Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,013,179	A→T	28.0%	Q19H (CAA→CAT)	USA300HOU_RS10140 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,013,179	0	A	T	28.0%	41.4 / 19.2	25	Q19H (CAA→CAT)	USA300HOU_RS10140	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (9/9);  new base T (4/3);  total (13/12)
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

TGGTTAGTATGTAAGTTAATTTAGTTATTTGCGAAATTGGATTATAATAGTATATATAATATTATGAAATGAGTGAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCAAGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAATTCCTGATGGGGATACTGTTCTTAAATTAAAGGACAATGCAACATATATTTCGCATCATAGAGGTATCACGCA  >  USA300TCH1516_ALE/2013041‑2013313                                                                                                                                           |                                                                                                                                       tGGTTAGTATGTAAGTTAATTTAGTTATTTGCGAAATTGGATTATAATAGTATATATAATATTATGAAATGAGTGAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCAAGa                                                                                                                                      <  2:21643/141‑1 (MQ=255) tGGTTAGTATGTAAGTTAATTTAGTTATTTGCGAAATTGGATTATAATAGTATATATAATATTATGAAATGAGTGAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCAAGa                                                                                                                                      <  1:49697/141‑1 (MQ=255)       gTATGTAAGTTAATTTAGTTATTTGCGAAATTGGATTATAATAGTATATATAATATTATGAAATGAGTGAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCAAGATCCAGc                                                                                                                                <  1:336493/141‑1 (MQ=255)             aaGTTAATTTAGTTATTTGCGAAATTGGATTATAATAGTATATATAATATTATGAAATGAGTGAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCATGATCCAGCAATGGc                                                                                                                          >  2:86044/1‑141 (MQ=255)                  aaTTTAGTTATTTGCGAAATTGGATTATAATAGTATATATAATATTATGAAATGAGTGAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCAAGATCCAGCAATGGCTTCTa                                                                                                                     <  2:87663/141‑1 (MQ=255)                    tttAGTTATTTGCGAAATTGGATTATAATAGTATATATAATATTATGAAATGAGTGAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCAAGATCCAGCAATGGCTTCTACg                                                                                                                   >  1:91789/1‑141 (MQ=255)                    tttAGTTATTTGCGAAATTGGATTATAATAGTATATATAATATTATGAAATGAGTGAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCAAGATCCAGCAATGGCTTCTACg                                                                                                                   >  1:91829/1‑141 (MQ=255)                     ttAGTTATTTGCGAAATTGGATTATAATAGTATATATAATATTATGAAATGAGTGAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCAAGATCCAGCAATGGCTTCTACGt                                                                                                                  >  2:33490/1‑141 (MQ=255)                                  aaaTTGGATTATAATAGTATATATAATATTATGAAATGAGTGAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCAAGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGc                                                                                                     >  1:94929/1‑141 (MQ=255)                                           tataATAGTATATATAATATTATGAAATGAGTGAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCAAGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCt                                                                                            <  1:351558/141‑1 (MQ=255)                                                           atatTATGAAATGAGTGAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGGCTTACAGCACTTGCAACTCAAGATCCAGCAATGGCTTCTACGTTTGGTGCAACCGCTACAACCCTTATCGTTGGTTCAttt                                                                            >  2:131314/1‑140 (MQ=255)                                                              ttatGAAATGAGTGAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCATGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAAtt                                                                         >  1:133551/1‑141 (MQ=255)                                                                   aaaTGAGTGAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCATGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAATTCCTGa                                                                    >  1:39958/1‑141 (MQ=255)                                                                        aGTGAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCGTACAGCACTTGCAACTCATGATCCTTCAAGTGCTTCTACTTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAATTCCTGATgggg                                                               >  1:225490/1‑141 (MQ=255)                                                                           gAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCAAGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAATTCCTGATGGGGATa                                                            >  2:261717/1‑141 (MQ=255)                                                                            aaCTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCAAGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAATTCCTGATGGGGATAc                                                           >  2:373245/1‑141 (MQ=255)                                                                                          cTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCAAGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAATTCCTGATGGGGATACTGTTCttaaattaa                                             <  2:273917/141‑1 (MQ=255)                                                                                                        gCAATTGGGGTGGGCCTTACAGCACTTGCAACTCAAGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAATTCCTGATGGGGATACTGTTCTTAAATTAAAGGACAATGCAACa                               <  2:95128/141‑1 (MQ=255)                                                                                                              ggggTGGGCCTTACAGCACTTGCAACTCAAGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAATTCCTGATGGGGATACTGTTCTTAAATTAAAGGACAATGCAACATATAtt                         <  1:308508/141‑1 (MQ=255)                                                                                                                ggTGGGCCTTACAGCACTTGCAACTCAAGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAATTCCTGATGGGGATACTGTTCTTAAATTAAAGGACAATGCAACATATATTTc                       <  2:119775/141‑1 (MQ=255)                                                                                                                 gTGGGCCTTACAGCACTTGCAACTCATGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAATTCCTGATGGGGATACTGTTCTTAAATTAAAGGACAATGCAACATATATTTCg                      <  2:327759/141‑1 (MQ=255)                                                                                                                  tGGGCCTTACCGCACTTGCAACTCCTGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTCATTCCTGATGGGGATACTCTGCTTAAATTAAAGGACAATGCCACATATATTTCGc                     <  2:225490/141‑1 (MQ=255)                                                                                                                                cTTGCAACTCATGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAATTCCTGATGGGGATACTGTTCTTAAATTAAAGGACAATGCAACATATATTTCGCATCATAGAGGTATc       <  2:133551/141‑1 (MQ=255)                                                                                                                                     aaCTCAAGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAATTCCTGATGGGGATACTGTTCTTAAATTAAAGGACAATGCAACATATATTTCGCATCATAGAGGTATCACGCa  >  2:371526/1‑141 (MQ=255)                                                                                                                                     aaCTCAAGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAATTCCTGATGGGGATACTGTTCTTAAATTAAAGGACAATGCAACATATATTTCGCATCATAGAGGTATCACGCa  >  2:57985/1‑141 (MQ=255)                                                                                                                                           |                                                                                                                                       TGGTTAGTATGTAAGTTAATTTAGTTATTTGCGAAATTGGATTATAATAGTATATATAATATTATGAAATGAGTGAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCAAGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAATTCCTGATGGGGATACTGTTCTTAAATTAAAGGACAATGCAACATATATTTCGCATCATAGAGGTATCACGCA  >  USA300TCH1516_ALE/2013041‑2013313

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