Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,173,363	Δ2 bp	intergenic (‑490/+918)	gatD ← / ← gatB	galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,173,363	0	C	.	85.7%	62.7 / 7.3	21	intergenic (‑490/+919)	gatD/gatB	galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component
Reads supporting (aligned to +/- strand):  ref base C (1/2);  new base . (14/4);  total (15/6)
Fisher's exact test for biased strand distribution p-value = 1.84e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.76e-01
*	NC_000913	2,173,364	0	C	.	85.7%	64.6 / 5.4	21	intergenic (‑491/+918)	gatD/gatB	galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component
Reads supporting (aligned to +/- strand):  ref base C (1/2);  new base . (14/4);  total (15/6)
Fisher's exact test for biased strand distribution p-value = 1.84e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.38e-01

TTAGCCGCCAGTTGGGTGTGCAAACCAATAGTTTGCGTCGCGATCCACAGGGTGATGCTCATAATGATGACACCCGAGATTAAGGTGCGGAACAGATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTG‑AGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCATTAGCAGCATCACTGCCGCCGTTTTTACCGCCAGCTGCAATACACCTTTGACATCGTAACCCGCGAGGATGCCGATAATCAGCCCCATCACAAAACCCACGGTGACAGGCTC  >  NC_000913/2173126‑2173612                                                                                                                                                                                                                                               ||                                                                                                                                                                                                                                                         ttAGCCGCCAGTTGGGTGTGCAAACCAATAGTTTGCGTCGCGATCCACAGGGAGATGCTCATAATGATGACACCCGAGATTAAGGTGCGGAACAGATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTG‑AGTGGGATAAAAATCAGGCTTGCCGATACCACC‑‑GCCGTATGTccc                                                                                                                                                                                                                                              >  2:2954/1‑249 (MQ=255)       gccAGTTGGGTGTGCAAACCAATAGTTTGCGTCGCGATCCACAGGGTGATGCTCATAATGATGACACCCGAGATTAAGGTGCGGAACAGATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTG‑AGTGGGATAAAAATCAGGCTTGCCGATACCACC‑‑GCCGTATGTCCCAgcagca                                                                                                                                                                                                                                       >  1:274818/1‑250 (MQ=255)        ccAGTTGGGTGTGCAAACCAATAGTTTGCGTCGCGATCCACAGGGTGCTGCTCATAATGATGACACCCGCGATTAAGGTGCGGAACAGATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGAGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTG‑AGTGGGATAAAAATCAGGCTTGACGATACCACC‑‑GCCGTATGTCCCAGCAGCAAc                                                                                                                                                                                                                                     >  2:294826/1‑251 (MQ=255)                gtgtGCAAACCAATAGTTGGCGTCGCGATCCACAGGGTGATGCTCATAAGGATGACCCCCGAGATTAAGGTGCGAAACAGATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTG‑AGTGGGATAAAAATCAGGCTTGCCGATACCACC‑‑GCCGTATGTCCCAGCAGCAACGCCGGATc                                                                                                                                                                                                                             <  1:294826/251‑1 (MQ=255)                                  tGCGACGCGATCCACAGGATGATGCTCATAATGATGACACCCGAGATTACGGTGCGAAACAGATTTCCACGATGCACGGCGCCCGCCATCGCAACGAAGACGACGATGGTGGCAAGCTCGCCAACAGGCCACAACTGATTACACGGCACACAAACAGCAATTCACATGGAG‑AGTGGGATAAAAATCAGGCTTGCCGAAACCACC‑‑GCCGTCTGTCCCAGCAGCCACGCCGGATAAAGGCCACTCAggcaatc                                                                                                                                                                                                           >  2:333177/1‑246 (MQ=255)                                           aTCCACAGGGTGATGCTCATAATGATGACACCCGAGATTAAGGTGCGGAACAGATTTCCACGATGCACGGCGACCGCCATCGCCACGACGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTG‑AGTGGGATAAAAATCAGGCTTGCCGATACCACC‑‑GCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGAccgcc                                                                                                                                                                                                  >  1:340218/1‑251 (MQ=255)                                                             aTAATGATGACACCCGAGATTAAGGTGCGGAACAGATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTG‑AGTGGGATAAAAATCAGGCTTGCCGATACCACC‑‑GCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACg                                                                                                                                                                                >  2:67802/1‑251 (MQ=255)                                                                                       gggaaacaagttcccccgaggcgcGGCGCCCGCCATCGCCGCGAAAAAGCAGAGGGTGGAAAGATCGCCAAGGGGCAGCGCCTGATTCCCCGGCCCACAAACTGCAATTAAAATGGTG‑GGTGGGATAAAAATCAGGCGGGCAGATAC‑‑CTCCGCCGTATGTCCCAGCAGCAACTCCGGATCAAGGCCAAGCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCg                                                                                                                                                      <  2:126448/228‑1 (MQ=255)                                                                                                                   aCCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTG‑AGTGGGATAAAAATCAGGCTTGCCGATACCACC‑‑GCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCAc                                                                                                                          >  1:99937/1‑251 (MQ=255)                                                                                                                    ccGCCATCGCCAGAAAAAAGCCAAGGGGGGCAAAATCCCAAAACGGCAGCACCTGATTACCCGGCCCACAAACAGCAATTAAAA‑GGTGGAGGGGGATAAAAATCAGGCTGGCCGATCCCACC‑‑GCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTGTAATCAcc                                                                                                                         <  2:127652/251‑1 (MQ=255)                                                                                                                    ccGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTG‑AGTGGGATAAAAATCAGGCTTGCCGATACCACC‑‑GCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCAcc                                                                                                                         >  1:222874/1‑251 (MQ=255)                                                                                                                           cGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTG‑AGTGGGATAAAAATCAGGCTTGCCGATACCACC‑‑GCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGAccgcc                                                                                                                                                                                                  >  2:88501/1‑171 (MQ=255)                                                                                                                           cGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTG‑AGTGGGATAAAAATCAGGCTTGCCGATACCACC‑‑GCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGAccgcc                                                                                                                                                                                                  <  1:88501/171‑1 (MQ=255)                                                                                                                                 gaagaaGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGAACACAAACAGCAATTAAAATGGTG‑AGTAGGATAAAAATCAGGCTTGCCGATACCACC‑‑GCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCATTagc                                                                                                             >  1:157248/1‑250 (MQ=255)                                                                                                                                      agCCGATGGCGGCAAGAGATCAAAACGGCAGCCCCTGCTTACCCGGCCCACAAACAACAACCACAATCGTG‑AGTGGGATAAAAATCAGGCTTGCCGATA‑‑ATCCCGCAGTATGTACCCGCCGCAACGCCGGATCAAGGCCAAGCCGGCACTCCTAACCGCAGAACTTAGCCTGTAAACGGCTACGCGCCTGCTTCGCGATAGGCGTTAAACAATCCATGACGGGATTAATCACACGTGGCATTAGCAGCATc                                                                                                       >  2:30577/1‑251 (MQ=255)                                                                                                                                                  cAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTG‑AGTGGGATAAAAATCAGGCTTGCCGATACCACC‑‑GCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCATTAGCAGCATCACTGCCGCCGtt                                                                                           >  1:276834/1‑251 (MQ=255)                                                                                                                                                      aTCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTG‑AGTGGGATAAAAATCAGGCTTGCCGATACCACC‑‑GCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCATTAGCAGCATCACTGCCGCCGttttt                                                                                        >  2:15810/1‑250 (MQ=255)                                                                                                                                                                                    cacacaAACAGCAATTAAAATGGTG‑AGTGGGATAAAAATCAGGCTTGCCGATACCACC‑‑GCCGTATGTACCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCATTAGCAGCATCACTGCCGCCGTTTTTACCGCCAGCTGCAATACAACTTTGACATCGt                                                         >  2:381616/1‑251 (MQ=255)                                                                                                                                                                                                 ataaaaaggggg‑AGTGGGATAAAAAACAGGCTTGCCGATACCACC‑‑GCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCATTAGCAGCATCACTGCCGCCGTTTTTACCGCCAGCTGCAATACACCTTTGACATCGTAACCCGCGAGGAt                                            <  1:377693/240‑1 (MQ=255)                                                                                                                                                                                                       agggTG‑AGGGGGATAAAAACCAGGCTGCCCGAT‑CC‑CCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCATTAGCAGCATCACTGCCGCCGTTTTTACCGCCAGCTGCAATACACCTTTGACATCGTAACCCGCGAGGATGCCGAt                                      <  1:356408/249‑1 (MQ=255)                                                                                                                                                                                                                                cTTGCCGATACCACC‑‑GCCGTATGTCCCAGAAGCAACGCCGCATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCATTAGCAGCATCACTGCCGCCGTTTTTACCGCCAGCTGCAATACACCTTTGACATCGTAACCCGCGCGGATGCCGATAATCAGCCCCATCACAAAACCCAc              >  2:209901/1‑251 (MQ=255)                                                                                                                                                                                                                                     gcggatccccccccCGTATGCCCCAGCAGAAACGCCGGATCAGGGCCAAGCAGGACCTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCATTAGCAGCATCACTGCCGCCGTTTTTACCGCCAGCTGCAATACACCTTTGACATCGTAACCCGCGAGGATGCCGATAATCAGCCCCATCACAAAACCCACGGt           <  2:138442/243‑1 (MQ=255)                                                                                                                                                                                                                                         ataccaccgccgTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCATTAGCAGCATCACTGCCGCCGTTTTTACCGCCAGCTGCAATACACCTTTGACATCGTAACCCGCGAGGATGCCGATAATCAGCCCCATCACAAAACCCACGGTgcc        >  2:160981/7‑248 (MQ=255)                                                                                                                                                                                                                                           ccccccGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCAAATCAGGAACCCCGGACCGCCGAACTTCGCCTGGAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCATTAGCATCATCACTGCCGCCGTTTTTACCGCCAGCTGCAAGACACCTTTGACATCGTAACCCGCGAGGATGCCGATAATCAGCCCCATCACAAAACCCACGGTGACAg      <  1:381616/248‑1 (MQ=255)                                                                                                                                                                                                                                              cccGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCATTAGCAGCATCACTGCCGCCGTTTTTACCGCCAGCTGCAATACACCTTTGACATCGTAACCCGCGAGGATGCCGATAATCAGCCCCATCACAAAACCCACGGTGACAGGCTc  <  1:183027/251‑1 (MQ=255)                                                                                                                                                                                                                                               ||                                                                                                                                                                                                                                                         TTAGCCGCCAGTTGGGTGTGCAAACCAATAGTTTGCGTCGCGATCCACAGGGTGATGCTCATAATGATGACACCCGAGATTAAGGTGCGGAACAGATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTG‑AGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCATTAGCAGCATCACTGCCGCCGTTTTTACCGCCAGCTGCAATACACCTTTGACATCGTAACCCGCGAGGATGCCGATAATCAGCCCCATCACAAAACCCACGGTGACAGGCTC  >  NC_000913/2173126‑2173612

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑