Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	2,992,923	C→T	pseudogene (227/375 nt)	pbl →	ECK2852:JW5457:b2854; predicted peptidoglycan‑binding enzyme

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,992,923	0	C	T	100.0%	287.4 / NA	77	pseudogene (227/375 nt)	pbl	ECK2852:JW5457:b2854; predicted peptidoglycan‑binding enzyme
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (0/77);  total (0/77)

CTTGTCTGAACATTAAAATAGGAACCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACG  >  W3110S.gb/2992899‑2992963                         |                                         gttGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:517609/64‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:307251/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:667253/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:614746/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:582853/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:545661/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:460675/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:445936/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:371897/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:321415/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:671900/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:253242/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:252881/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:2410/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:220339/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1875470/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1850647/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1837415/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1822766/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:883637/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:995184/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:968260/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:959895/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:953403/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:919589/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:901146/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:892991/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:890851/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:886449/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1761489/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:848920/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:829909/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:828700/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:817467/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:747938/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:724062/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:705058/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:691132/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1247000/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1387265/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1373297/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1334698/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1332359/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1331616/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1277927/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1274161/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1272477/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1260135/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1390195/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1245151/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1244966/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1226343/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1206103/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1185359/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1184064/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1151671/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1110821/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1421703/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1725736/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1711290/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1686589/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1659370/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1655715/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1609221/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1560406/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1539639/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1511269/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:149832/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1491631/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1457483/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1450805/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1445962/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:144456/65‑1 (MQ=255) cTTGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:107158/65‑1 (MQ=255)  ttGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1196783/64‑1 (MQ=255)  ttGTCTGAACATTAAAATAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:1688633/64‑1 (MQ=255)                  aTAGGAATCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACg  <  1:303791/48‑1 (MQ=255)                         |                                         CTTGTCTGAACATTAAAATAGGAACCGAGATTTTATATAACCATTTTTCACGTTGTGGAGTAACG  >  W3110S.gb/2992899‑2992963

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑