Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,013,179	A→T	31.1%	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	31.1%	37.8 / 22.1	32	Q19H (CAA→CAT)	USA300HOU_RS10140	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (13/9);  new base T (4/6);  total (17/15)
Fisher's exact test for biased strand distribution p-value = 4.50e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.25e-01

CATGGTTAGTATGTAAGTTAATTTAGTTATTTGCGAAATTGGATTATAATAGTATATATAATATTATGAAATGAGTGAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCAAGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAATTCCTGATGGGGATACTGTTCTTAAATTAAAGGACAATGCAACATATATTTCGCATCATAGAGGTATCACGCA  >  USA300TCH1516_ALE/2013039‑2013313                                                                                                                                             |                                                                                                                                       cATGGTTAGTATGTAAGTTAATTTAGTTATTTGCGAAATTGGATTATAATAGTATATATAATATTATGAAATGAGTGAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCaa                                                                                                                                        >  2:16757/1‑141 (MQ=255)          tATGTAAGTTAAATTAGTTATTTGCGAAATTGGATTATAATAGTATATATAATATTATGAAATGAGTGAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCAAGATCCAGCa                                                                                                                               <  1:152860/141‑1 (MQ=255)                 ttaaaTTTAGGTATTTGCAAAATTGGATTATAATAGTATATATAATATTATGAACTGAGCGGTCGGTGATGGACACTGCAACACTTATCGCAATTGGGGTGGGCCTTACATCACTTGCAACTCATGATCCAGCAATTGCtt                                                                                                                        <  2:122256/138‑1 (MQ=255)                 gTTAATTTAGTTATTTGCGAAATTGGATTATAATAGTATATATAATATTATGAAATGAGTGAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCGACTCAAGATCCAGCAATGGCtt                                                                                                                        <  2:252009/141‑1 (MQ=255)                       ttAGTTATTTGCGAAATTGGATTATAATAGTATATATAATATTATGAAATGAGTGAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCAAGATCCAGCAATGGCTTCTACGt                                                                                                                  >  1:107280/1‑141 (MQ=255)                       ttAGTTATTTGCGAAATTGGATTATAATAGTATATATAATATTATGAAATGAGTGAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCAAGATCCAGCAATGGCTTCTACGt                                                                                                                  >  2:8487/1‑141 (MQ=255)                        tAGTTATTTGCGAAATTGGATTATAATAGTATATATAATATTATGAAATGAGTGAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCATGATCCAGCAATGGCTTCTACGtt                                                                                                                 >  2:127694/1‑141 (MQ=255)                         aGTTATTTGCGAAATTGGATTATAATAGTATATATAATATTATGAAATGAGTGAAATGATATAAACACGGCAAAACATATTTCAATTGGGGTAGAGCGTACAGCACTTGCAACTCAACATCCAGCAACAGGTTCTACGttt                                                                                                                >  1:241981/1‑141 (MQ=255)                              tttGCGAAATTGGATTATAATAGTATATATAATATTATGAAATGAGTGAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCAAGATCCAGCAATGGCTTGTACGTTTGGTGc                                                                                                           >  1:279753/1‑141 (MQ=255)                                   gAAATTGGATTATAATAGTATATATAATATTATGAAATGAGTGAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCATGATCCAGCAATGGCTTCTACGTTTGGTGCAACAg                                                                                                      <  2:100890/141‑1 (MQ=255)                                          gATTATAATAGTATATATAATATTATGAAATGAGTGAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCATGATCCAGCAATGGCTTCTACGTTTGGTGCAACACCTACAAc                                                                                               >  1:256289/1‑141 (MQ=255)                                          gATTATAATAGTATATATAATATTATGAAATGAGTGAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCAAGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAAc                                                                                               >  2:274030/1‑141 (MQ=255)                                                           taataTTATGAAATGAGTGAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCAAGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCAt                                                                              >  1:8981/1‑141 (MQ=255)                                                               tttattaAAGGAGTGAACGGATATGGACACTGCAACACATATCGCAATTGTGGTGGGCCTTACTGCACTTGCAACTCAAGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAATCCTTATTGTTGGTTCATTAAt                                                                          <  2:236365/140‑1 (MQ=255)                                                               attatGAAATGAGTGAACTGATATGGACACTGCAACACATATCGCAATTGCGGTGGGCCTTACGGCACTTGCAACTCAAGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAAGCCTTATTGTTGGTTCATTAAt                                                                          <  2:236268/141‑1 (MQ=255)                                                                    gAAATGAGTGAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCAAGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAAGTCCTg                                                                     <  1:346618/141‑1 (MQ=255)                                                                          aGTGAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCATGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAATTCCTGATgggg                                                               >  2:345295/1‑141 (MQ=255)                                                                           gTGAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCAAGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAATTCCTGATGGGGa                                                              <  1:47591/141‑1 (MQ=255)                                                                                  gATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCAAGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAATTCCTTATGGGGATACTGtt                                                       >  1:11073/1‑141 (MQ=255)                                                                                  gATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCAAGATCCAACAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCCTTGGGTAATTAATTCATGCTCGGCATACTGtt                                                       >  2:60163/1‑141 (MQ=255)                                                                                    tatGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCAAGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAATTCCTGATGGGGATACTGTTCt                                                     <  1:8487/141‑1 (MQ=255)                                                                                          cacTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCATGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAATTCCTGATGGGGATACTGTTCttaaatt                                               >  2:27724/1‑141 (MQ=255)                                                                                              gCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCAAGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAATTCCTGATGGGGATACTGTTCTTAAATTAAAg                                           >  1:258800/1‑141 (MQ=255)                                                                                                   acaTATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCAAGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAATTCCTGATGGGGATACTGTTCTTAAATTAAAGGACaa                                      <  1:157717/141‑1 (MQ=255)                                                                                                       aaccataTTGGGTTGTGCCTTCTAGCACTTGCAACTCATCATCCAGCAATGGCTTCGACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAATTCCTGATGGGGATACTGTTCTTAAATTAAAGGACAATGCa                                  <  2:329471/135‑1 (MQ=255)                                                                                                         cGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCATGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAATTCCTGATGGGGATACTGTTCTTAAATTAAAGGACAATGCAAc                                <  1:201662/141‑1 (MQ=255)                                                                                                                  ggTGGGCCTTACAGCACTTGCAACTCAAGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAATTCCTGATGGGGATACTGTTCTTAAATTAAAGGACAATGCAACATATATTTc                       >  1:47728/1‑141 (MQ=255)                                                                                                                  ggTGGGCCTTACAGCACTTGCAACTCAAGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAATTCCTGATGGGGATACTGTTCTTAAATTAAAGGACAATGCAACATATATTTc                       >  1:277653/1‑141 (MQ=255)                                                                                                                    tGGGCCTTACAGCACTTGCAACTCATGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAATTCCTGATGGGGATACTGTTCTTAAATTAAAGGACAATGCAACATATATTTCGc                     <  1:345295/141‑1 (MQ=255)                                                                                                                    tGGGCCTTACAGCACTTGCAACTCAAGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAATTCCTGATGGGGATACTGTTCTTAAATTAAAGGACAATGCAACATATATTTCGc                     >  1:337994/1‑141 (MQ=255)                                                                                                                          ttACAGCACTTGCAACTCATGATCCAGCAACGGCTTCTACGTTGGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAATTCCTTAGGGGGACACTGTTCTTAAATTAAAGGACAATGCAACATATATTTCGCATCATa               <  1:330936/141‑1 (MQ=255)                                                                                                                                       aaCTCAAGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAATTCCTGATGGGGATACTGTTCTTAAATTAAAGTACAATGCAACATATATTTCGCATCATAGAGGTATCACGCa  >  2:145359/1‑141 (MQ=255)                                                                                                                                       aaCTCAAGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAATTCCTGATGGGGATACTGTTCTTAAATTAAAGGACAATGCAACATATATTTCGCATCATAGAGGTATCACGCa  <  1:187645/141‑1 (MQ=255)                                                                                                                                             |                                                                                                                                       CATGGTTAGTATGTAAGTTAATTTAGTTATTTGCGAAATTGGATTATAATAGTATATATAATATTATGAAATGAGTGAACTGATATGGACACTGCAACACATATCGCAATTGGGGTGGGCCTTACAGCACTTGCAACTCAAGATCCAGCAATGGCTTCTACGTTTGGTGCAACAGCTACAACCCTTATCGTTGGTTCATTAATTCCTGATGGGGATACTGTTCTTAAATTAAAGGACAATGCAACATATATTTCGCATCATAGAGGTATCACGCA  >  USA300TCH1516_ALE/2013039‑2013313

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: ‑