Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,623,125	T→C	A331T (GCA→ACG)	lplA ←	lipoate‑‑protein ligase A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,623,125	0	T	C	91.7%	29.6 / ‑3.7	12	A331T (GCA→ACG)	lplA	lipoate‑‑protein ligase A
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base C (9/2);  total (10/2)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.85e-01

CGATCCCGCTGGCGCAGCAGTTCTGGCAAACGGTCGCCAGAGATCCGCGTATCAGCGAGGCGTTTCGCCACATTGCGCAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAACTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCTTTTTCCTGTTCCGGGAAGTCAACCAACAGCGCTTCGCACTCCTGTTGCAGCATATCTGCGCGGTACAGGCAGCCTTGCAGTCGTCCGGCGAGGGCTTCCAGCGGCGCGGGGTTGAGGCTGTCGGTAAACACCTGGGCGCGGGTGATATGGCCTTTTTCAACGTCGAAATGCAGTTCCACGCCGCCCCAGGTAAAGCGTTCATCCAGCAGATGC  >  NC_000913/4622964‑4623359                                                                                                                                                                  |                                                                                                                                                                                                                                           cGATCCCGCTGGCGCAGCAGTTCTGGCAAACGGTCGCCAGAGATCCGCGTATCAGCGAGGCGTTTCGCCACATTGCGCAAGAAATGCCGTAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAACTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCTTTTTCCTGTTCCGGGAAGTCAACCAACAGCGCTTCGCACTCCTGTTGCAGCATATCTGCGCGGTAc                                                                                                                                                     >  1:278554/1‑249 (MQ=255)                                                                                                                             tttaatcagcgagttACCTTACCGCCCCCGCTATCCACGTCGACAACTTCCGTAGCTCTTTTTCCTGGTCCGGGAAGTCAACCAACAGCGCTTCGCACTCTTGTTGCAGCATATCCGCGCGGTACAGGCAGCCTTGCAGTCGCCCGGCGAGGGCTTCCAGCGGCGCGGGGTTGAGGCTGTCGGTAAACACCTGGGCGCGGGTGATATGGCCTTTTTCAACGTCGAAATGCAGTTCCACGCCGCCCCAgct                        >  1:48782/15‑248 (MQ=255)                                                                                                                                   cagcgagttACCTTACCGCCCCCGCTATCCACGTCGACAACTTCCGTAGCTCTTTTTCCTGGTCCGGGAAGTCAACCAACAGCGCTTCGCACTCTTGTTGCAGCATATCCGCGCGGTACAGGCAGCCTTGCAGTCGCCCGGCGAGGGCTTCCAGCGGCGCGGGGTTGAGGCTGTCGGTAAACACCTGGGCGCGGGTGATATGGCCTTTTTCAACGTCGAAATGCAGTTCCACGCCGCCCCAGCTAAAGCGt                 >  1:283879/9‑251 (MQ=255)                                                                                                                                    agcgagttACCTTACCGCCCCCGCTATCCACGTCGACAACTTCCGTAGCTCTTTTTCCTGGTCCGGGAAGTCAACCAACAGCGCTTCGCACTCTTGTTGCAGCATATCCGCGCGGTACAGGCAGCCTTGCAGTCGCCCGGCGAGGGCTTCCAGCGGCGCGGGGTTGAGGCTGTCGGTAAACACCTGGGCGCGGGTGATATGGCCTTTTTCAACGTCGAAATGCAGTTCCACGCCGCCCCAGCTAAAGCGtt                >  1:575533/8‑251 (MQ=255)                                                                                                                                      cgagttACCTTACCGCCCCCGCTATCCACGTCGACAACTTCCGTAGCTCTTTCTCCTGGTCCGGGAAGTCAACCAACAGCGCTTCGCACTCTTGTTGCAGCATATCCGCGCGGTACAGGCAGCCTTGCAGTCGCCCGGCGAGGGCTTCCAGCGGCGCGGGGTTGAGGCTGTCGGTAAACACCTGGGCGCGGGTGATATGGCCTTTTTCAACGTCGAAATGCAGTTCCACGCCGCCCCAGCTAAAGCGTTc               >  1:565100/6‑250 (MQ=255)                                                                                                                                        agttACCTTACCGCCCCCGCTATCCACGTCGACAACTTCCGTAGCTCTTTTTCCTGGTCCGGGAAGTCAACCAACAGCGCTTCGCACTCTTGTTGCAGCATATCCGCGCGGTACAGGCAGCCTTGCAGTCGCCCGGCGAGGGCTTCCAGCGGCGCGGGGTTGAGGCTGTCGGTAAACACCTGGGCGCGGGTGATATGGCCTTTTTCAACGTCGAAATGCAGTTCCACGCCGCCCCAGCTAAAGCGTTCATc            >  1:66009/4‑251 (MQ=255)                                                                                                                                          ttACCTTACCGCCCCCGCTATCCACGTCGACAACTTCCGTAGCTCTTTTTCCTGGTCCGGGAAGTCAACCAACAGCGCTTCGCACTCTTGTTGCAGCATATCCGCGCGGTACAGGCAGCCTTGCAGTCGCCCGGCGAGGGCTTCCAGCGGCGCGGGGTTGAGGCTGTCGGTAAACACCTGGGCGCGGGTGATATGGCCTTTTTCAACGTCGAAATGCAGTTCCACGCCGCCCCCGCTAAAGCGTTCATccc          >  2:286819/2‑250 (MQ=255)                                                                                                                                              cTTACAGCCCACGCTGTCCACGTCGACAACTTCCGTAGCTCTTTTTCCTGGTCCGGGAAGTCCACCAACAGCGCTTCGCACTCTTGTTGCAGCATATCCGCGCGGTACAGGCAGCCTTGCAGTCGCCCGGCGAGGGCTTCCAGAGGCGCGGGGTTGAGGCTGTCGGTAAACACCTGGGCGCGGGGGGTATGGCCTTTTTCAACGTCGAAATGCAGTTCCACGCCGCCCCAGCCCACGCGTTCATCcaaca       >  2:546301/1‑247 (MQ=255)                                                                                                                                                taccgCCCCCGCTATCCACGTCGACAACTTCCGTAGCTCTTTTTCCTGGTCCGGGAAGTCAACCAACAGCGCTTCGCACTCTTGTTGCAGCATATCCGCGCGGTACAGGCAGCCTTGCAGTCGCCCGGCGAGGGCTTCCAGCGGCGCGGGGTTGAGGCTGTCGGTAAACACCTGGGCGCGGGTGATATGGCCTTTTTCAACGTCGAAATGCAGTTCCACGCCGCCCCAGCTAAAGCGTTCATCcagcag      <  1:405603/245‑1 (MQ=255)                                                                                                                                                 accgCCCCCGCTATCCACGTCGACAACTTCCGTAGCTCTTTTTCCTGGTCCGGGAAGTCAACCAACAGCGCTTCGCACTCTTGTTGCAGCATATCCGCGCGGTACAGGCAGCCTTGCAGTCGCCCGGCGAGGGCTTCCAGCGGCGCGGGGTTGAGGCTGTCGGTAAACACCTGGGCGCGGGTGATATGGCCTTTTTCAACGTCGAAATGCAGTTCCACGCCGCCCCAGCTAAAGCGTTCATCCAGCAGAt    <  1:199255/247‑1 (MQ=255)                                                                                                                                                 accgCCCCCGCTATCCACGTCGACAACTTCCGTAGCTCTTTTTCCTGGTCCGGGAAGTCAACCAACAGCGCTTCGCACTCTTGTTGCAGCATATCCGCGCGGTACAGGCAGCCTTGCAGTCGCCCGGCGAGGGCTTCCAGCGGCGCGGGGTTGAGGCTGTCGGTAAACACCTGGGCGCGGGAGATATGGCCTTTTTCAACGTCGAAATGCAGTTCCACGCCGCCCCAGCTAAAGCGTTCATCCAGCAGATg   >  1:656407/4‑251 (MQ=255)                                                                                                                                                  tcgCCCCCGCTATCCACGTCGACAACTTCCGTAGCTCTTTTTCCTGATCCGAGAAAGCAACCAACAGCGCTTCGCACTCTTGTTGCAGAATATCCGCGCGGTCCAGGCAGCCTTGCAGTCGCCCGGCGCGGTCTTCCAGCGGCGCGGGGTTGAGGCTGTCGGTAACCACCTGGGCGCGGGCGATCTGGCCTTTTTCAACGTCGCACTACCGTTCCACGCCGCCCCAGCTAAAGCTATCATCcagccgttgg  >  2:496789/3‑245 (MQ=255)                                                                                                                                                                  |                                                                                                                                                                                                                                           CGATCCCGCTGGCGCAGCAGTTCTGGCAAACGGTCGCCAGAGATCCGCGTATCAGCGAGGCGTTTCGCCACATTGCGCAAGAAATGCCGGAAAAAATCCGGCAAATCGAAGAGAAAGTTGCCCGCATGGGCGGGTAACTACCTTACAGCCCCCGCCATCCATGCCGATAACTCCCGTAGCTCTTTTTCCTGTTCCGGGAAGTCAACCAACAGCGCTTCGCACTCCTGTTGCAGCATATCTGCGCGGTACAGGCAGCCTTGCAGTCGTCCGGCGAGGGCTTCCAGCGGCGCGGGGTTGAGGCTGTCGGTAAACACCTGGGCGCGGGTGATATGGCCTTTTTCAACGTCGAAATGCAGTTCCACGCCGCCCCAGGTAAAGCGTTCATCCAGCAGATGC  >  NC_000913/4622964‑4623359

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑