Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,981,089	T→G	41.8%	T105P (ACT→CCT)	USA300HOU_RS09870 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,981,089	0	T	G	41.8%	4.3 / 6.7	16	T105P (ACT→CCT)	USA300HOU_RS09870	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (6/3);  new base G (4/3);  total (10/6)
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

TCTTCTTTAGCATTTCTGTTAAAGTATGTTTCAGCTTCTCTCATTTTAGAAGTACCGAAAATTGGTTGGTTATCTGGATTTAATACACGATAAATATTGCTTACTTTGTTACTTTGTAAAATGTACCCATTACGAGTCTCAATGTTATTCCAATAAATATCACTTGTTGGTGCATGGTTTGGATATGCACAGTGATTTCTTGAAATTGTTTGAACGATTTCTAATGGATCACAGCCAAATGTACTGTTTAATACTTCAGAGTCTCTGAA  >  USA300TCH1516_ALE/1980953‑1981221                                                                                                                                         |                                                                                                                                     tcttctTTAGCATTTCTGTTAAAGTATGTTTCAGCTTCTCTCATTTTAGAAGTACCGAAAATTGGTTGGTTATCTGGATTTAATACACGATAAATATTGCTTACTTTGTTACTTTGTAAAATGTACCCATTACGAGGCTCa                                                                                                                                  >  2:84186/1‑141 (MQ=255)     cttTAGCATTTCTGTTAAAGTATGTTTCAGCTTCTCTCATTTTAGAAGTACCGAAAATTGGTTGGTTATCTGGATTTAATACACGATAAATATTGCTTACTTTGTTACTTTGTAAAATGTACCCATTACGAGTCTCAATGt                                                                                                                              >  1:109574/1‑141 (MQ=255)                   ttAAAGTATGTTTCAGCTTCTCTCATTTTAGAAGTACCGAAAATTGGTTGGTTATCTGGATTTAATACACGATAAATATTGCTTACTTTGTTACTTTGTAAAATGTACCCATTACGAGGCTCAATGTTATTCCaataaata                                                                                                                >  1:287340/1‑141 (MQ=255)                    tAAAGTATTTTTCAGCTTCTCTAATTTAAGAAGTACCGAAAATTGGTTGGTTATCTGGATTTAATACACGATAAATATTGCTTACTTTGTTACTTTGTAAAATGTACCAATTACGAGGCAAAAAGTAATTCCGAAAAatat                                                                                                               <  2:37743/141‑1 (MQ=255)                      aaGTATGTTTCAGCTTCTCTCATTTTATAAGTACCGAAAATTGGTTGGTTATCTGGATTTAATACACGATAAATATTGCTTACTTTGTTACTTTGTAAAATGTACCCATTACGAGTCTCAATGTTATTCCAATAAATATCa                                                                                                             <  2:184255/141‑1 (MQ=255)                           tGTTTCAGCTTCTCTCATTTTAGAAGTACCGAAAATTGGTTGGTTATCTGGATTTAATACACGATAAATATTGCTTACTTTGTTACTTTGTAAAATGTACCCATTACGAGTCTCAATGTTATTCCAATAAATATCACttgt                                                                                                        >  2:137428/1‑141 (MQ=255)                            gTTTCAGCTTCTCTCATTTTAGAAGTACCGAAAATTGGTTGGTTATCTGGATTTAATACACGATAAATATTGCTTACTTTGTTACTTTGTAAAATGTACCCATTACGAGTCTCAATGTTATTCCAATAAATATCACttgtt                                                                                                       >  1:288218/1‑141 (MQ=255)                                            ttttAGAAGTACCGAAAATTGGTTGGTTATCTGGATTTAATACACGATAAATATTGCTTACTTTGTTACTTTGTAAAATGTACCCATTACGAGTCTCAATGTTATTCCAATAAATATCACTTGTTGGTGCATGGTTTGGat                                                                                       >  1:107068/1‑141 (MQ=255)                                                          aaaaTTGGTTGGTTATCTGGATTTAATACACGATAAATATTGCTTACTTTGTTACTTTGTAAAATGTACCCATTACGAGGCTCAATGTTATTCCAATAAATATCACTTGTTGGTGCATGGTTTGGATATGCACCGTGAttt                                                                         >  1:99157/1‑141 (MQ=255)                                                                                          aTAAATATTGCTTACTTTTTTACTTTGTAAAATGTACCCATTACGAGTCTCAATGTTATTCCAATAAATATCACTTGTTGGTGCATGGTTTGGATATGCACAGTGATTTCTTGAAATTGTTTGAACGATTTCTAATGGATc                                         <  1:119049/141‑1 (MQ=255)                                                                                               tatTCCTTACTTTGTTACTGTGGAAAATGTACTCATTACGAGGCTTATTGTTATTCTAATTAATATCTCTTGTTGTTGCATGGTTTAGTTACGCACAGTGATTTCTTTAAATTGTTTGAACGATTTCTAATGGATGACAgg                                    <  2:191578/141‑2 (MQ=255)                                                                                                          ttgttactttgtAAAATGTACCCATTACGAGTCTCAATGTTATTCCAATAAATATCACTTGTTGGTGCATGGTTTGGATATGCACAGTGATTTCTTGAAATTGTTTGAACGATTTCTAATGGATCACAGCCAAATGTACTg                         >  2:105219/1‑141 (MQ=255)                                                                                                             ttactttgtAAAATGTACCCATTACGAGGCTCAATGTTATTCCAATAAATATCACTTGTTGGTGCATGGTTTGGATATGCACAGTGATTTCTTGAAATTGTTTGAACGATTTCTAATGGATCACAGCCAAATGTACTGttt                      <  1:191486/141‑1 (MQ=255)                                                                                                                  ttgtAAAATGTACCCATTACGAGGCTCAATGTTATTCCAATAAATATCACTTGTTGGTGCAGGGTTTGGATATGCACAGTGATTTCTTGAAATGGTTTGAACGATTTCTAATGGATGACAGCCAAATGTGCTGTTTAATAc                 >  1:4518/1‑141 (MQ=255)                                                                                                                     tAAAATGTACCCATTACGAGTCTCAATGTTATTCCAATAAATATCACTTGTTGGTGCATGGTTTGGATATGCACAGTGATTTCTTGAAATTGTTTGAACGATTTCTAATGGATCACAGCCAAATGTACTGTTTAATACTTc              <  1:232450/141‑1 (MQ=255)                                                                                                                                 aTTACGAGTCTCAATGTTATTCCAATAAATATCACTTGTTGGTGCATGGTTTGGATATGCACAGTTATTTCTTGAAATTTTTTGAACGGTTTCTAATGGATTACAGCCAAATGTACTGTTTAATAATTCAGTGTCTCTGaa  >  2:19568/1‑141 (MQ=255)                                                                                                                                         |                                                                                                                                     TCTTCTTTAGCATTTCTGTTAAAGTATGTTTCAGCTTCTCTCATTTTAGAAGTACCGAAAATTGGTTGGTTATCTGGATTTAATACACGATAAATATTGCTTACTTTGTTACTTTGTAAAATGTACCCATTACGAGTCTCAATGTTATTCCAATAAATATCACTTGTTGGTGCATGGTTTGGATATGCACAGTGATTTCTTGAAATTGTTTGAACGATTTCTAATGGATCACAGCCAAATGTACTGTTTAATACTTCAGAGTCTCTGAA  >  USA300TCH1516_ALE/1980953‑1981221

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: ‑