Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,096,622	(G)7→8	intergenic (+570/+166)	ycdU → / ← serX	hypothetical protein/tRNA‑Ser

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,096,615	1	.	G	92.9%	22.8 / ‑2.7	14	intergenic (+563/+173)	ycdU/serX	hypothetical protein/tRNA‑Ser
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base G (3/10);  total (4/10)
Fisher's exact test for biased strand distribution p-value = 2.86e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.57e-01

TCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTGACTCGCTTC  >  NC_000913/1096537‑1096635                                                                                |                     tctcATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGAttagag        >  1:6066172/1‑89 (MQ=1) tctcATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGAc         >  2:8208042/1‑93 (MQ=255) tctcAACCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGAc         <  2:6254929/93‑1 (MQ=11)  ctcATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACt        <  1:8208043/93‑1 (MQ=12)  ctcATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACt        <  1:3744862/93‑1 (MQ=255)  ctcATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACt        >  1:4430262/1‑93 (MQ=255)  ctcATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACt        <  2:3923479/93‑1 (MQ=255)   tcATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACtc       >  2:9618023/1‑93 (MQ=16)   tcATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTGACtcg      >  1:457338/1‑93 (MQ=34)   tcATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACtc       >  2:10029064/1‑93 (MQ=255)    cacccccccGGTGTGTGCAATATACGAAAAAAAAGCCCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACtcg      <  1:3104841/90‑1 (MQ=11)     aTCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACtcgc     <  2:3191898/93‑1 (MQ=16)       ccccccGGTGTGTGGAATATACGAAAAAAAAGCCCGCACTTTCGTACGAGCTTTTCTTTAAATATGGGGGTGAGGGGGGGGATTGACtcgctt   <  2:3168284/93‑1 (MQ=11)        cccccGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACtcgcttc  <  2:3780637/93‑1 (MQ=12)        cccccGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACtcgcttc  <  1:2617235/93‑1 (MQ=12)         ccccGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACtcg      <  1:576666/88‑1 (MQ=9)         ccccGGTGTGTGCAATATACGAAAAAAAAGCCCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACtcg      >  2:576666/1‑88 (MQ=11)                                                                                |                     TCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTGACTCGCTTC  >  NC_000913/1096537‑1096635

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑