Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	1	1,339,535	C→T	intergenic (‑221/‑133)	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	1,339,535	0	C	T	100.0%	90.8 / NA	35	intergenic (‑221/‑133)	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 T (17/18);  total (17/18)

CTTCTGTTAAGGATTGCTCAAACATTGATAAAACTCTTTCTTGAAGA‑TGAGTTTGCCCATTTTTTGATTTAGCTTGATTTAACATATTTTCTCCAACGCGCGCGGATTGTAATAATGATCTATCTTGGAATCATACAACAAAATTGCCAAAAGGTAAAAGGCCCAAGGGAGCCCTATCGGGCTAAGGGTAAAATTTAAGGATAACCTTCCCAAGGGAAAGGTCTTACCTAAAAAGGTCAAAAGGCCTTTTCAAAAGGCTGGAACTACACTCACTATATTTGTTCGTTTTTAATGATCACTTATTTGTTGTTTTGATGTCCATCACTTGTATTCTGCAACATTAAACAGTTCCCCTTACTAAAACATGAAGCAACTATAATGTTTTCTATTTTTCATAAAATGCTAAGTAAAAAAAGTAATACCGAATCCCTTGGTATTTCTACCCAGCCAACACTGTCGGTG  >  1/1339290‑1339751                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                         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‑‑TACCTTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAAcaacccgcaccatat                                                                                                                                                                                          >  1:143591/3‑237 (MQ=255)                gttCAAACACTGATAATACTCTTTCTTGAAAG‑TGAGTTTGCTCATTTTTTAATTTAGCTTGATTTAACATATTTTCTCCAA‑‑‑‑CACGGAT‑‑‑‑CTA‑‑CA‑‑TACCTTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAAcaacccgcaccatat                                                                                                                                                                                          >  1:392502/3‑237 (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‑‑TACCTTGAAATCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAACAACCCGCACCATAtttatctgtttt                                                                                                                                                                               >  1:307693/1‑242 (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)                                                                                                                                  aaTCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAACAACCCGCACCATATTTATCTGTTTTTAATGATCACTTATTTGTTGTTTTGATATTCATCACTTGTATTCTGCAACATTAAATAACACCCCTTACTAAGATATGAAGCAACtatgt                                                                                     <  1:210347/251‑3 (MQ=255)                                                                                                                                    tCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAAc                                                                                                                                                                                                        <  1:223244/134‑1 (MQ=255)                                                                                                                                    tCATACAACAAAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAACAACCCGCACCATATTTATCTGTTTTTAAt                                                                                                                                                                           >  1:582822/1‑163 (MQ=255)                                                                                                                                         caacaaAACCGCAAAAAGGTAAAAGGAACAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAACAACCCGCACCATATTTATCTGTTTTTAATGATCACTTATTTGTTGTTTTGATATTCATCACTTGTATTCTGCAACATTAAATAACACCCCTTACTAAGATATGAAGCAACtatgttttccat                                                                              <  1:234863/251‑10 (MQ=255)                                                                                                                                                                aggaacAAGGGAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAACAACCCGCACCATATTTATCTGTTTTTAATGATCACTTATTTGTTGTTTTGATATTCATCACTTGTATTCTGCAACATTAAATAACACCCCTTACTAAGATATGAAGCAACT‑‑‑ATGTTTTCCATTTTTCATAAAATCCTAAGTaaaa                                                    >  1:416088/6‑251 (MQ=255)                                                                                                                                                                          gAGCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAACAACCCGCACCATAtttatc                                                                                                                                                                                     >  1:786621/1‑112 (MQ=255)                                                                                                                                                                            gCCCTAGCGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAACAACCCGCACCATATTTATCTGTTTTTAATGATCACTTATTTGTTGTTTTGATATTCATCACTTGTATTCTGCAACATTaaataacaccccttacta                                                                                                        <  1:63624/190‑16 (MQ=255)                                                                                                                                                                               ctagcGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAACAACCCGCACCATATTTATCTGTTTTTAATGATCACTTATTTGTTGTTTTGATATTCATCACTTGTATTCTGCAACATTAAATAACACCCCTTACTaag                                                                                                      <  1:572970/185‑2 (MQ=255)                                                                                                                                                                                 agcGGGCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAACAACCCGCACCATATTTATCTGTTTTTAATGATCACTTATTTGTTGTTTTGATATTCATCACTTGTATTCTGCAACATTAAATAACACCCCTTACTAAGATATGAAGCAACT‑‑‑ATGTTTTCCATTTTTCATAAAATCCTAAGTAAAAAATCTAATAc                                          <  1:98711/242‑1 (MQ=255)                                                                                                                                                                                      gCTAAGGGTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAACAACCCGCACCATATTTATCTGTTTTTAATGATCACTTATTTGTTGTTTTGATATTCATCACTTGTATTCTGCAACATTAAATAACCCCCCTTACTAAGATATGAAGCAACT‑‑‑ATGTTTTCCATTTTTCATAAAATCCTAAGTAAAAAATCTAATACCGAATCCTTTga                              >  1:442552/1‑250 (MQ=255)                                                                                                                                                                                           gggTAAAATTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAACAACCCGCACCATATTTATCTGTTTTTAATGATCACTTATTTGTTGTTTTGATATTCATCACTTGTATTCTGCAACATTAAATAACACCCCTTACTAAGATATGAAGCAACT‑‑‑ATGTTTTCCATTTTTCATAAAATCCTAAGTAAAAAATCTAATACCGAATCCTTTGATAtta                         >  1:131650/1‑250 (MQ=255)                                                                                                                                                                                                 aaTTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAACAACCCGCACCATATTTATCTGTTTTTAATGATCACTTATTTGTTGTTTTGATATTCATCACTTGTATTCTGc                                                                                                                                <  1:737542/145‑1 (MQ=255)                                                                                                                                                                                                 aaTTTAAGGATAACCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAACAACCCGCACCATATTTATCTGTTTTTAATGATCACTTATTTGTTGTTTTGATATTCATCACTTGTATTCTGCAACATTAAATAACACCCCTTACTAAGATATGAAGCAACT‑‑‑ATGTTTTCCATTTTTCATAAAATCCTAAGTAAAAAATCTAATACCGAATCCTTTGATATTACTatcc                   <  1:839919/251‑4 (MQ=255)                                                                                                                                                                                                            aaCCTTTCCAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAACAACCCGCACCATATTTATCTGTTTTTAATGATCACTTATTTGTTGTTTTGATATTCATCAc                                                                                                                                           >  1:65838/1‑123 (MQ=255)                                                                                                                                                                                                                  tccAAGGGAAAGGTCTTACCTGAAAAGGCCAAAAGGCTTTTTCAAAAGGCAGGAACAACCCGCACCATATTTATCTGTTTTTAATGATCACTTATTTGTTGTTTTGATATTCATCACTTGTATTCTGCAACATTAAATAACACCCCTTACTAAGATATGAAGCAACT‑‑‑ATGTTTTCCATTTTTCATAAAATCCTAAGTAAAAAATCTAATACCGAATCCTTTGATATTACTATCCAACCGACACtaccaatg  <  1:787157/250‑8 (MQ=255)                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                         CTTCTGTTAAGGATTGCTCAAACATTGATAAAACTCTTTCTTGAAGA‑TGAGTTTGCCCATTTTTTGATTTAGCTTGATTTAACATATTTTCTCCAACGCGCGCGGATTGTAATAATGATCTATCTTGGAATCATACAACAAAATTGCCAAAAGGTAAAAGGCCCAAGGGAGCCCTATCGGGCTAAGGGTAAAATTTAAGGATAACCTTCCCAAGGGAAAGGTCTTACCTAAAAAGGTCAAAAGGCCTTTTCAAAAGGCTGGAACTACACTCACTATATTTGTTCGTTTTTAATGATCACTTATTTGTTGTTTTGATGTCCATCACTTGTATTCTGCAACATTAAACAGTTCCCCTTACTAAAACATGAAGCAACTATAATGTTTTCTATTTTTCATAAAATGCTAAGTAAAAAAAGTAATACCGAATCCCTTGGTATTTCTACCCAGCCAACACTGTCGGTG  >  1/1339290‑1339751

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑