Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_007793	1,442,893	T→C	Y16C (TAT→TGT)	SAUSA300_RS07125 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007793	1,442,893	0	T	C	98.8%	214.0 / ‑5.1	80	Y16C (TAT→TGT)	SAUSA300_RS07125	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base C (77/2);  total (78/2)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.53e-01

AGTAGTTGAAAATGATTATCAATACCATATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTTATAAC  >  NC_007793/1442866‑1442990                            |                                                                                                   tcctattGAAAATGATTATCAATACCACATAGAACATCACCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGcc                            >  1:4183077/6‑100 (MQ=255)  ccgcaggAAAATGATTATCAATACCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGcca                           >  1:5083488/7‑99 (MQ=255)   ctattGAAAATGATTATCAATCCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCg                          <  1:4608532/97‑1 (MQ=255)    tcctccaaaTTATTATC‑TTACCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCgca                        <  1:5324794/94‑3 (MQ=255)         gcaaTGATTATCAATACCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAg                   >  1:442024/3‑100 (MQ=255)              catgaccAATACCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAGATATTCCCCTTTTATATGCCCGTAA‑AAGACAat              >  1:1250114/7‑100 (MQ=255)               aTTATCAATACCACATAGAACATCCCCTCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTagatcggaaga              >  1:609080/1‑90 (MQ=255)                  aTCAATACCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGatcggaaga          >  1:4445033/1‑92 (MQ=255)                    cAATACCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGt        >  1:5533571/1‑100 (MQ=255)                     aaTACCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGtt       >  1:4382396/1‑100 (MQ=255)                      ctACCATATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTCTTATATGCCCGTAA‑AAGACAATATACGTta      >  1:3732662/2‑100 (MQ=255)                      aTACCACATAGAACATCCTCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTta      >  1:1215871/1‑100 (MQ=255)                      aTACCACATAGAACATCCCCCCCACCACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTta      >  1:5047304/1‑100 (MQ=255)                      aTACCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCACATATTCCCCTTTTTTATGCCCGTAA‑TAGACAATATACGTta      >  1:5640738/1‑100 (MQ=255)                      aTACCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGGCAATATACGTta      >  1:3529859/1‑100 (MQ=255)                      aTACCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACagatcggaaga      >  1:4094106/1‑90 (MQ=255)                      aTACCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACagatcggaaga      >  1:4392441/1‑90 (MQ=255)                      aTACCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAagatcggaag      >  1:3975423/1‑94 (MQ=255)                      aTACCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTta      >  1:4607826/1‑100 (MQ=255)                      aTACCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTta      >  1:1465378/1‑100 (MQ=255)                      aTACCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTta      >  1:4227490/1‑100 (MQ=255)                      aTACCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTta      >  1:792044/1‑100 (MQ=255)                      aTACCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTta      >  1:2067969/1‑100 (MQ=255)                      aTACCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTta      >  1:4596603/1‑100 (MQ=255)                      aTACCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTta      >  1:3242822/1‑100 (MQ=255)                      aTACCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTta      >  1:5603251/1‑100 (MQ=255)                      aTACCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTta      >  1:4654632/1‑100 (MQ=255)                      aTACCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTta      >  1:3504073/1‑100 (MQ=255)                      aTACCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTta      >  1:2249204/1‑100 (MQ=255)                      aTACCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTta      >  1:22452/1‑100 (MQ=255)                       tACCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtat     >  1:177056/1‑100 (MQ=255)                       tACCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtat     >  1:2521386/1‑100 (MQ=255)                       tACCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtat     >  1:4950932/1‑100 (MQ=255)                       tACCACATAGAACATCCCCCCCACAACGTTTCGCTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtat     >  1:4877144/1‑100 (MQ=255)                       caCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtat     >  1:3945244/2‑100 (MQ=255)                       caCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtat     >  1:2657272/2‑100 (MQ=255)                       atccACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAT‑AAGACAATATACGTtat     >  1:1698053/3‑100 (MQ=255)                       agccACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtat     >  1:2356049/3‑100 (MQ=255)                       aaCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATTCCCGTAA‑AAGACAATATACGTtat     >  1:1665807/2‑100 (MQ=255)                       aaCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtat     >  1:2885427/2‑100 (MQ=255)                        cccACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAAGAAAACAataaaacgttc     >  1:523998/2‑92 (MQ=255)                        cccACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:3636847/2‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTTTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:233689/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATCTTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:5559293/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAagatcggaagag    >  1:4621080/1‑92 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:5237576/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:4724074/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:2314205/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:2276862/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:2189104/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:5094306/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:5124916/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:923002/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:2049178/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:1778651/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:616188/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:640286/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:1505988/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:3694628/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:4172372/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:3709657/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:3879545/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:1154694/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:321246/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:4053331/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:3158566/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:4155448/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:2366738/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:311973/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:2985945/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:2909958/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:4432074/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:2853076/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:4499490/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:2560140/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTCATATGCCCGTAA‑AAGACAATATACGTtata    >  1:1960348/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGACATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:3891804/1‑100 (MQ=255)                        aCCACATAGAACATCCCCCCCACAACGTTTCGCTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTtata    >  1:514138/1‑100 (MQ=255)                        aCCACATAGAACAT‑CCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTTATaa   >  1:592052/1‑100 (MQ=255)                         ccACATAGAACAT‑CCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCCAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTTATaac  >  1:3117673/1‑100 (MQ=255)                            |                                                                                                   AGTAGTTGAAAATGATTATCAATACCATATAGAACATCCCCCCCACAACGTTTCGTTCTTGTTGGATTGGTCATTTTCAAATATTCCCCTTTTATATGCCCGTAA‑AAGACAATATACGTTATAAC  >  NC_007793/1442866‑1442990

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑