Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP009974	1,897,951	G→T	intergenic (‑5729/‑2868)	RPPX_08470 ← / → RPPX_08480	tryptophan synthase subunit beta/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009974	1,897,951	0	G	T	93.8%	17.2 / ‑5.9	16	intergenic (‑5729/‑2868)	RPPX_08470/RPPX_08480	tryptophan synthase subunit beta/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base T (3/12);  minor base A (1/0);  total (4/12)
Fisher's exact test for biased strand distribution p-value = 2.50e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCAGGACGCAGGCCAGATCAGTCTGGGCATCACGTCCGCTGTGGATATAGACGGTCACACCTTTGAGAACCTGGAACTGGGTGGTGCTGCTTCGGTTCAAGTGACCGACACCACCGACGAAGTAGTGGCCAAGCTGACCGCGACCCCGTCGGTCACCGAAGGGGTGG  >  CP009974/1897804‑1897970                                                                                                                                                    |                    ccAGGAGGCTGGCCAGATCAGTCTGGGTTTCTCGTCCGGTGTCGGCGTCGACGGTCACACCCTCGCGAACCTTGCACTGGGCGCTGCTGCTCCGGGCCAGGCGACCAACACCCTCGCCGAAGTGTTGGCCAAGCTGACCGCGACCCCTTCg                  <  2:3387889/151‑1 (MQ=9)        gctggCCAGATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCg           >  2:2468115/4‑151 (MQ=1)          tggCCAGATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGaa         <  1:377474/150‑1 (MQ=11)           ggCCAGATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAg        <  2:3927595/151‑1 (MQ=11)            gCCAGATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAgg       <  1:4941884/151‑1 (MQ=11)            gCCAGATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAgg       >  1:832766/1‑151 (MQ=11)            gCCAGATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAgg       <  2:1620187/151‑1 (MQ=11)             ccAGATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAggc      <  1:3369970/151‑2 (MQ=11)             ccAGATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAggc      <  1:655805/151‑2 (MQ=11)             ccAGATCAGTCTGGGCATCACGTCCGCAGTGGATGTAGGCGGTCACACCTTGAACTAGCTGGAACCGGGCGGAGCTGCTACGGATCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCATCGGACAccacaggc      >  2:2733626/1‑145 (MQ=2)              cAGATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAggcg     <  2:1309881/151‑3 (MQ=11)                gATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAggcggt   <  1:4683847/151‑5 (MQ=11)                gATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAggcggt   <  2:3309825/151‑5 (MQ=11)                 aTCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAggcggtg  <  1:1790126/151‑6 (MQ=11)                 aTCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAggcggtg  <  2:3244116/151‑6 (MQ=11)                 aTCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAggcggtg  >  2:4473820/1‑146 (MQ=11)                                                                                                                                                    |                    CCAGGACGCAGGCCAGATCAGTCTGGGCATCACGTCCGCTGTGGATATAGACGGTCACACCTTTGAGAACCTGGAACTGGGTGGTGCTGCTTCGGTTCAAGTGACCGACACCACCGACGAAGTAGTGGCCAAGCTGACCGCGACCCCGTCGGTCACCGAAGGGGTGG  >  CP009974/1897804‑1897970

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: ‑