Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,226,031	G→T	15.2%	V40L (GTA→TTA)	USA300HOU_RS06095 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,226,031	0	G	T	15.2%	63.6 / 2.5	29	V40L (GTA→TTA)	USA300HOU_RS06095	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (13/11);  new base T (2/3);  total (15/14)
Fisher's exact test for biased strand distribution p-value = 6.51e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACTTAAGAGGAGAAAGTTTATGAAAAAGACACTGGGATGTTTACTTTTAATTATGCTTTTAGTCGTAGCAGGTTGTTCTTTTGGTGGGAATCATAAATTATCATCAAAGAAATCAGAAGAATCAAAACAAGAAACTGTAAAAAAAGAATCGGAAGAAGAGAAAGATCCAGATTTAGAGAAATATGAAGAAATAGAGAAGAAAATGAAAGGAATTAAAGATGCGCCATCTCTTGATAAGTTGGATCCATTAATGACAGAAAAGTCGTTTACGAA  >  USA300TCH1516_ALE/1225895‑1226167                                                                                                                                         |                                                                                                                                         aCTTAAGAGGAGAAAGTTTATGAAAAAGAAACTGGGATGTTTCATTTTAATTATTCTTTTTGTCGTAGCAGGTTGTTCTTTTGGTGGGGATCATAAATTATCATCGAAGAAATACGAAGAATCAAAACAAGAAACTGTaaa                                                                                                                                      >  2:38951/1‑141 (MQ=255)         ggagAAAGTTTATGAAAAAGACACTGGGATGTTTACTTTTAATTATGCTTTTAGTCGTAGCAGGTTTTTCTTTTGGTGGGAATCAGAAATTATCATCAAAGAAATCAGAAGAATCAAAACAATAAACTGTAAAAAAAGAAt                                                                                                                              <  2:113350/141‑1 (MQ=255)            gaAAGTTTATGAAAAAGACACTGGGATGTTTACTTTTAATTATGCTTTTAGTCGTAGCAGGTTGTTCTTTTGGTGGGAATCATAAATTATCATCAAAGAAATCAGAAGAATCAAAACAAGAAAATGTAAAAAAAGAATCgg                                                                                                                           >  2:151635/1‑141 (MQ=255)             aaaGTTTATGAAAAAGACACTTGGATGTTTACTTTTAATTATTCTTTTAGTCGTAGCAGGTTGTTCTTTTGGTGGGAATCATAAATTATCATCAAAGAAATCAGAAGAATCAAAACAAGAAACTGTAAAAAAAGAATCGga                                                                                                                          <  1:327367/141‑1 (MQ=255)                    aTGAAAAAGACACTGGGATGTTTACTTTTAATTATGCTTTTAGTCGTAGCAGGTTGTTCTTTTGGTGGGAATCATAAATTATCATCAAAGAAATCAGAAGAATCAAAACAAGAAACTGTAAAAAAAGAATCGGAAGAagag                                                                                                                   >  2:138968/1‑141 (MQ=255)                       aaaaaGACACTGGGATGTTTACTTTTAATTATGCTTTTAGTCGTAGCAGGTTGTTCTTTTGGTGGGAATCATAAATTATCATCAAAGAAATCAGAAGAATCAAAACAAGAAACTGTAAAAAAAGAATCGGAAGAAGAGaaa                                                                                                                <  2:319274/141‑1 (MQ=255)                         aaaGACACTGGGATGTTTACTTTTAATTATGCTTTTAGTCGTAGCAGGTTGTTCTTTTGGTGGGAATCATAAATTAGCATCAAATAAATCAGAAGAATCAAAACAAGAAACTGTAAAAAAAGAATCGGAAAAAGAGAAAGa                                                                                                              >  2:122221/1‑141 (MQ=255)                                       gTTTACTTTTAATTTTGCTTTTAGTCGTAGCAGGTTGTTCTTTTGGTGGGAATCATAAATTATCATCAAAGAAATCAGAAGAATCAAAACAAGAAACTGTAAAAAAAGAATCGGAAGAAGAGAAAGATCCAGATTTAgaga                                                                                                <  2:129349/141‑1 (MQ=255)                                                 aaTTATGCTTTTAGTCGTAGCAGGTTGTTCTTGTGGTGGGAATCATAAATTATCATCAAAGAAATCAGAAGAATCAAAACAAGAAACTTTAAAAAAAGAATCGGAAGAAGAGAAAGATCCAGATTTAGAGAAATATgaaga                                                                                      <  2:3978/141‑1 (MQ=255)                                                      tGCTTTTAGTCGTAGCAGGTTGTTCTTATGGTGGGAATCATAAATTATCATCAAAGAAATCAGAAGAATCAAAACAAGAAACTGTAAAAAAAGAATCGGAAGAAGAGAAAGATCCAGATTTAGAGAAATATGAAGAAATag                                                                                 <  2:216518/141‑1 (MQ=255)                                                             aGTCGTAGCAGGTAGTTCTTTTGGTGGGAATCATAAATTATCATCAAAGAAATCAGAAGAATCAAAACAAGAAACTTTAAAAAAAGAATCGGAAGAAGAGAAAGATCCAGATTTAGAGAAATATGAAGAAATAGAgaagaa                                                                          <  2:248479/141‑1 (MQ=255)                                                              gTCGTAGCAGGTTGTTCTTTTGGTGGGAATCATAAATTATCATCAAAGAAATCAGAAGAATCAAAACAAGAAACTGTAAAAAAAGGATCGGAAGAAGAGAAAGATCCAGATTTAGAGAAATATGAAGAAATAGAGAAGaaa                                                                         >  1:198036/1‑141 (MQ=255)                                                                       ggTTGTTCTTTTGGTGGGAATCATAAATTATCATCAAAGAAATCAGAAGAATCAAAACAAGAAACTTTAAAAAAAGAATCGGAAGAAGAGAAAGATCCAGATTTAGAGAAATATGAAGAAATAGAGAAGAAAATGAAAGGa                                                                >  2:279221/1‑141 (MQ=255)                                                                              cTTTTGGTGGGAATCATAAATTATCATCAAAGAAATCAGAAGAATCAAAACAAGAAACTGTAAAAAAAGAATCGGAAGAAGAGAAAGATCCAGATTTAGAGAAATATGAAGAAATAGAGAAGAAAATGAAAGGAATTAAAg                                                         >  2:250749/1‑141 (MQ=255)                                                                                tttGGTGGGAATCATAAATTATCATCAAAGAAATCAGAAGAATCAAAACAAGAAACTGTAAAAAAAGAATCGGAAGAAGAGAAAGATCCAGATTTAGAGAAATATGAAGAAATAGAGAAGAAAATGAAAGGAATTAAAGAt                                                       >  1:24119/1‑141 (MQ=255)                                                                                               aaaTTATCATCAAAGAAATCAGAAGAATCAAAACAAGAAACTGTAAAAAAAGAATCGGAAGAAGAGAAAGATCCAGATTTAGAGAAATATGAAGAAATAGAGAAGAAAATGAAAGGAATTAAAGATGCGCCATCTCTTGAt                                        <  1:227363/141‑1 (MQ=255)                                                                                                     tcatcaAAGAAATCAGAAGAATCAAAACAAGAAACTGTAAAAAAAGAATCGGAAGAAGAGAAAGATCAAGATTTAGAGAAATATGAAGAAATAGAGAAGAAAATGAAAGGAATTAAAGATGCGCCATCTCTTGATAAGTTg                                  >  2:53590/1‑141 (MQ=255)                                                                                                         caAAGAAATCAGAAGAATCAAAACAAGAAACTGTAAAAAAAGAATCGGAAGAAGAGAAAGATCCAGATTTAGAGAAATATGAAGAAATAGAGAAGAAAATGAAAGGAATTAAAGATGCGCCATCTCTTGATAAGTTGGATc                              <  1:186024/141‑1 (MQ=255)                                                                                                            aGAAATCAGAAGAATCAAAACAAGAAACTGTAAAAAAAGAATCGGAAGAAGAGAAAGATCCAGATTTAGAGAAATATGAAGAAATAGAGAAGAAAATGAAAGGAATTAAAGATGCGCCATCTCTTGATAAGTTGGATCCAt                           >  2:195189/1‑141 (MQ=255)                                                                                                             gAAATCAGAAGAATCAAAACAAGAAACTGTAAAAAAAGAATCGGTAGAAGAGAAAGATCCAGATTTAGAGAAATATGAAGAAATAGAGAAGAAAATGAAAGGAATTAAAGATGCGCCATCTCTTGATAAGTTGGATCCAtt                          >  1:237294/1‑141 (MQ=255)                                                                                                                 tCAGAAGAATCAAAACAAGAAACTTTATAAAAAGAATCGTAAGAAGAGAAAGATCCAGATTTAGAGAAATATGAAGAAATAGAGAAGAAAATGAAAGGAATTAAAGATGCGCCATCTCTTGATAAGTTGGATCCATTAATg                      >  1:86649/1‑141 (MQ=255)                                                                                                                    gaagaaTCAAAACAAGAAACTGTAAAAAAAGAATCGGAAGAAGAGAAAGATCCAGATTTAGAGAAATATGAAGAAATAGAGAAGAAAATGAAAGGAATTAAAGATGCGCCATCTCTTGATAAGTTGGATCCATTAATGACa                   >  2:102238/1‑141 (MQ=255)                                                                                                                    gaagaaTCAAAACAAGAAACTGTAAAAAAAGAATCGGAAGAAGAGAAAGATCCAGATTTAGAGAAATATGAAGAAATAGAGAAGAAAATGAAAGGAATTAAAGATGCGCCATCTCTTGATAAGTTGGATCCATTAATGACa                   <  1:259901/141‑1 (MQ=255)                                                                                                                     aagaaTCAAAACAAGAAAAGGTAAACAAAGAATCGGAAGAAGAGAAAGATCCAGATTTAGATAAATATGAAGAAATAGAGAAGAAAATGAAAGGAATTAAAGATGCGCCATCTCTTGATAAGTTGGATCCATTAATGACAg                  <  1:43170/141‑1 (MQ=255)                                                                                                                       gaaTCAAAACAAGAAACTGTAATGTAGTAATCGGAAGAAGAGAAAGATCCAGATTTAGAGAAATATGAAGAAATAGAGAAGAAAATGAAAGGAATTAAAGATGCGCCATCTCTTGATAAGTTGGATCCATTAATGACAGaa                >  1:82464/1‑141 (MQ=255)                                                                                                                          tCAAAACAAGAAACTGTAAAAAAAGAATCGGAAGAAGAGAAAGATCCAGATTTAGAGAAATATGAAGAAATAGAGAAGAAAATGAAAGGAATTAAAGATGCGCCATCTCTTGATAAGTTGGATCCATTAATGACAGAAAAg             <  1:138968/141‑1 (MQ=255)                                                                                                                           cAAAACAAGAAACTTTAAAAAAAGAATCGGAAGAAGAGAAAGATCCAGATTTAGAGAAATATGAAGAAATAGAGAAGAAAATGAAAGGAATTAAAGATGCGCCATCTCTTGATAAGTTGGATCCATTAATGACAGAAAAGt            <  1:279221/141‑1 (MQ=255)                                                                                                                                cAAGAAACTGTAAAAAAAGAATCGGAAGAAGAGAAAGATCCAGATTTAGAGAAATATGAAGAAATAGAGAAGAAAATGAAAGGAATTAAAGATGCGCCATCTCTTGATAAGTTGGATCCATTAATGACAGAAAAGTCGttt       >  2:238791/1‑141 (MQ=255)                                                                                                                                     aaCGGTAAAAAAAGAATCGGAAGAAGAGAAAGATCCAGATTTAGAGAAATATGAAGAAATACAGAAGAAAATGAAAGGAATTAAAGATGCGCCATCTCTTGATAAGTTGGATACATTAATGACAGAAAAGTCGTTTACGaa  <  1:223199/141‑1 (MQ=255)                                                                                                                                         |                                                                                                                                         ACTTAAGAGGAGAAAGTTTATGAAAAAGACACTGGGATGTTTACTTTTAATTATGCTTTTAGTCGTAGCAGGTTGTTCTTTTGGTGGGAATCATAAATTATCATCAAAGAAATCAGAAGAATCAAAACAAGAAACTGTAAAAAAAGAATCGGAAGAAGAGAAAGATCCAGATTTAGAGAAATATGAAGAAATAGAGAAGAAAATGAAAGGAATTAAAGATGCGCCATCTCTTGATAAGTTGGATCCATTAATGACAGAAAAGTCGTTTACGAA  >  USA300TCH1516_ALE/1225895‑1226167

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑