Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_007793	861,284	T→G	S713A (TCA→GCA)	SAUSA300_RS04165 →	clumping factor A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007793	861,284	0	T	G	85.7%	13.9 / 11.9	49	S713A (TCA→GCA)	SAUSA300_RS04165	clumping factor A
Reads supporting (aligned to +/- strand):  ref base T (5/2);  new base G (42/0);  total (47/2)
Fisher's exact test for biased strand distribution p-value = 1.79e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.83e-01

CCGACAGTGATTCCGA‑CTCAGACAGCGATTCAGATTCCGACAGTGATTCCGACTCAGATAGCGATTCCGACTCAGATAGCGACTCAGATTCAGACAGCGATTCAGATTCAGACAGCGATTCAGATTCAGATAGCGATTCAGATTCCGACAGTGACTCAGATTCCGACAGTGA  >  NC_007793/861195‑861366                                                                                           |                                                                                   ccGACAGTGATTCCGA‑CTCAGACAGCGATTCAGATTCCGACAGTGATTCCGACTCAGATAGCGATTCCGACTCAGATAGCGACtcagattcagacagcga                                                                          >  1:5894872/1‑100 (MQ=255) ccGACAGTGATTCCGA‑CTCAGACAGCGATTCAGATTCCGACAGTGATTCCGACTCAGATAGCGATTCCGACTCAGATAGCGACtcagattcagacagcga                                                                          >  1:5984512/1‑100 (MQ=255) ccGACAGTGATTCCGA‑CTCAGACAGCGATTCAGATTCCGACAGTGATTCCGACTCAGATAGCGATTCCGACTCAGATAGCGACtcagattcagacagcga                                                                          >  1:1707068/1‑100 (MQ=255)    aCAGTGATTCCGA‑CTCAGACAGCGATTCAGATTCCGACAGTGATTCCGACTCAGATAGCGATTCCGACTCAGATAGCGACtcagattcagacagcgattc                                                                       <  1:5384588/100‑1 (MQ=255)     gtgctcttCCGATCTCAGACTGCGATTCAGATTCCGACAGTGATTCCGACTCAGAGAGCGATTCCGACTCAGATAGCGACtcagattcagacagcgattc                                                                       <  1:1843102/94‑1 (MQ=18)          aTTCCGA‑CTCAGACAGCGATTCAGATTCCGACAGTGATTCCGACTCAGATAGCGATTCCGACTCAGATAGCGACtcagattcagacagcgattcagattc                                                                 <  1:1353248/100‑1 (MQ=255)                    cAGACAGCGATTCAGATTCCGACAGTGATTCCGACTCAGATAGCGATTCCGACTCAGATAGCGACtcagattcagacagcgattcagattcagacagcgt                                                        <  1:2281732/100‑2 (MQ=255)                    cAGACAGCGATTCAGATTCCGACAGTGATTCCGACTCAGATAGCGATTCCGACTCAGATAGCGACtcagattcagacagcgattcagattcagacagcga                                                        >  1:2309217/1‑100 (MQ=255)                      gACAGCGATTCAGATTCCGACAGTGATTCCGACTCAGATAGCGATTCCGAATCAGACAGCGATtcagaatcagacagcgattcagattcagacagcactc                                                      <  1:6188734/100‑5 (MQ=14)                             aTTCAGATTCCGACAGTGATTCCGACTCAGATAGCGATTCCGAATCAGATAGCGACTCAGATTCagacagcggttaagattcagacagcgattcagattc                                               <  1:5099195/100‑1 (MQ=255)                                               actcagacgcagatagcgactcagacgcagatagcgaCTCTGATGCGGACAGCGACTCAGATTCAGACAGCGATTCAGACGCAGATAGCGATtcagattc                             >  1:3223972/6‑100 (MQ=11)                                               actcagacgcagatagcgactcagacgcagatagcgaCTCTGATGCGGACAGCGACTCAGATTCAGACAGCGATTCAGACGCAGATAGCGATtcagattc                             >  1:6005269/6‑100 (MQ=11)                                                ctccgacgcggatagcgattcagacgcagatagcgaCTCTGATGCGGACAGCGACTCAGATTCAGACAGCGATTCAGACGCAGATAGCGATtctgatgcg                            >  1:6320660/2‑97 (MQ=11)                                                ctcagacgcagatagcgactcagacgcagatagcgaCTCTGATGCGGACAGCGACTCAGATTCAGGCAGCGATTCAGACGCAGATAGCGATtcagattca                            >  1:4376284/5‑99 (MQ=2)                                                ctcagacgcagatagcgactcagacgcagatagcgaCTCTGATGCGGACAGCGACTCAGATTCAGACAGCGATTCAGACGCAGATAGCGATtcagattca                            >  1:2862888/5‑99 (MQ=11)                                                 cccgacgcagatagcgattcagacgcagatagcgaCTCTGATGCGGACAGCGACTCAGATTCAGACAGCGATTCAGACGCAGATAGCGATtctgatgagg                           >  1:6565282/2‑96 (MQ=11)                                                 ccagacgcagatagcgattcagacgcagatagcgaCTCTGATGCGGACAGCGACCCAGATTCAGACAGCGATTCAGACGCAGATAGCGATtctgatgcgg                           >  1:5681087/4‑96 (MQ=2)                                                  tcgacgcagatagcgattctgatgcggacagcgaTTCAGACGCAGATAGCGATTCTGATGCAGACAGCGATTCAGACGCAGATAGCGATtctgatgcgga                          >  1:1988997/2‑95 (MQ=0)                                                  ccgacgcagatagcgattcagacgcagatagcgaCTCTGATGCGGACAGCGACTCAGATTCAGACAGCGATTCAGACGCAGATAGCGATtctgatgcgga                          >  1:4809324/1‑95 (MQ=11)                                                  ccgacgcagatagcgactcagacgcagatagcgaCTCTGATGCGGACAGCGACTCAGATTCAGACAGCGATTCAGACGCAGATAGCGAttcagattcaga                          >  1:6298685/1‑100 (MQ=11)                                                  cagacgcagatagcgattcagatgcagatagcgaCTCTTATGCGGACAGCGATTCAGATTCAGACAGCGATTCAGACGCAGATATCGACtctgatccgga                          >  1:1114000/3‑95 (MQ=2)                                                  cagacgcagatagcgattcagacgcagatagcgaCTCTGATGCGGACAGCGACTCAGATGCAGACAGCGATTCAGACGCAGATAGCGATtcagatgcgga                          >  1:2930363/3‑95 (MQ=11)                                                  acaggccagatagcgattcggactcagacagcgaTTCAGATTCAGACAGCGACTCAGACTCGGATAGCGATTCAGATTCAGATAGCGATtcggatgccga                          >  1:3215289/7‑100 (MQ=17)                                                   ttatgcggacagcgattcagacgcagatagcgaTTCTGATGCGGACAGCGATTCAGACGCAGATAGCGATTCAGATTCAGATAGCGACtctgatgcggac                         >  1:3373702/11‑100 (MQ=2)                                                   gctggcagatagcgattctgatgcggacagcgaTTCAGACGCAGATAGCGATTCTGATGCGGACAGCGATTCAGACGCAGATAGCGATtcagatgcggac                         >  1:1593857/6‑100 (MQ=0)                                                   gcatgcggacagcgattcagacgcagatagcgaTTCTGATGCGGACAGCGATTCAGACGCAGATAGCGATTCAGATTCAGATAGCGATtctgatgcggac                         >  1:854059/11‑100 (MQ=2)                                                   ctacgcagatagcgattcagacgcagatagcgaCTCTGATGCGGACAGCGACTCAGATTCAGACAGCGATTCAGACGCAGATAGCGATtctgatgcggac                         >  1:5161789/6‑100 (MQ=2)                                                   atacccagacagcgattcagacgcagatagcgaTTCTGATGCGGACAGCGATTCAGACGCAGATAGCGATTCAGATTCAGATAGCGATtctgatgcggac                         >  1:3834989/6‑100 (MQ=2)                                                   acttgcggacagcgattcagacgcagatagcgaTTCTGATGCGGACAGCGATTCAGACGCAGATAGCGCTTCAGATTCAGATAGCGATtctgatgcggac                         >  1:1411407/11‑100 (MQ=2)                                                    cttgcggacagcgattcagacgcagatagcgaTTCTGATGCGGACAGCGATTCAGACGCAGATAGCGATTCAGATTCAGATAGCGATtctgatgcggaca                        >  1:4059584/10‑100 (MQ=2)                                                    atagcagatagcgattcagacgcagatagcgaCTCTGATGCGGACAGCGACTCAGATTCAGACAGCGATTCAGACGCAGATAGCGATtctgatgcggaca                        >  1:212505/5‑100 (MQ=11)                                                    aacgcagatagcgattcagacgcagatagcgaCTCTGATGCGGACAGCGACTCAGATTCAGACAGCGATTCAGACGCAGATAGCGATtctgatgcggaca                        >  1:4617694/5‑100 (MQ=11)                                                     tggcggacagcgattcagacgcagatagcgaTTCTGATGCGGACAGCGATTCAGACGCAGATAGCGATTCAGATTCAGATAGCGATtctgttgcggacag                       >  1:1695453/9‑100 (MQ=2)                                                     atgcggacagcgattcagacgcagatagcgaTTCTGATGCGGACAGCGATTCAGACGCAGATAGCGATTCAGATTCAGATAGCGATtctgatgcggacgg                       >  1:222164/9‑98 (MQ=2)                                                     atgcggacagcgattcagacgcagatagcgaTTCTGATGCGGACAGCGACTCAGATTCAGACAGCGATTCAGACGCAGATAGCGATtctgatgcggacag                       >  1:2419208/9‑100 (MQ=0)                                                     atgcggacagcgattcagacgcagatagcgaTTCAGATTCAGATAGCGCTTCTGATGCGGACAGCGATTCAGACGCAGATAGCGATtcagatgcggacag                       >  1:3545128/9‑100 (MQ=2)                                                     acgcagatagcgattcagacgcagatagcgaCTCTGATGCGGACAGCGACTCAGATTCAGACAGCGATTCAGACGCAGATAGCGATtctgatgcggacag                       >  1:4009698/4‑100 (MQ=11)                                                     acgcagatagcgattcagacgcagatagcgaCTCTGATGCGGACAGCGACTCAGATTCAGACAGCGATTCAGACGCAGATAGCGATtctgatgcggacag                       >  1:46060/4‑100 (MQ=11)                                                      cccggacagcgattcagacgcagatagcgaTTCTGATGCGGACAGCGATTCAGACGCAGATAGCGATTCAGATTCAGATAGCGATtctgctgcggacagc                      >  1:6467550/8‑99 (MQ=2)                                                       tcagacagcgattcagacgcagatagcgaTTCTGATGCGGACAGCGGTTCAGACGCAGACAGCGATTCAGATTCAGATAGCGATtctgatgcggacagcg                     >  1:6446463/1‑98 (MQ=2)                                                       gcagatagcgattcagacgcagatagcgaCTCTGATGCGGACAGCGACTCAGATTCAGACAGCGATTCAGACGCAGATAGCGATtctgatgcggacagcg                     >  1:5575882/2‑98 (MQ=11)                                                       gcagacagcgactcagacgcagatagcgaTTCAGATGCGGACAGCGATTCAGATGCAGACAGCGATTCAGACGCAGATAGCGATtctgatgcggacagcg                     >  1:13679/2‑98 (MQ=0)                                                        cagatagcgattctgatgcggacagcgaTTCAGACGCAGATAGCGATTCTGATGCGGACAGCGATTCAGACGCAGATAGCGATtcagatgcggacagatc                    >  1:2678235/1‑97 (MQ=0)                                                        cagatagcgattctgatgcggacagcgaTTCAGACGCAGATAGCGATTCTGATGCGGACAGCGATTCAGACGCAGATAGCGATtcagatgcggacaagat                    >  1:3266672/1‑96 (MQ=0)                                                        cagatagcgattcagacgcagatagcgaCTCTGATGCGGACAGCGACTCAGATTCAGACAGCGATTCAGACGCAGATAGCGATtctgatgcggacagcga                    >  1:1601736/1‑100 (MQ=11)                                                        cagatagcgattcagacgcagatagcgaCTCTGATGCGGACAGCGACTCAGATTCAGACAGCGATTCAGACGCAGATAGCGATtctgatgcggacagcga                    >  1:2970730/1‑100 (MQ=11)                                                        cagatagcaattctgatgcggacagcgaTTCAGACGCAGATAGCGATTCTGATGCGGACAGCGATTCAGACGCAGATAGCGATtcagatgcggacagatc                    >  1:400038/1‑97 (MQ=0)                                                         tgatagcgattcagacgcagatagcgaCTCTGATGCGGACAGCGACTCAGATTCAGACAGCGATTCAGACGCAGATAGCGATtctgatgcggacagcgat                   >  1:351069/2‑99 (MQ=2)                                                         agatagcgattctgatgcggacagcgaTTCAGACGCAGATAGCGATTCTGATGCGGACAGCGATTCAGACGCAGATAGCGATtcagatgcggacagatcg                   >  1:201217/1‑96 (MQ=0)                                                         agatagcgattcagacgcagatagcgaCTCTGATGCGGACAGCGACTCAGATTCAGACAGCGATTCAGACGCAGATAGCGATtctgatgcggacagcgat                   >  1:4029303/1‑99 (MQ=11)                                                         agatagcgattcagacgcagatagcgaCTCTGATGCGGACAGCGACTCAGATTCAGACAGCGATTCAGACGCAGATAGCGATtctgatgcggacagcgac                   >  1:6428510/1‑100 (MQ=11)                                                           acagcgactcagacgcagatagcgaTTCAGATGCGGACAGCGATTCAGACGCAGACAGCGATTCAGACGCAGATAGCGATtctgatgctgacagtgattc                 >  1:4580885/3‑100 (MQ=2)                                                               tcttccagacgcagatagcgaTTCAGATGCGGACAGCGATTCAGACGCAGACAGCGATTCAGACGCAGATAGCGATtctgatgcggacagcgattcagac             >  1:1669020/8‑99 (MQ=0)                                                                     tgactcagatagcgaCTCAGATTCAGACAGCGATTCAGATTCAGACAGCGATTCAGATTCAGATAGCGATtcagattccgacagtgactcagattccgac       >  1:2897119/2‑100 (MQ=255)                                                                     cgacgcagatagcgaCTCTGATGCGGACAGCGACTCAGATTCAGACAGCGATTCAGACGCAGAGAGCGATtctgatgcagacagcgactcagacgcagat       >  1:3399920/1‑93 (MQ=0)                                                                     agacgcagatagcgaTTCAGATTCAGATAGCGATTCTGATTCGGACAGCGATTCAGAAGCATATAGCGATtcagattcgtacagcgaatcagtcgcattt       >  1:4743930/2‑92 (MQ=2)                                                                       actcagatagcgaCTCAGATTCAGACAGCGATTCAGATTCAGACAGCGATTCAGATTCAGATAGCGATtcagattccgacagtgactcagattccgacag     <  1:2399346/100‑1 (MQ=255)                                                                          cagatagcgaCTCAGATTCAGACAGCGATTCAGATTCAGACAGCGATTCAGATTCAGATAGCGATtcagattccgacagtgactcagattccgacagtga  >  1:2402623/1‑100 (MQ=255)                                                                                           |                                                                                   CCGACAGTGATTCCGA‑CTCAGACAGCGATTCAGATTCCGACAGTGATTCCGACTCAGATAGCGATTCCGACTCAGATAGCGACTCAGATTCAGACAGCGATTCAGATTCAGACAGCGATTCAGATTCAGATAGCGATTCAGATTCCGACAGTGACTCAGATTCCGACAGTGA  >  NC_007793/861195‑861366

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑