Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	1	1,339,417	G→A	intergenic (‑103/‑251)	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	1,339,417	0	G	A	100.0%	88.3 / NA	34	intergenic (‑103/‑251)	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 G (0/0);  new base A (20/14);  total (20/14)

ACATCTTCATGTGAGTAAGTCTTAATTTTTCCATTTAAGACACCTTGTAAAAAGCGCTGCTCTTCTGTTAAGGATTGCTCAAACATTGATAAAACTCTTTCTTGAAGA‑TGAGTTTGCCCATTTTTTGATTTAGCTTGATTTAACATATTTTCTCCAACGCGCGCGGATTGTAATAATGATCTATCTTGGAATCATACAACAAAATTGCCAAAAGGTAAAAGGCCCAAGGGAGCCCTATCGGGCTAAGGGTAAAATTTAAGGATAACCTTCCCAAGGGAAAGGTCTTACCTAAAAAGGTCAAAAGGCCTTTTCAAAAGGCTGGAACTACACTCACTATATTTGTTCGTTTTTAATGATCACTTATTTGTTGTTTTGATGTCCATCACTTGTATTCTGCAACATTAAACAGTTCCCCTTACTAAAACATGAAGCAAC  >  1/1339229‑1339663                                                                                                                                                                                              |                                                                                                                                                                                                                                                       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                                                                                                                                                                      >  1:708263/1‑248 (MQ=255)          tgtgAGTAGGTCTTAATTTTGCCATTCAAGACACCTTGTAAAAAGCGTTGCTCTTCAGTTAAGGACTGTTCAAACACTGATAATACTCTTTCTTGAAAG‑TGAGTTTGCTCATTTTTTAATTTAGCTTGATTTAACATATTTTCTCCAA‑‑‑‑CACGGAT‑‑‑‑CTA‑‑CA‑‑TACCTTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCtttc                                                                                                                                                                      >  1:768890/1‑248 (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)                                                                                                                                                                     ctccaacacggatctacatacctTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAACAACCCGCACCATATTTATCTGTTTTTAATGATCACTTATTTGTTGTTTTGATATTCATCACTTGTATTc                                           >  1:397000/22‑231 (MQ=255)                                                                                                                                                                     ctccaacacggatctacatacctTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAACAACCCGCACCATATTTATCTGTTTTTAATGATCACTTATTTGTTGTTTTGATATTCATCACTTGTATTCTGCAACATTaaat                              >  1:690409/22‑243 (MQ=255)                                                                                                                                                                               gatctacatacctTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAACAACCCGCACCATATTTATCTGTTTTTAAt                                                                                   >  1:660186/12‑181 (MQ=255)                                                                                                                                                                               gatctacatacctTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAACAACCCGCACCATATTTATCTGTTTTTAATg                                                                                  <  1:792599/171‑1 (MQ=255)                                                                                                                                                                               gatctacatacctTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAACAACCCGCACCATATTTATCTGTTTTTAATGATCACTTATTTGTTGTTTTGATATTCATCACTTGTATTCTGCAACATTaaat                              <  1:604511/223‑2 (MQ=255)                                                                                                                                                                               gatctacatacctTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAACAACCCGCACCATATTTATCTGTTTTTAATGATCACTTATTTGTTGTTTTGATATTCATCACTTGTATTCTGCAACATTAAATAACACCCCTTACTaag              <  1:626096/239‑2 (MQ=255)                                                                                                                                                                                   tacatacctTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAACAACCCGCACCATATTTATCTGTTTTTAATGATCACTTATTTGTTGTTTTGATATTCATCACTTGTATTCTGCAACATTAAATAACACCCCTTACTaagatatg         >  1:541017/8‑245 (MQ=255)                                                                                                                                                                                    acatacctTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAACAACCCGCACCATATTTATCTGTTTTTAATGATCACTTATTTGTTGTTTTGATATTCATCACTTGTATTCTGCAACATTaaataac                           <  1:197498/226‑5 (MQ=255)                                                                                                                                                                                      atacctTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAACAACCCGCACCATATTTATCTGTTTTTAATGATCACTTATTTGTTGTTTTGATATTCATCACTTGTATTCTGCAACATTAAATAACACCCCTTACTAAGATATGAAg      <  1:190343/247‑1 (MQ=255)                                                                                                                                                                                          ctTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAACAACCCGCACCATATTTATCTGTTTTTAATGATCACTTATTTGTTGTTTTGATATTCATCACTTGTATTCTGCAACATTAAATAACACCCCTTACTAAGATATGAAGCAAc  <  1:360243/251‑1 (MQ=255)                                                                                                                                                                                              |                                                                                                                                                                                                                                                       ACATCTTCATGTGAGTAAGTCTTAATTTTTCCATTTAAGACACCTTGTAAAAAGCGCTGCTCTTCTGTTAAGGATTGCTCAAACATTGATAAAACTCTTTCTTGAAGA‑TGAGTTTGCCCATTTTTTGATTTAGCTTGATTTAACATATTTTCTCCAACGCGCGCGGATTGTAATAATGATCTATCTTGGAATCATACAACAAAATTGCCAAAAGGTAAAAGGCCCAAGGGAGCCCTATCGGGCTAAGGGTAAAATTTAAGGATAACCTTCCCAAGGGAAAGGTCTTACCTAAAAAGGTCAAAAGGCCTTTTCAAAAGGCTGGAACTACACTCACTATATTTGTTCGTTTTTAATGATCACTTATTTGTTGTTTTGATGTCCATCACTTGTATTCTGCAACATTAAACAGTTCCCCTTACTAAAACATGAAGCAAC  >  1/1339229‑1339663

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: ‑