Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,337,959	C→T	intergenic (‑125/‑283)	adhR ← / → USA300HOU_RS11940	HTH‑type transcriptional regulator AdhR/Hyaluronate lyase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,337,959	0	C	T	100.0%	40.6 / NA	12	intergenic (‑125/‑283)	adhR/USA300HOU_RS11940	HTH‑type transcriptional regulator AdhR/Hyaluronate lyase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (8/4);  total (8/4)

CTTCTTTAGTTTTCATTGCGACTATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAATTTGGGTGATCGATT  >  USA300TCH1516_ALE/2337819‑2338102                                                                                                                                             |                                                                                                                                                cttcttTAGTTTTCATTGCGACTATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCg                                                                                                                                        <  1:816467/150‑1 (MQ=255) cttcttTAGTTTTCATTGCGACTATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCg                                                                                                                                        >  2:816467/1‑150 (MQ=255)      ttAGTTTTCATTGCGACTATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTa                                                                                                                                  <  2:1048624/151‑1 (MQ=255)            ttCATTTCGACTATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACt                                                                                                                            <  3:262/151‑1 (MQ=255)               aTTGCGACTATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTa                                                                                                                         >  1:455151/1‑151 (MQ=255)                                                          gTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAg                                                                              >  2:730096/1‑151 (MQ=255)                                                                      atTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTTAAAATTTTATAACTTAATTCTTTAAAATTATATAATCATTAAGATTTATTAtttt                                                                  >  2:557904/1‑151 (MQ=255)                                                                                                          cTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAGTTTTTTGAAAATTATTTTAGTTGCAAttttttg                              >  4:346178/1‑149 (MQ=255)                                                                                                          cTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTgg                              >  3:357539/1‑151 (MQ=255)                                                                                                                  taaatttGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCg                      >  1:529530/1‑151 (MQ=255)                                                                                                                                  ttAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAATTTGGGTGATc      <  1:557904/151‑1 (MQ=255)                                                                                                                                      cATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTTAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAATTTGGGTGATCGAtt  >  4:73291/1‑151 (MQ=255)                                                                                                                                             |                                                                                                                                                CTTCTTTAGTTTTCATTGCGACTATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAATTTGGGTGATCGATT  >  USA300TCH1516_ALE/2337819‑2338102

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑