Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,144,194	C→T	P150P (CCG→CCA)	USA300HOU_RS10940 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,144,194	0	C	T	96.7%	61.0 / NA	30	P150P (CCG→CCA)	USA300HOU_RS10940	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base T (19/10);  total (20/10)
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

TGACGGGTTAGGATTTGGCTTATTAGGGTCTGGTTTTGGATTCGGATTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTT‑‑‑ATTA‑‑‑GGGTCTGGTTTTGGATCTGGATTTGGTTTCGGGTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATCCGGTTTTGGTTTCGGGTTATCTGGATCTGGTTTAGGATTCGGACTTGGGTTTTGGTTATTTGGGTCTG  >  USA300TCH1516_ALE/2144068‑2144327                                                                                                                                     |                                                                                                                                      cgACGGGTTAGGATTTGGCTCATTAGGGCCTGGTTTTGGCTTCGGATTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATAAGGATTTGGATTCGGGTTata                                                                                                                               >  2:774597/2‑140 (MQ=11)                                                                            cgggttaggATTTGGCTT‑‑‑ATTA‑‑‑GGGTCTGGTTTTGGATTCGGATTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATCCGGTTTTGGTTTCGGGTTatctgg                                              >  1:168999/8‑141 (MQ=14)                                                                            cgggttaggATTTGGCTT‑‑‑ATTA‑‑‑GGGTCTGGTTTTGGATTCGGATTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGG‑TTTAGATCCGGTTTTGGTTTCGGGTTatctgga                                             <  4:161156/134‑1 (MQ=14)                                                                             gggttaggATTTGGCTT‑‑‑ATTA‑‑‑GGGTCTGGTTTTGGATTCGGATTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATCCGGTTTTGGTTTCGGGTTatctgga                                             >  3:86978/7‑141 (MQ=14)                                                                             gggttaggATTTGGCTT‑‑‑ATTA‑‑‑GGGTCTGGTTTTGGATTCGGATTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATCCGGTTTTGGTTTCGGGTTatctgga                                             <  2:546520/135‑1 (MQ=14)                                                                                ttaggATTTGGCTT‑‑‑ATTA‑‑‑GGGTCTGGTTTTGGATTCGGATTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTGTGGGTTATCGGGGTCTGGTTTTGGATCCGGTTTTGGTTTCGGGTTatctggatct                                          >  3:236664/4‑141 (MQ=11)                                                                                  aggATTTGGCTT‑‑‑ATTA‑‑‑GGGTCTGGTTTTGGATTCGGATTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATCCGGTTTTGGTTTCGGGTTatctggatctgg                                        >  1:302086/2‑141 (MQ=14)                                                                                   ggATTTGGCTT‑‑‑ATTA‑‑‑GGGTCTGGTTTTGGATTCGGATTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATCCGGTTTTGGTTTCGGGTTATCTGGATCTGGt                                       <  2:112535/141‑1 (MQ=14)                                                                                   ggATTTGGCTT‑‑‑ATTA‑‑‑GGGTCTGGTTTTGGATTCGGATTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATCCGGTTTTGGTTTCGGGTTATCTGGATCTGGt                                       <  2:722002/141‑1 (MQ=14)                                                                                      tttGGCTT‑‑‑ATTA‑‑‑GGGTCTGGTTTTGGATTCGGATTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATCCGGTTTTGGTTTCGGGTTATCTGGATCTGGTTTa                                    <  1:146674/141‑1 (MQ=14)                                                                                      tttGGCTT‑‑‑ATTA‑‑‑GGGTCTGGTTTTGGATTCGGATTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATCCGGTTTTGGTTTCGGGTTATCTGGATCTGGTTTa                                    >  3:354086/1‑141 (MQ=14)                                                                                         ggCTT‑‑‑ATTA‑‑‑GGGTCTGGTTTTGGATTCGGATTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATCCGGTTTTGGTTTCGGGTTATCTGGATCTGGTTTAGGa                                 >  1:110015/1‑141 (MQ=17)                                                                                            tt‑‑‑atta‑‑‑GGGTCTGGTTTTGGATTCGGATTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTGGGTTTATCTGGGTCTGGTTTTGGATCCGGTTTTGGTTTCGGGTTATCTGGATCTGGTTTAGGATTc                              >  3:337314/1‑141 (MQ=14)                                                                                             t‑‑‑atca‑‑‑GGGCCTGGCTTTGGCTTCGGATTTGGCGTTGGTTTATCTGGATTCGGTTTTGGATCCGGATTTGGCTTCGGTTTATCTGGGGCTGGGTTTGGATCCGGTGTTGGTTGCGGGTTATCTGGACCTGGTTTTGGATTCg                             >  2:744337/1‑141 (MQ=9)                                                                                                 atta‑‑‑GGGTCTGGTTTTGGATTCGGATTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATCCGGTTTTGGTTTCGGGTTATCTGGATCTGGTTTAGGATTCgg                            >  2:908325/1‑141 (MQ=17)                                                                                                   ta‑‑‑GGGTCTGGTTTTGGATTCGGATTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATCCGGTTTTGGTTTCGGGTTATCTGTATCTGGTTTAGGATTCGGAc                          <  3:42489/141‑1 (MQ=17)                                                                                                    a‑‑‑GGGTCTGGTTTTGGATTCGGATTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATCCGGTTTTGGTTTCGGGTTATCTGGATCTGGTTTAGGATTCGGACt                         >  1:530991/1‑141 (MQ=17)                                                                                                    a‑‑‑GGGTCTGGTTTTGGATTCGGATTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATCCGGTTTTGGTTTCGGGTTATCTGGATCTGGTTTAGGATTCGGACt                         <  1:430260/141‑1 (MQ=17)                                                                                                        gggTCTGGTTTTGGATTCGGATTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATCCGGTTTTGGTTTCGGGTTATCTGGATCTGGTTTAGGATTCGGACtt                        <  2:588003/141‑1 (MQ=17)                                                                                                         ggTCTGGTTTTGGATTCGGATTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATCCGGTTTTGGTTTCGGGTTATCTGGATCTGGTTTAGGATTCGGACTTg                       >  1:569769/1‑141 (MQ=17)                                                                                                           tCTGGTTTTGGATTCGGATTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATCCGGTTTTGGTTTCGGGTTATCTGGATCTGGTTTAGGATTCGGACTTggg                     >  1:27971/1‑141 (MQ=18)                                                                                                             tGGTTTTGGATTCGTAATTGGCTTTGGTTTATCTGGATCTGGTTTTAGATCCGGATTTGGCTTTGGTTTATCTAGGTCTGGTTTTTGATTCGGCTTTTGTTTCGGGTTATCTGGATCTGGTTTCGGACTCGGACCTTGGtt                   >  4:236006/1‑141 (MQ=17)                                                                                                               gTTTTGGATTCGGATTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATCCGGTTTTGGTTTCGGGTTATCTGGATCTGGTTTAGGATTCGGACTTGGGtttt                 >  4:213359/1‑141 (MQ=17)                                                                                                                 tttGGATTCGGATTTGGCTATGGTTAATCGGGTGCGGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATCCGGTTTTGGTTTCGGGTTATCTGGATCTGGTTTAGGATTCGGACTTGGGTTTTgg               >  2:233240/1‑141 (MQ=18)                                                                                                                  ttGGATTCGGATTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATCCGGTGTTGGTTTCGGGTTATCTGGATCTGGTTTAGGATTCGGACTTGGGTTTTGGt              >  4:106235/1‑141 (MQ=18)                                                                                                                         cggATTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATCCGGTTTTGGTTTCGGGTTATCTGGATCTGGTTTAGGATTCGGACTTGGGTTTTGGTTATTTgg       <  1:434625/140‑1 (MQ=255)                                                                                                                          ggATTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATCCGGTTTTGGTTTCGGGTTATCTGGATCTGGTTTAGGATTCGGACTTGGGTTTTGGTTATTTggg      >  3:221457/1‑141 (MQ=255)                                                                                                                          ggATTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATCCGGTTTTGGTTTCGGGTTATCTGGATCTGGTTTAGGATTCGGACTTGGGTTTTGGTTATTTggg      >  4:236567/1‑141 (MQ=255)                                                                                                                            aTTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATCCGGTTTTGGTTTCGGGTTATCTGGATCTGGTTTAGGATTCGGACTTGGGTTTTGGTTATTTGGGTc    <  1:179966/141‑1 (MQ=255)                                                                                                                              ttGGCTTTGGTTTAGCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATCCGGTTTTGGTTTCGGGTTATCTGGATCTGGTTTAGGATTCGGACTTGGGTTTTGGTTATTTGGGTCTg  >  2:845330/1‑141 (MQ=255)                                                                                                                                     |                                                                                                                                      TGACGGGTTAGGATTTGGCTTATTAGGGTCTGGTTTTGGATTCGGATTTGGCTTTGGTTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTT‑‑‑ATTA‑‑‑GGGTCTGGTTTTGGATCTGGATTTGGTTTCGGGTTATCTGGATCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATCCGGTTTTGGTTTCGGGTTATCTGGATCTGGTTTAGGATTCGGACTTGGGTTTTGGTTATTTGGGTCTG  >  USA300TCH1516_ALE/2144068‑2144327

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑