Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	110,225	T→C	G28G (GGT→GGC)	USA300HOU_RS00515 →	putative lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	110,225	0	T	C	94.1%	43.5 / NA	17	G28G (GGT→GGC)	USA300HOU_RS00515	putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base C (8/8);  minor base A (0/1);  total (8/9)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACAAAAACAAATCATTTTAAAAAGAAGAGAGTTGTAAGATGATGAAACGATTAAACAAATTAGTGTTAGGCATTATTTTTCTGTTTTTAGTCATTAGTATCACTGCTGGTTGTGGCATAGGTAAAGAAGCGGAAGTTAAGAAAAGCTTTGAAAAAACATTGAGTATGTACCCTATTAAAAATCTAGAGGATTTATACGATAAGGAAGGCTATCGTGATGATCAGTTTGATAAAAATGATAAAGGTACATGGATTAT  >  USA300TCH1516_ALE/110104‑110359                                                                                                                          |                                                                                                                                       acaaaaacaaaTCATTTTAAAAAGAAGAGATTTGTAAGATGATGAAACGATTAAACATATAAGTGTTAGGCATTATTTTTCTGTTTTTACTAATTAGTATCACTGCTGGTTGTTGTATAGTCATAGAAGCGGAAGATCAGa                                                                                                                     >  2:193130/1‑141 (MQ=17)              aTTTTAAAAAGAAGTGTGGTCGAAGATGATGAATCGATTAATACAATTAGTGTTAGGGATTTTTTTTCTGTTTTTAGTCAATAGTATCACTGCTGGTTGTGGCATAGGCAAAGAAGCGGAAGGTAAGAAAAGCTTTGaaag                                                                                                        <  2:133270/141‑2 (MQ=14)                     aaaGAAGAGAGTTGTAAGATGATGAAACGATTAAACAAATTAGTGTTAGGCATTATTTTTCTGTTTTTAGTCATTAGTATCACTGCTGGTTGTGGCATAGGCAAAGAAGCGGAAGTTAAGAAAAGCTTTGAAAAAACATTg                                                                                                 >  1:44907/1‑141 (MQ=255)                                              aaCGATTAATCAAATTAGTGTTAGGCATTATTTTTCTGTTTTTAGTCATTAGTATCACTGCGGGTTGTGGCATAGGCAAAGAAGCGGAAGTTAAGAAAAGCTTTGAAAAAACATTGAGTATGTACCCTATTAAAAATCTag                                                                        <  1:81378/141‑1 (MQ=255)                                              aaCGATTAAACAAATTAGTGTTAGGCATTATTTTTCTGTTTTTAGTCATTAGTATCACTGCTGGTTGTGGCATAGGCAAAGAAGCGGAAGTTAAGAAAAGCTTTGAAAAAACATTGAGTATGTACCCTATTAAAAATCTag                                                                        <  2:2188/141‑1 (MQ=255)                                                    tAAACAAATTAGTGTTAGGCATTATTTTTCTGTTTTTAGTCATTAGTATCACTGCTGGTTGTGGCATAGGCAAAGAAGCGGAAGTTAAGAAAAGCTTTGAAAAAACATTGAGTATGTACCCTATTAAAAATCTAGAGGAtt                                                                  <  2:163809/141‑1 (MQ=255)                                                        cAAAGTAGTGTTAGGCATTATTTTTCTGTTTTTAGTTATTAGTATCACTGCTGGTTGTGGCATAGGCAAAGAAGCGGAAGTTAAGAAAAGCTTTGAAAAAACATTGAGTATGTACCCTATTAAAAATCTAGAGGATTtata                                                              <  2:117596/141‑1 (MQ=255)                                                               gtgtTAGGCATTATTTTTCTGTTTTTAGTCATTAGTATCACTGCTGGTTGTGGCATAGGCAAAGAAGCGGAAGTTAAGAAAAGCTTTGAAAAAACATTGAGTATGTACCCTATTAAAAATCTAGAGGATTTATACGATaag                                                       >  1:84611/1‑141 (MQ=255)                                                                 gtTAGGCATTATTTTTCTGTTTTTAGTCATTAGTATCACTGCTGGTTGTGGCATAGGCAAAGAAGCGGAAGTTAAGAAAAGCTTTGAAAAAACATTGAGTATGTACCCTATTAAAAATCTAGAGGATTTATACGATaaggg                                                     >  1:57409/1‑140 (MQ=255)                                                                              tttATGTTTAGAGTAATGATTATCACTGGTGTTAGTGGCATAGGAAAAGAAGCGGAAGTTAATAAAAGCTTTGAAAAAACAGTGAGTATGTACCCTATTAAAAATCTAGAGGATTTATACGATAAGGAAGGCTATCGtgat                                        <  2:241645/141‑1 (MQ=14)                                                                                          ttaaTTAGTATCACTGCTGGGTGTGGAATAGTCAAAGAAGCAGAAGATAATAAAAGCTTTGAAAAAACATTGAGTATGTACTCTATTAAAAATCTAGAGGATTTATACGATAAGGAATGCTATCGTGATGATCAGTTTGAt                            <  2:260974/138‑1 (MQ=17)                                                                                                      aCTGCTGGTTGTGGCATAGGCAAAGAAGCGGAAGTTAAGAAAAGCTTTGAAAAAACATTGAGTATGTACCCTATTAAAAATCTAGAGGATTTATACGATAAGGAAGGCTATCGTGATGATCAGTTTGATAAATCTGATaaa                >  1:36723/1‑141 (MQ=255)                                                                                                             gTTGTGGCATAGGCAAAGAAGCGGAAGTTAAGAAAAGCTTTGAAAAAACATTGAGTATGTACCCTATTAAAAATCTAGAGGATTTATACGATAAGGAAGGCTATCGTGATGATCAGTTTGATAAAAATGATAAAGGTACAt         >  1:116375/1‑141 (MQ=255)                                                                                                               tgtgGCATAGGCAAAGAAGCGGAAGTTAAGAAAAGCTTTGAAAAAACATTGAGTATGTACCCTATTAAAAATCTAGAGGATTTATACGATAAGGAAGGCTATCGTGATGATCAGTTTGATAAAAATGATAAAGGTACATgg       <  1:171288/141‑1 (MQ=255)                                                                                                                 gggaaTAGGCAAAGAAGCGGAAGTTAAGAAAAGCTTTGAAAAAACATTGAGTATGTACCCTATTAAAAATCTAGAGGATTTATACGATAAGGAAGGCTATCGTGATGATCAGTTTGATAAAAATGATAAAGGTACATGGAt     <  2:171958/137‑1 (MQ=255)                                                                                                                    cATAGGCAAAGAAGCGGAAGTTAAGAAAAGCTTTGAAAAAACATTGAGTATGTACCCTATTAAAAATCTAGAGGATTTATACGATAAGGAAGGCTATCGTGATGATCAGTTTGATAAAAATGATCAAGGTACATGGATtat  >  1:234238/1‑141 (MQ=255)                                                                                                                    cATAGGCAAAGAAGCGGAAGTTAAGAAAAGCTTTGAAAAAACATTGAGTATGTACCCTATTAAAAATCTAGAGGATTTATACGATAAGGAAGGCTATCGTGATGATCAGTTTGATAAAAATGATAAAGGTACATGGATtat  >  2:64316/1‑141 (MQ=255)                                                                                                                          |                                                                                                                                       ACAAAAACAAATCATTTTAAAAAGAAGAGAGTTGTAAGATGATGAAACGATTAAACAAATTAGTGTTAGGCATTATTTTTCTGTTTTTAGTCATTAGTATCACTGCTGGTTGTGGCATAGGTAAAGAAGCGGAAGTTAAGAAAAGCTTTGAAAAAACATTGAGTATGTACCCTATTAAAAATCTAGAGGATTTATACGATAAGGAAGGCTATCGTGATGATCAGTTTGATAAAAATGATAAAGGTACATGGATTAT  >  USA300TCH1516_ALE/110104‑110359

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑