Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	104,186	T→C	V6A (GTA→GCA)	USA300HOU_RS00495 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	104,186	0	T	C	93.8%	45.8 / NA	16	V6A (GTA→GCA)	USA300HOU_RS00495	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base C (5/10);  minor base A (0/1);  total (5/11)
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

ATTTTTGTTATCATAGAGTTAATAAATATAATAAATTAAACAAGTAACTTTACAAAAATTAGAATGATTCAATTCAATCATAATTGTTTGAAAATAGAGGTGAGCAGGTGAACGATATGTTAATTAGTCTTGTAATCCCAGTTTTTGCTTTGTTAGTTATTGGTGGTATTATTTGGATGATTATAGAAGGTATAGTACATATTTCAAAAAAGAATAAAGCAATTGATAACTTTTTTAACCAAGTTAATA  >  USA300TCH1516_ALE/104054‑104302                                                                                                                                     |                                                                                                                     aTTTATGTTATCATAGAGTTAATAAATATAATAAATTAAACAAGTAACTTTACAAAAATTAGAATGATTCAATTCAATCATAATTGTTTGAAAATAGAGGTGAGCAGGTGAACGATATGTTAATTAGTCTTGCACTCCCAg                                                                                                              >  2:35954/1‑141 (MQ=255)     ttGTTATCATAGAGTTAATAAAGATAATAAATTAAACAAGTAACTTTACAAAAATTAGAATGATTCAATTCAATCATAATTGTTTGAAAATAGAGGTGAGCAGGTGAACGATATGTTAATTAGTCTTGCAATCCCAGtttt                                                                                                          <  2:76842/141‑1 (MQ=255)                gagTTAATAAATATAATAAATTAAACAAGTAACTTTACAAAAATTAGAATGATTCAATTCAATCATAATTGTTTGAAAATAGAGGTGAGCAGGTGAACGATATGTTAATTAGTCTTGCAATCCCAGTTTTTGCTTTgttag                                                                                               <  1:103231/141‑1 (MQ=255)                    taataaATATAATAAATTAAACAAGTAACTTTACAAAAATTAGAATGATTCAATTCAATCATAATTGTTTGAAAATAGAGGTGAGCAGGTGAACGATATGTTAATTAGTCTTGCAATCCCAGTTTTTGCTTTGTTAGTTAt                                                                                           >  1:17285/1‑141 (MQ=255)                           tataATAAATTAAACAAGTAACTTTACAAAAATTAGAATGATTCAATTCAATCATAATTGTTTGAAAAGAGAGGTGAGCAGGTGAACGATATGTTAATTAGTCTTGCAATCCCAGTTTTTGCTTTGTTAGTTATTggtggt                                                                                    >  2:158594/1‑141 (MQ=255)                             taatacAGTAAACAAGTAACTGTACAAAAATTAGAAGGATTCAATTCAATCAGAATTGTTTGAAAATAGAGGTGAGCAGGTGAACGATATGTTAATTAGTCTTGCAATCCCAGTTTTTGCTTTGTTAGTTATTGGTGGtat                                                                                  <  1:33401/141‑1 (MQ=255)                                taaATTAAACAAATAACTTTACAAAAATTAGAATGATTCAATTCAATCATAATTGTTTGAAAATAGAGGTGAGCAGGTGAACGATATGTTAATTAGTCTTGCAATCCCAGTTTTTGCTTTGTTAGTTATTGGTGGtattat                                                                               <  1:175909/141‑1 (MQ=255)                                                   tACAAAAATTAGAATGATTCAATTCAATCATAATTGTTTGAAAATAGAGGTGAGCAGGTGAACGATATGTTAATTAGTCTTGCAATCCCAGTTTTTGCTTTGTTAGTTATTGGTGGTATTATTTGGATGATTATAGAAGGt                                                            <  1:88660/141‑1 (MQ=255)                                                              gAATGATTCAATTCAATCATAATTGTATGAAAATAGAGGTGAGCAGGTGAACGATATGTTAATTAGTCTTGCAATCCCAGTTTTTGCTTTGTTAGTTATTGGTAGTATTATTTGGATGATTATAGAAGGTATAGTACatat                                                 <  2:257758/141‑1 (MQ=255)                                                              gAAGGATTCAATGCAATCATAATTGTGTGAAAATAGAGGTGAGCAGGTTAACGATATGTTAATTAGTCTTGCAATCCCAGTTTTTGCTTTGTTAGTTATTGGTGGTATTATTTGGATGATTATAGAAGGTATAGTACatat                                                 <  2:243931/141‑1 (MQ=255)                                                                    ttcaattcaaTCATAATTGTTTGAAAATAGAGGTGAGCAGGTGAACGATATGTTAATTAGTCTTGCAATCCCAGTTTTTGCTTTGTTAGTTATTGGTGGTATTATTTGGATGATTATAGAAGGTATAGTACATATTTCaaa                                           <  1:240530/141‑1 (MQ=255)                                                                                            aaaTAGAGGTGAGCAGGTGAACGATATGTTAATTAGTCTTGCAATCCCAGTTTTTGCTTTGTTAGTTATTGGTGGTATTATTTGGATGATTATAGAAGGTATAGTACATATTTCAAAAAAGAATAAAGCAATTGATAACtt                   >  1:178621/1‑141 (MQ=255)                                                                                                    gTGAGCAGGTGAACGATATGTTAATTAGTCTTGCAATCCCAGTTTTTGCTTTGTTAGTTATTGGTGGTATTATTTGGATGATTATAGAAGGTATAGTACATATTTCAAAAAAGAATAAAGCAATTGATAACTTTTTTAAcc           <  1:158594/141‑1 (MQ=255)                                                                                                       agaaGGTGAAATGTATGTTAATTAGTTTTGAAATACCAGTTTTTGCTTTGTTAGTTATTGGTGGTATTATTTGGATGATTATAGAAGGTATAGTACATATTTGATGTAAGTATAAAGCAATTGATAACTTTTTTAACCAAg        <  2:19859/138‑1 (MQ=255)                                                                                                          aGGTGAACGATATGTTAATTAGTCTTGCAATCCCAGTTTTTGCTTTGTTAGTTATTGGTGGTATTATTTGGATGATTATAGAAGGTATAGTACATATTTCAAAAAAGAATAAAGCAATTGATAACTTTTTTAACCAAGTta     <  1:165351/141‑1 (MQ=255)                                                                                                             tGAACGATATGTTAATTAGACTTGCAATACCCGTTTAGGCGATGTTAGTTATTGGTGGTATTATTTGGATGATTATAGAAGGTATAGTACCTATTTCAAAAAAGAATAAAGCCATTGATAACTTTTTTAACCAAGTtaata  >  1:79708/1‑141 (MQ=255)                                                                                                                                     |                                                                                                                     ATTTTTGTTATCATAGAGTTAATAAATATAATAAATTAAACAAGTAACTTTACAAAAATTAGAATGATTCAATTCAATCATAATTGTTTGAAAATAGAGGTGAGCAGGTGAACGATATGTTAATTAGTCTTGTAATCCCAGTTTTTGCTTTGTTAGTTATTGGTGGTATTATTTGGATGATTATAGAAGGTATAGTACATATTTCAAAAAAGAATAAAGCAATTGATAACTTTTTTAACCAAGTTAATA  >  USA300TCH1516_ALE/104054‑104302

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑