=255)                                                                                                                                                           tataaaaaacaaaaaaTACGAAC‑AA‑TACCCAGAACTTTACTAGTTTATTATTTGGTTAAAAAAAAAAAAGG‑TTCACAAAAAAAAA‑T‑TTCC‑TTTAACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTGATCAACTCGCTTGAACAAATCATTCCCGGTa                                                                             <  1:928614/229‑1 (MQ=255)                                                                                                                                                                               cac‑aACTACCAGGAACTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTGATCAACTCGCTTGAACAAATCATT‑CCGGTACAGCTGCTGAATTTGATTTCa                                                        >  2:248469/1‑239 (MQ=255)                                                                                                                                                                                    aCTACCAGGAACTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTGATCAACTCGCTTGAACAAATCATTCCCGGTACAGCTGCTGa                                                                   >  2:928614/1‑225 (MQ=255)                                                                                                                                                                                     cTACCAGGAACTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGAGGATGAAATCCCGGCGCTGGCTGAACAAGATGACGATAGCg                                                                                                              >  2:300445/1‑181 (MQ=255)                                                                                                                                                                                        ccAGGAATTTATCAGGTTGA‑TATCTGGCTAAAAAAAAAGAAGTTTTCAAAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTGATCAACTCGCTTGAACAAATCATTCCCGGTACAGCTGCTGAATTTGATTTCAAtcatca                                                 <  2:490410/239‑1 (MQ=255)                                                                                                                                                                                           tgtcacttttcagtgtttattCTGGGTGGAAAAAACGAAGGTTTTAAAAAAAAAAA‑TATACG‑TTG‑CCCGCCAATGCATAGCAACTTCTGCAGCCAGAGTTTACGGTAGAACAACGTCGTGAGCTTGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTGATCAACTCGATTGAACAAATCATTCCCGGTACAGCGGCTGAATTTGATTTCAATCATCAg                                                <  1:616056/219‑1 (MQ=255)                                                                                                                                                                                               cTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTGAt                                                                                                          >  2:346233/1‑175 (MQ=255)                                                                                                                                                                                               cTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTGATCAACTCGCTTGAACAAATCATTCCCGGTACACCTGCTGAATTTAATTTCAATAATCAGCAAAtt                                          >  1:733807/1‑239 (MQ=255)                                                                                                                                                                                                 tATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAACAA‑T‑TCCA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGCAATCCCGGCGCTGCCTGAAAATAAAGACGATAGCGTGCTCAACACGCTTGAACAAATAATTCCCGGTACAGCTGCTAAATTTGATTCAAACAATAAGCACCTTaa                                        >  1:984837/1‑239 (MQ=255)                                                                                                                                                                                                  aTCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTGATCAACTCGCTTGAACAAATCATTCCCGGTACAGCTGCTGAATTTGATTTCAATCATCAGCAACTTAAt                                       >  2:839878/1‑239 (MQ=255)                                                                                                                                                                                                       gTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGAGGATGAACTCCCGGCGCTGGCTGACAAAGATGACGATAGCGTGATCAACTCGCTTGAACAAATCATTCCCGGGACAGCTGCTGAATTTATTTTCAATCATAAGCACCTACATTTGa                                   >  1:754460/1‑238 (MQ=255)                                                                                                                                                                                                          gA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGa                                                                                                                                                 >  2:986799/1‑125 (MQ=255)                                                                                                                                                                                                          gA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTg                                                                                                            >  1:184336/1‑162 (MQ=255)                                                                                                                                                                                                          gA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTGATCAACTCGCTTGAACAAATCATTCACGGTACAGCTGCTGAATTTGATTTCAATCATCAGCAACTTAATTTGAGCAt                               >  2:287549/1‑239 (MQ=255)                                                                                                                                                                                                          gA‑TATCTGGCTGAATAAAAAGAAGGTTTCAAAGCAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACACCTACGAGAGCTGGGTATTAAGGCGGATGAAATCCCGGCGCTGACTGAAAAAGATGACGCTCACGTGCTCACATCGCTTAGACAAATCCTTCCCGGTACACCGGCTGAATTTGATTTCAACAATCAGCCACTTAATTTgcaca                                >  1:674308/1‑234 (MQ=255)                                                                                                                                                                                                          aa‑tatCTGGCTGAATAAAAAGAAGGTTCCAAAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTg                                                                                                            <  2:184336/161‑1 (MQ=255)                                                                                                                                                                                                                 gtgtaaaaaaaaaaGAAGTTTTACCAAAAAAATA‑T‑TACT‑TTG‑CCCGCCAATGCGGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTGATCAACTCGCTTGAACAAATCATTCCCGGTACAGCTGCTGAATTTGATTTCAATCATCAGCAACTTAATTTGAGCATTCCCCa                         <  1:627871/230‑1 (MQ=255)                                                                                                                                                                                                                   gcaaaaaaaaaaGATGGTTTCAAAAAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTGATCAACTCGCTTGAACAAATCATTCCCGGTACAGCTGCTGAATTTGATTTCAATCATCAGCAACTTAATTTGAGCATTCCCCaaa                       <  1:992353/232‑1 (MQ=255)                                                                                                                                                                                                                   gCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGCTAGCGGGATCAACTCGCTTGAACAAATCATTCCCGGTACAGATGCGGAATTTAATTTCAATCATAAGCAACTTAATTTTAACATTCCCCcaa                       >  1:133989/1‑239 (MQ=255)                                                                                                                                                                                                                   gCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGGATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTGCTCAACCGGCTTTAACAAATCATCCCCGGTACACCTCCTGAATTGGATTTCAATCACCACAAAATAAATATGAGAATTCCCaaaa                       >  1:546794/1‑239 (MQ=255)                                                                                                                                                                                                                    cgaaaaaaaaaaaaGGTTTTAAAAAAAAAAA‑T‑TTCACTTT‑CCCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTGATCAACTCGCTTGAACAAATCATTCCCGGTACAGCTGCTGAATTTGATTTCAATCATCAGCAACTTAATTTGAGCATTCCCCaaa                       <  1:141714/233‑1 (MQ=255)                                                                                                                                                                                                                        aaaaaaaaaaGTTTCCACAAAAAAAAT‑T‑TCCA‑TTT‑CCCGCCAATGCAGAGCCACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTGATCAACTCGCTTGAACAAATCATTCCCGGTACAGCTGCTGAATTTGATTTCAATCATCAGCAACTTAATTTGAGCATTCCCCAAATTGCa                  <  1:758648/237‑1 (MQ=255)                                                                                                                                                                                                                        aaaaaaaGTAGTTCTCACAAAAAAATA‑T‑TATT‑TTT‑CCCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACATCTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTGATCAACTCGCTTGAACAAATCATTCCCGGTACAGCTGCTGAATTTGATTTCAATCATCAGCAACTTAATTTGAGCATTCCCCAAATTGCa                  <  1:713532/237‑1 (MQ=255)                                                                                                                                                                                                                        aaaaaaaGGAGTTTTCAAAAAAAAAAA‑T‑TACA‑TTA‑TCCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTGATCAACTCGCTTGAACAAATCATTCCCGGTACAGCTGCTGAATTTGATTTCAATCATCAGCAACTTAATTTGAGCATTCCCCAAATTGCa                  <  2:754460/237‑1 (MQ=255)                                                                                                                                                                                                                        aTAAAAAGAAGGTTTCACAAAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTGATCAACTCGCTTGAACAAATCATTCCCGGTACAGCTGCTGAATTTGATTTCAATCATCAGCAACTTAATTTGAGCATTCCCCAAATTGCa                  <  2:733807/239‑1 (MQ=255)                                                                                                                                                                                                                                aagGTTTCA‑AAAAAAAAA‑T‑GTCATTTT‑ACCGCCAATGCAGAGCAACTTTGGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGATGAAAAAGATGACGATAGCGTGATCAACTCGCTTGAACAAATCATTCCCGGTACAGCTGCTGAATTTGATTTCAATCATCAGCAACTTAATTTGAGCATTTCCCAAATTGCACTGTACCg          <  2:997828/239‑1 (MQ=255)                                                                                                                                                                                                                                 agGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTGATCAACTCGCTTGAACAAATCATTCCCGGTACAGCTGCTGAATTTGATTTCAATCATCAGCAACTTAATTTTAGCATTCCCCAAATTGCACTGTa             >  2:141714/1‑235 (MQ=255)                                                                                                                                                                                                                                        acaAAAAAAAA‑T‑TACA‑TTG‑CCCCCCAAGGCAGAGCAACTTCTGCAGCCAAAGTTTACGGTAGAACAACTACGTGCGCTGGGTATTAAGGTTGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTGATCAACTCGCTTGAACAAATCATTCCCGGTACAGCTGCTGAATTTGATTTCAATCATCAGCAACTTAATTTGAGCATTCCCCAAATTGCACTGTACCGTGATGCaa  <  1:777798/239‑1 (MQ=255)                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                                  CGAAACAGTTGGCGCTCATCATCAAACGTTGTTTGCCGATGGTGCTCACTGGCAGCGGCATGCTTTGCACTACCGCTAACGCCGAAGAGTATTATTTCGACCCCATTATGCTGGAAACCACAAAAA‑GTGGTATGC‑AAACAACCGATCTGTCGCGTTTTTC‑AAAAAAATATGCAC‑AACTACCAGGAACTTATCAGGTTGA‑TATCTGGCTGAATAAAAAGAAGGTTTCACAGAAAAAAA‑T‑TACA‑TTT‑ACCGCCAATGCAGAGCAACTTCTGCAGCCACAGTTTACGGTAGAACAACTACGTGAGCTGGGTATTAAGGTGGATGAAATCCCGGCGCTGGCTGAAAAAGATGACGATAGCGTGATCAACTCGCTTGAACAAATCATTCCCGGTACAGCTGCTGAATTTGATTTCAATCATCAGCAACTTAATTTGAGCATTCCCCAAATTGCACTGTACCGTGATGCAA  >  NC_000913/3288849‑3289313

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑