Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	3,790	G→A	A29T (GCA→ACA)	USA300HOU_RS00015 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	3,790	0	G	A	100.0%	78.2 / NA	21	A29T (GCA→ACA)	USA300HOU_RS00015	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (14/7);  total (14/7)

AAAGGTATAATATATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAGCAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAATTACCTGAAGATGCTGGTTCTTTCTTAATCATTCATCAA  >  USA300TCH1516_ALE/3660‑3930                                                                                                                                   |                                                                                                                                             aaaGGTATAATATATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAg                                                                                                                            >  1:108093/1‑149 (MQ=255)      tataATATATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGATACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGtt                                                                                                                       <  1:271058/149‑1 (MQ=255)      tataATATATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGtt                                                                                                                       <  1:271068/149‑1 (MQ=255)           tatatTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGt                                                                                                                  >  1:52324/1‑149 (MQ=255)           tatatTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGt                                                                                                                  >  1:38925/1‑149 (MQ=255)                           aaaGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTg                                                                                                  >  1:140393/1‑149 (MQ=255)                                         attattTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCGAAAAACAGAAGGGATTATGGAATCTGGTGGTCAAACAAAATGGTTCTCGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTcg                                                                                    >  1:100315/1‑149 (MQ=255)                                          ttattTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTcgc                                                                                   >  1:110302/1‑149 (MQ=255)                                              tttGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTa                                                                               >  1:103222/1‑149 (MQ=255)                                                             tGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATc                                                                >  1:7204/1‑149 (MQ=255)                                                                    gAAGGAGACATTAAGTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAACCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCg                                                         <  1:117588/149‑1 (MQ=255)                                                                                 aTTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCa                                            >  1:238248/1‑149 (MQ=255)                                                                                 aTTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCa                                            >  1:242653/1‑149 (MQ=255)                                                                                  tttAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCGAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAg                                           <  1:234146/149‑1 (MQ=255)                                                                                    tAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAACATCATTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGaa                                         <  1:277661/149‑1 (MQ=255)                                                                                                             gATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAATTACCTGAAGATGCTGGttctttct                <  1:73920/149‑1 (MQ=255)                                                                                                                    gAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAATTACCTGAAGATGCTGGTTCTTTCTTAAtcat         >  1:110994/1‑149 (MQ=255)                                                                                                                       tCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAATTACCTGAAGATGCTGGTTCTTTCTTAAtcattca      <  1:215127/149‑1 (MQ=255)                                                                                                                         tggtggTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAATTACCTGAAGATGCTGGTTCTTTCTTAATCATtcatc    >  1:36456/1‑149 (MQ=255)                                                                                                                          ggtggtCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAATTACCTGAAGATGCTGGTTCTTTCTTAATCATtcatca   >  1:13673/1‑149 (MQ=255)                                                                                                                           gtggtCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAATTACCTGAAGATGCTGGTTCTTTCTTAATCATTCATCaa  >  1:164064/1‑149 (MQ=255)                                                                                                                                   |                                                                                                                                             AAAGGTATAATATATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAGCAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAATTACCTGAAGATGCTGGTTCTTTCTTAATCATTCATCAA  >  USA300TCH1516_ALE/3660‑3930

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑