Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	575,770	G→A	100%	pseudogene (339/1128 nt)	nmpC ←	DLP12 prophage region; ECK0544:JW5078:b0553; truncated outer membrane porin

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	575,770	0	G	A	100.0%	13.3 / NA	7	pseudogene (339/1128 nt)	nmpC	DLP12 prophage region; ECK0544:JW5078:b0553; truncated outer membrane porin
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (3/4);  total (3/4)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GTTTTATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCA  >  W3110S.gb/575756‑575806               |                                     tttttATCTTTGGAATAACCTTGAGATTCAGcacg                  <  1:3627245/34‑1 (MQ=25) gTTTTATCTTTGGAAGAACCTTGAGATTCAGcacg                  <  1:1365039/35‑1 (MQ=38) gTTTTATCTTTGGAAGAACCTTGAGATTCAGcacg                  <  1:1398046/35‑1 (MQ=38) gTTTTATCTTTGGAAGAACCTTGAGATTCAGcacg                  <  1:364866/35‑1 (MQ=38)      gtCTTTGGAAGAACCTTGAGATTCAGCACGGTTGCCTTTGAATTCa  >  1:2020308/2‑46 (MQ=255)      gtCTTTGGAAGAACCTTGAGATTCAGCACGGTTGCCTTTGAATTCa  >  1:2267107/2‑46 (MQ=255)      gtCTTTGGAAGAACCTTGAGATTCAGCACGGTTGCCTTTGAATTCa  >  1:463178/2‑46 (MQ=255)               |                                     GTTTTATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCA  >  W3110S.gb/575756‑575806

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑