Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_012967	4,201,911	C→T	100%	A217T (GCG→ACG)	iclR ←	glyoxylate bypass operon transcriptional repressor IclR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_012967	4,201,911	0	C	T	96.1%	45.9 / ‑6.1	18	A217T (GCG→ACG)	iclR	glyoxylate bypass operon transcriptional repressor IclR
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (9/8);  minor base A (0/1);  total (9/9)
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
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AATACACGCTGCAAGGCAACGTAGCCCCAGCGCATGTTCCTCATCGTCAAATGAATAAC  >  NC_012967/4201879‑4201937                                 |                           aaTACACGCTGCAAGGCAACGTAGCCCCCGCGTATg                         >  2:225789/1‑36 (MQ=37)  aTACACGCTGCAAGGCAACGTAGCCCCAGCGTATGt                        >  2:440666/1‑36 (MQ=38)   tACACGCTGCAAGGCAACGTAGCCCCAGCGTATGtt                       <  2:388340/36‑1 (MQ=38)    acacGCTGCAAGGCAACGTAGCCCCAGCGTATGtta                      >  1:539173/1‑35 (MQ=38)     cacGCTGCAAGGCAACGTAGCCCCAGCGTATGTTcc                     >  1:322309/1‑36 (MQ=38)         cTGCAAGGCAACGTAGCCCCAGCGTATGTTCCTCAt                 >  1:863483/1‑36 (MQ=38)           gaaaGGCAACGTAGCCCCAGCGTATGTTCCTCATCg               <  1:118627/34‑1 (MQ=37)           gCAAGGCAACGTAGCCCCAGCGTATGTTCCTCATCg               >  1:813299/1‑36 (MQ=38)             aaGGCAACGTAGCCCCAGCGTATGTTCCTCATCGTc             <  1:837876/36‑1 (MQ=38)             aaGGCAACGTAGCCCCAGCGTATGTTCCTCATCGTc             >  2:331397/1‑36 (MQ=38)              atgCAACGTAGCCCCAGCGTATGTTCCTCATCGTCa            <  2:773282/34‑1 (MQ=37)              aGGCAACGTAGCCCCAGCGTATGTTCCTCATCGTCa            <  2:622822/36‑1 (MQ=38)                gaaaCGAAGCCCCAGCGAATGTTCCTCATCGTCaaa          <  2:604152/34‑1 (MQ=25)                  aaCGTAGCCCCAGCGTATGTTCCTCATCGTCATATg        >  2:689957/1‑36 (MQ=37)                  aaCGTAGCCCCAGCGTATGTTCCTCATCGTCAAATg        <  1:134193/36‑1 (MQ=38)                      tAGCCCCAGCGTATGTTCCTCATCGTCAAATGAATa    <  2:829144/36‑1 (MQ=38)                        gCCCCAGCGTATGTTCCTCATCGTCAAATGAATAAc  <  1:393560/36‑1 (MQ=38)                        gCCCCAGCGTATGTTCCTCATCGTCAAATGAATAAc  >  2:904714/1‑36 (MQ=38)                                 |                           AATACACGCTGCAAGGCAACGTAGCCCCAGCGCATGTTCCTCATCGTCAAATGAATAAC  >  NC_012967/4201879‑4201937

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑