Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP028101	1,262,493	2 bp→TG	pseudogene (1086‑1087/1276 nt)	C7Y58_06050 →	ISL3 family transposase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP028101	1,262,493	0	C	T	100.0%	14.1 / NA	11	pseudogene (1086/1276 nt)	C7Y58_06050	ISL3 family transposase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (1/10);  total (1/10)
*	CP028101	1,262,494	0	A	G	100.0%	13.7 / NA	11	pseudogene (1087/1276 nt)	C7Y58_06050	ISL3 family transposase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (1/10);  total (1/10)

AAAATGATGATAGCACTAAAAACTCTTAAGAAACATATGAACTATATTGAGAATATGTTTGAATCAAATATTACTAATGGAGTAATAGAGGGTTTAAATAACAAAATAAAATCAATAAAAAGAACAGCATTTGGATATTCAAATTTTAGCAATTTT  >  CP028101/1262480‑1262635              ||                                                                                                                                              aaaaTGATGATAGTGCTAAAAACTCTTAAGAAACATATGAACTATATTGAGAATATGTTTGAATCAAATATTACTAATGGAGTAATAGAGGGTTTAAATAACAAAATAAAATCAATAAAAAGAACAGCATTTGGATATTCAAATTTTAGc        <  1:2010375/150‑1 (MQ=2) aaaaTGATGATAGTGCTAAAAACTCTTAAGAAACATATGAACTATATTGAGAATATGTTTGAATCAAATATTACTAATGGAGTAATAGAGGGTTTAAATAACAAAATAAAATCAATAAAAAGAACAACATTTGGATATTCAAATTTTAGc        <  2:2102395/150‑1 (MQ=2)  agatgatgATAGTGCTAAAAACTCTTAAGAAACATATGAACTATATTGAGAATATGTTTGAATCAAATACTACTAATGGAGTAATAGAGGGTTTAAATAACAAAATAAAATCAATAAAAAGAACAGCATTTGGATATTCAAATTTTAGCa       <  2:2389870/148‑1 (MQ=255)  aaaTGATGATAGTGCTAAGAACTCTTAAGAAACATATGAACTATATTGAGAATATGTTCGAATCAAATATTACTAATGGAGTAATAGAGGGTTTAAATAACAAAATAAAATCAATAAAAAGAACAGCATTTGGATATTCAAATTTTAGCa       <  1:2317899/150‑1 (MQ=11)  aaaTGATGATAGTGCTAAAAACTCTTAAGAAACATATGAACTATATTGAGAATATGTTTGAATCCAATATTACTAATGGAGTAATAGAGGGTTTAAATAACAAAATAAGATCAATAAAAAGAACAGCATTTGGATATTCGAATTTTAGCa       <  2:2389868/150‑1 (MQ=11)     tgatgaTAGTGCTAAAGACTCTTAAGAAACATATGAACTATATTGAGAATATGTTTGAATCAAATATTACTAATGGAGTAATAGAGGGTTTAAATAACAAAATAAAATCAATAAAAAGAACAGCATTTGGATAGTCAAATTTTAGCAAtt    <  2:2961374/150‑1 (MQ=11)     tgatgaTAGTGCTAAAAACTCTTAAGAAACATATGAACTATATTGAGAATATGTTTGAATCAAATATTACTAATGGAGTAATAGAGGGTTTAAATAACAAAATAAAATCAATAAAAAGAACAGCATTTGGATATTCAAATTTTAGCAAtt    <  2:2897567/150‑1 (MQ=12)     tgatgaTAGTGCTAAAAACTCTTAAGAAACATATGAACTATATTGAGAATATGTTTGAATCAAATATTACTAATGGAGTAATAGAGGGTTTAAATAACAAAATAAAATCAATAAAAAGAACAGCATTTGGATATTCAAATTTTAGCAAtt    <  2:376325/150‑1 (MQ=12)     tgatgaTAGTGCTAAAAACTCTTAAGAAACATATGAACTATATTGAGAATATGTTTGAATCAAATATTACTAATGGAGTAATAGAGGGTTTAAATAACAAAATAAAATCAATAAAAAGAACAGCATTTGGATATTCAAATTTTAGCAAtt    <  2:376326/150‑1 (MQ=12)       atgatAGTGCTAAAAACTCTTAAGAAACATATGAACTATATTGAGAATATGTTTGAATCAAATATTACTAATGGAGTAATAGAGGGTTTAAATAACAAAATAAAATCAATAAAAAGAACAGCATTTGGATATTCAAATTTTAGCAAtttt  <  1:1466780/150‑1 (MQ=12)       atgatAGTGCTAAAAACTCTTAAGAAACATATGAACTATATTGAGAATATGTTTGAATCAAATATTACTAATGGAGTAATAGAGGGTTTAAATAACAAAATAAAATCAATAAAAAGAACAGCATTTGGATATTCAAATTTTAGCAAtctt  >  1:2288640/1‑147 (MQ=255)              ||                                                                                                                                              AAAATGATGATAGCACTAAAAACTCTTAAGAAACATATGAACTATATTGAGAATATGTTTGAATCAAATATTACTAATGGAGTAATAGAGGGTTTAAATAACAAAATAAAATCAATAAAAAGAACAGCATTTGGATATTCAAATTTTAGCAATTTT  >  CP028101/1262480‑1262635

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑