Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	1	1,339,409	Δ2 bp	intergenic (‑95/‑258)	unknown ← / → unknown	Haemophilus‑specific protein, uncharacterized/Pyruvate/2‑oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component, and related enzymes

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	1	1,339,408	0	T	.	100.0%	96.9 / NA	24	intergenic (‑94/‑260)	unknown/unknown	Haemophilus‑specific protein, uncharacterized/Pyruvate/2‑oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component, and related enzymes
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (16/8);  total (16/8)
*	1	1,339,409	0	C	.	100.0%	96.9 / NA	24	intergenic (‑95/‑259)	unknown/unknown	Haemophilus‑specific protein, uncharacterized/Pyruvate/2‑oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component, and related enzymes
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (16/8);  total (16/8)

ACATCTTCATGTGAGTAAGTCTTAATTTTTCCATTTAAGACACCTTGTAAAAAGCGCTGCTCTTCTGTTAAGGATTGCTCAAACATTGATAAAACTCTTTCTTGAAGA‑TGAGTTTGCCCATTTTTTGATTTAGCTTGATTTAACATATTTTCTCCAACGCGCGCGGATTGTAATAATGATCTATCTTGGAATCATACAACAAAATTGCCAAAAGGTAAAAGGCCCAAGGGAGCCCTATCGGGCTAAGGGTAAAATTTAAGGATAACCTTCCCAAGGGAAAGGTCTTACCTAAAAAGGTCAAAAGGCCTTTTCAAAAGGCTGGAACTACACTCACTATATTTGTTCGTTTTTAATG  >  1/1339229‑1339583                                                                                                                                                                                     ||                                                                                                                                                                               acctCTTCATGTGAGTAGGTCTTAATTTTGCCATTCAAGACACCTTGTAAAAAGCGTTGCTCTTCAGTTAAGGACTGTTCAAACACTGATAATACTCTTTCTTGAAAG‑TGAGTTTGCTCATTTTTTAATTTAGCTTGATTTAACATATTTTCTCCAA‑‑‑‑CACGGAT‑‑‑‑CTA‑‑CA‑‑TACCTTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGAt                                                                                              >  1:109841/4‑251 (MQ=255)   ctCTTCATGTGAGTAGGTCTTAATTTTGCCATTCAAGACACCTTGTAAAAAGCGTTGCTCTTCAGTTAAGGACTGTTCAAACACTGATAATACTCTTTCTTGAAAG‑TGAGTTTGCTCATTTTTTAATTTAGCTTGATTTAACATATTTTCTCCAA‑‑‑‑CACGGAT‑‑‑‑CTA‑‑CA‑‑TACCTTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATaa                                                                                            >  1:692483/2‑251 (MQ=255)          tgtgAGTAGGTCTTAATTTTGCCATTCAAGACACCTTGTAAAAAGCGTTGCTCTTCAGTTAAGGACTGTTCAAACACTGATAATACTCTTTCTTGAAAG‑TGAGTTTGCTCATTTTTTAATTTAGCTTGATTTAACATATTTTCTCCAA‑‑‑‑CACGGAT‑‑‑‑CTA‑‑CA‑‑TACCTTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCtttc                                                                                      >  1:768890/1‑248 (MQ=255)          tgtgAGTAGGTCTTAATTTTGCCATTCAAGACACCTTGTAAAAAGCGTTGCTCTTCAGTTAAGGACTGTTCAAACACTGATAATACTCTTTCTTGAAAG‑TGAGTTTGCTCATTTTTTAATTTAGCTTGATTTAACATATTTTCTCCAA‑‑‑‑CACGGAT‑‑‑‑CTA‑‑CA‑‑TACCTTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCtttc                                                                                      >  1:708263/1‑248 (MQ=255)          cgtagctttgtcgtAATTTTGCCATTCAAGACACCTTGTAAAAAGCGTTGCTCTTCAGTTAAGGACTGTTCAAACACTGATAATACTCTTTCTTGAAAG‑TGAGTTTGCTCATTTTTTAATTTAGCTTGATTTAACATATTTTCTCCAA‑‑‑‑CACGGAT‑‑‑‑CTA‑‑CA‑‑TACCTTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAAcc                                                                                          <  1:164276/233‑1 (MQ=255)                                cATTCAAGACACCTTGTAAAAAGCGTTGCTCTTCAGTTAAGGACTGTTCAAACACTGATAATACTCTTTCTTGAAAG‑TGAGTTTGCTCATTTTTTAATTTAGCTTGATTTAACATATTTTCTCCAA‑‑‑‑CACGGAT‑‑‑‑CTA‑‑CA‑‑TACCTTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTgaaa                                                               <  1:137420/251‑1 (MQ=255)                                    caaGACACCTTGTAAAAAGCGTTGCTCTTCAGTTAAGGACTGTTCAAACACTGATAATACTCTTTCTTGAAAG‑TGAGTTTGCTCATTTTTTAATTTAGCTTGATTTAACATATTTTCTCCAA‑‑‑‑CACGGAT‑‑‑‑CTA‑‑CA‑‑TACCTTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTgaaa                                                               <  1:702711/246‑1 (MQ=255)                                                              cttcaGTTAAGGACTGTTCAAACACTGATAATACTCTTTCTTGAAAG‑TGAGTTTGCTCATTTTTTAATTTAGCTTGATTTAACATATTTTCTCCAA‑‑‑‑CACGGAT‑‑‑‑CTA‑‑CA‑‑TACCTTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGaa                                 >  1:150462/1‑251 (MQ=255)                                                                   gTTAAGGACTGTTCAAACACTGATAATACTCTTTCTTGAAAG‑TGAGTTTGCTCATTTTTTAATTTAGCTTGATTTAACATATTTTCTCCAA‑‑‑‑CACGGAT‑‑‑‑CTA‑‑CA‑‑TACCTTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAAcaac                             >  1:11348/1‑247 (MQ=255)                                                                   gTTAAGGACTGTTCAAACACTGATAATACTCTTTCTTGAAAG‑TGAGTTTGCTCATTTTTTAATTTAGCTTGATTTAACATATTTTCTCCAA‑‑‑‑CACGGAT‑‑‑‑CTA‑‑CA‑‑TACCTTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAAcaac                             >  1:612114/1‑247 (MQ=255)                                                                             gttCAAACACTGATAATACTCTTTCTTGAAAG‑TGAGTTTGCTCATTTTTTAATTTAGCTTGATTTAACATATTTTCTCCAA‑‑‑‑CACGGAT‑‑‑‑CTA‑‑CA‑‑TACCTTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAg                                                                                                 >  1:254176/3‑172 (MQ=255)                                                                             gttCAAACACTGATAATACTCTTTCTTGAAAG‑TGAGTTTGCTCATTTTTTAATTTAGCTTGATTTAACATATTTTCTCCAA‑‑‑‑CACGGAT‑‑‑‑CTA‑‑CA‑‑TACCTTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCtttcc                                                                                     >  1:589814/3‑181 (MQ=255)                                                                             gttCAAACACTGATAATACTCTTTCTTGAAAG‑TGAGTTTGCTCATTTTTTAATTTAGCTTGATTTAACATATTTTCTCCAA‑‑‑‑CACGGAT‑‑‑‑CTA‑‑CA‑‑TACCTTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCa                                                                                    <  1:144612/183‑1 (MQ=255)                                                                             gttCAAACACTGATAATACTCTTTCTTGAAAG‑TGAGTTTGCTCATTTTTTAATTTAGCTTGATTTAACATATTTTCTCCAA‑‑‑‑CACGGAT‑‑‑‑CTA‑‑CA‑‑TACCTTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAAcaacccgcaccatat                  >  1:392502/3‑237 (MQ=255)                                                                             gttCAAACACTGATAATACTCTTTCTTGAAAG‑TGAGTTTGCTCATTTTTTAATTTAGCTTGATTTAACATATTTTCTCCAA‑‑‑‑CACGGAT‑‑‑‑CTA‑‑CA‑‑TACCTTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAAcaacccgcaccatat                  >  1:143591/3‑237 (MQ=255)                                                                                  aaCACTGATAATACTCTTTCTTG‑AGAGTGAGTTTGCTCATTTTTTAATTTAGCTTGATTTAACATATTTTCTCCAA‑‑‑‑CACGGAT‑‑‑‑CTA‑‑CA‑‑TACCTTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAACAACCCGCACCATAtttatc             <  1:800660/251‑4 (MQ=255)                                                                                      ctGATAATACTCTTTCTTGAAAG‑TGAGTTTGCTCATTTTTTAATTTAGCTTGATTTAACATATTTTCTCCAA‑‑‑‑CACGGAT‑‑‑‑CTA‑‑CA‑‑TACCTTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAAcaacc                            <  1:239658/231‑5 (MQ=255)                                                                                        gATAATACTCTTTCTTGAAAG‑TGAGTTTGCTCATTTTTTAATTTAGCTTGATTTAACATATTTTCTCCAA‑‑‑‑CACGGAT‑‑‑‑CTA‑‑CA‑‑TACCTTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAAcc                                                                                          >  1:73243/1‑168 (MQ=255)                                                                                        gATAATACTCTTTCTTGAAAG‑TGAGTTTGCTCATTTTTTAATTTAGCTTGATTTAACATATTTTCTCCAA‑‑‑‑CACGGAT‑‑‑‑CTA‑‑CA‑‑TACCTTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTc                                                                         >  1:117744/1‑185 (MQ=255)                                                                                        gATAATACTCTTTCTTGAAAG‑TGAGTTTGCTCATTTTTTAATTTAGCTTGATTTAACATATTTTCTCCAA‑‑‑‑CACGGAT‑‑‑‑CTA‑‑CA‑‑TACCTTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTgaaa                                                               >  1:99293/1‑195 (MQ=255)                                                                                        gATAATACTCTTTCTTGAAAG‑TGAGTTTGCTCATTTTTTAATTTAGCTTGATTTAACATATTTTCTCCAA‑‑‑‑CACGGAT‑‑‑‑CTA‑‑CA‑‑TACCTTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAACAACCCGCACCATAtttatctgtttt       >  1:307693/1‑242 (MQ=255)                                                                                         ataataCTCTTTCTTGAAAG‑TGAGTTTGCTCATTTTTTAATTTAGCTTGATTTAACATATTTTCTCCAA‑‑‑‑CACGGAT‑‑‑‑CTA‑‑CA‑‑TACCTTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTgaaaa                                                              <  1:609691/195‑1 (MQ=255)                                                                                         ataataCTCTTTCTTGAAAG‑TGAGTTTGCTCATTTTTTAATTTAGCTTGATTTAACATATTTTCTCCAA‑‑‑‑CACGGAT‑‑‑‑CTA‑‑CA‑‑TACCTTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAACAACCCGCACCATAtttatctgttttt      >  1:654575/1‑241 (MQ=255)                                                                                             taCTCTTTCTTGAAAG‑TGAGTTTGCTCATTTTTTAATTTAGCTTGATTTAACATATTTTCTCCAA‑‑‑‑CACGGAT‑‑‑‑CTA‑‑CA‑‑TACCTTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAACAACCCGCACCATATTTATCTGTTTTTAATg  <  1:353378/250‑1 (MQ=255)                                                                                                                                                                                     ||                                                                                                                                                                               ACATCTTCATGTGAGTAAGTCTTAATTTTTCCATTTAAGACACCTTGTAAAAAGCGCTGCTCTTCTGTTAAGGATTGCTCAAACATTGATAAAACTCTTTCTTGAAGA‑TGAGTTTGCCCATTTTTTGATTTAGCTTGATTTAACATATTTTCTCCAACGCGCGCGGATTGTAATAATGATCTATCTTGGAATCATACAACAAAATTGCCAAAAGGTAAAAGGCCCAAGGGAGCCCTATCGGGCTAAGGGTAAAATTTAAGGATAACCTTCCCAAGGGAAAGGTCTTACCTAAAAAGGTCAAAAGGCCTTTTCAAAAGGCTGGAACTACACTCACTATATTTGTTCGTTTTTAATG  >  1/1339229‑1339583

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑