Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP009974	1,897,927	A→G	intergenic (‑5705/‑2892)	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	1,897,927	0	A	G	94.7%	17.8 / ‑4.7	19	intergenic (‑5705/‑2892)	RPPX_08470/RPPX_08480	tryptophan synthase subunit beta/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base G (6/12);  total (7/12)
Fisher's exact test for biased strand distribution p-value = 3.68e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

GGGCGATGACGTCTACCAGGACGCAGGCCAGATCAGTCTGGGCATCACGTCCGCTGTGGATATAGACGGTCACACCTTTGAGAACCTGGAACTGGGTGGTGCTGCTTCGGTTCAAGTGACCGACACCACCGACGAAGTAGTGGCCAAGCTGACCGCGACCCCGTCGGTCACCGAAGGGGTGG  >  CP009974/1897789‑1897970                                                                                                                                           |                                            aggCGATGACGTCTACAACGATGCTGGCCAGATCAGCCTGGGAATCAATTCGGCGGTAGACGCCACCGGCGCAACGTTCGCGAACCTGCAGTTGGGCGGTGCGGCTACTGCTCAAGTCACCGACACCACCGACGAAGTAGTGGCCaaccgg                                 >  2:3850860/2‑147 (MQ=255)           gTCTACCAGGACGCTGGCCAGATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGAccc                       >  2:4599376/1‑151 (MQ=1)           gTCTACCAGGACGCTGGCCAGATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGAccc                       >  1:4348110/1‑151 (MQ=11)                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       <  2:1620187/151‑1 (MQ=11)                           gCCAGATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAgg       >  1:832766/1‑151 (MQ=11)                           gCCAGATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAgg       <  1:4941884/151‑1 (MQ=11)                            ccAGATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAggc      <  1:655805/151‑2 (MQ=11)                            ccAGATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAggc      <  1:3369970/151‑2 (MQ=11)                            ccAGATCAGTCTGGGCATCACGTCCGCAGTGGATGTAGGCGGTCACACCTTGAACTAGCTGGAACCGGGCGGAGCTGCTACGGATCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCATCGGACAccacaggc      >  2:2733626/1‑145 (MQ=2)                             cAGATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAggcg     <  2:1309881/151‑3 (MQ=11)                               gATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAggcggt   <  2:3309825/151‑5 (MQ=11)                               gATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAggcggt   <  1:4683847/151‑5 (MQ=11)                                aTCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAggcggtg  <  1:1790126/151‑6 (MQ=11)                                aTCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAggcggtg  <  2:3244116/151‑6 (MQ=11)                                aTCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAggcggtg  >  2:4473820/1‑146 (MQ=11)                                                                                                                                           |                                            GGGCGATGACGTCTACCAGGACGCAGGCCAGATCAGTCTGGGCATCACGTCCGCTGTGGATATAGACGGTCACACCTTTGAGAACCTGGAACTGGGTGGTGCTGCTTCGGTTCAAGTGACCGACACCACCGACGAAGTAGTGGCCAAGCTGACCGCGACCCCGTCGGTCACCGAAGGGGTGG  >  CP009974/1897789‑1897970

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: ‑