Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,028,269	G→A	84.5%	P126S (CCA→TCA)	USA300HOU_RS10230 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,028,269	0	G	A	84.5%	46.4 / 4.0	26	P126S (CCA→TCA)	USA300HOU_RS10230	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (2/2);  new base A (10/12);  total (12/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.04e-01

TGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACGCACAATAAGTAATAATAAAAAGACGAACAAG  >  USA300TCH1516_ALE/2028136‑2028405                                                                                                                                      |                                                                                                                                         tGCACGTTGCCTAAAATGTGTCTAATAACAATGGTATGATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGATGTTCGt                                                                                                                                   <  2:383863/141‑1 (MQ=255)     cTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGATGTACGGTGCt                                                                                                                               >  1:209686/1‑141 (MQ=255)       ttACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGATGTACGTTGCTCa                                                                                                                             <  2:42579/141‑1 (MQ=255)       ttACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGATGTACGTTGCTCa                                                                                                                             >  1:89013/1‑141 (MQ=255)                    gtCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGATGTACGTTGCTCACCAAACCACtttt                                                                                                                >  1:140606/1‑141 (MQ=255)                                  gTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTTTACGTTGCTCACCAAACCACTTTTGTTTAATACAAGAt                                                                                                  >  2:134550/1‑141 (MQ=255)                                  gTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAACGAt                                                                                                  >  2:79841/1‑141 (MQ=255)                                  gTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGATGTACGTTGCTCACCAAACCACTTTTGTTTAATACAAAAt                                                                                                  >  2:286523/1‑141 (MQ=255)                                  gTATTATTTTCCTGAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGAAAGCAAGTCCAGGTTGAATTTGTACATCTTCCCACTTATATACGTTGACTGATGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGAt                                                                                                  <  2:167381/141‑1 (MQ=255)                                            ccTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGATGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCa                                                                                        <  1:19619/141‑1 (MQ=255)                                                 atatTTGCAGGTTTTGTTGAGTCGATATGGACGTCGCACAGTGCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGATGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAAcc                                                                                   <  2:145426/141‑1 (MQ=255)                                                      tGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGATGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATc                                                                              <  2:48745/141‑1 (MQ=255)                                                                  tAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGATGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCTCGactcc                                                                  >  2:264079/1‑139 (MQ=255)                                                                          tatGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGATGTACGTTGCTCACCAACCCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTg                                                          >  2:28983/1‑141 (MQ=255)                                                                             gTAGTTCTCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGATGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGtt                                                       <  2:385218/141‑1 (MQ=255)                                                                             gTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGATGTACGTTGCTAACAGGATTGGGGTTGTTTAATTCATAAGTGTCAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGtt                                                       <  1:302799/141‑1 (MQ=255)                                                                                          tCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTAt                                          <  2:381359/141‑1 (MQ=255)                                                                                             aTGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGATGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTaa                                       <  2:16801/141‑1 (MQ=255)                                                                                                   aaTTTGTACATCTTCCCACTTATATACATAAACTGATGTACGGTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACg                                 <  2:309107/141‑1 (MQ=255)                                                                                                      ttGTACATCTTCCCACTAATATACATAAACTGATGTACGTTGCTCATCAAACCACTTTTGTTTAATAAAAAATGGTGAAGTCATAACCTCATACATCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACGcac                              <  2:197472/141‑1 (MQ=255)                                                                                                            aTCTTCCCACTTATATACATAAACTGATGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACGCACAATAAg                        >  1:30402/1‑141 (MQ=255)                                                                                                             tCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCACCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACGCACAATAAGt                       <  1:209668/141‑1 (MQ=255)                                                                                                                 cccACTTATATACATAAACTGATGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCCTCCGTCGCAACTACTTTTTTTGGTTTAATCTTCTGGATGAAAGATCGCACAGTAAGtacta                   >  1:173751/1‑141 (MQ=255)                                                                                                                     cTTATATACATAAACTGATGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCACCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTAATAAATAACTCACAATAAGtcataataa               >  2:119735/1‑141 (MQ=255)                                                                                                                      ttATATACATAAACTGATGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACGCACAATAAGAAATAATaaa              >  1:332406/1‑141 (MQ=255)                                                                                                                                  aCTGATGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACGCACAATAAGTAATAATAAAAAGACGAACAAg  <  2:140606/141‑1 (MQ=255)                                                                                                                                      |                                                                                                                                         TGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACGCACAATAAGTAATAATAAAAAGACGAACAAG  >  USA300TCH1516_ALE/2028136‑2028405

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: ‑