Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP028101	2,124,069	G→A	pseudogene (429/1185 nt)	C7Y58_10215 →	IS3 family transposase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP028101	2,124,069	0	G	A	100.0%	11.9 / NA	9	pseudogene (429/1185 nt)	C7Y58_10215	IS3 family transposase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (4/5);  total (4/5)

TAAGAAAAATGATAAAGTATTATCTGAAAAAGAAAAAATTAAACTATTAGAAGATGAAATAATTTATCTTAAAGCTGAGAATGAATACTTAAAAAAATTGAGAGCTCTAGTTCAAGAAAGGGAGCTAAAAGAGAAGAAAAAGTAAGAGTAATAGCAGAACTTAGAGCTAAATATCCTTTCAAAATACTATTAAAGATTGCTGGAATATCAAGATCAGTATACTATTACTATATTAATAAAAAGGATTTTGATGAGAAGAATAAAGATATTATTGAAAAAATTAGAGAAATTTAC  >  CP028101/2123827‑2124120                                                                                                                                                                                                                                                   |                                                    caaGAAAAATGATAAAGTATTATCTGAAAAAGAAAAAATTAAACTATTAGAAGATGAAATAATTTATCTTAAAGCTGAGAATGAATACTTAAAAAAATTGAGAGCTCTAGTTCAAGAAAGGGAGCTAAAAGAGAAGAAAAAGTAAGAGTAATAGCAGAACTTAGAGCTAAATATCCTTTCAAAATACTATTAAAGATTGCTGGAATATCAAGATCAGTATACTATTACTATATTAATAAAAAAGATTTtga                                             >  2:502683/2‑251 (MQ=14)        aaTGATAAAGTAATATCTGAAAAAGAAAAAATTAAACTATTAGAAGATGAAATAATTTATCTTAAAGCAGAGAATGAATACTTAAAAAAATTGAGAGCTCTAGTTCAAGAAAGGGAGCTAAAAGAGAAGAAAAAGTAAGAGTAATAGCAGAACTTAGAGCTAAATATCCTTTCAAAATACTATTAAAGATTGCTGGAATATCAAGATCAGTATACTATTACTATATTAATAAAAAAGATTTTGATGagaag                                      <  2:192304/251‑1 (MQ=14)             tAAAGTATTATCTGAAAAAGAAAAAATTAAACTATTAGAAGATGAAATAATTTATCTTAAAGCTGAGAATGAATACTTAAAAAAATTGAGAGCTCTAGTTCAAGAAAGGGAGCTAAAAGAGAAGAAAAAGTAAGAGTAATAGCAGAACTTAGAGCTAAATATCCTTTCAAAATACTATTAAAGATTGCTGGAATATCAAGATCAGTATACTATTACTATATTAATAAAAAAGATTTTGATGAGAAGAATaa                                 <  1:502683/251‑1 (MQ=14)             tAAAGTATTATCTGAAAAAGAAAAAATTAAACTATTAGAAGATGAAATAATTTATCTTAAAGCTGAGAATGAATACTTAAAAAAATTGAGAGCTCTAGTTCAAGAAAGGGAGCTAAAAGAGAAGAAAAAGTAAGAGTAATAGCAGAACTTAGAGCTAAATATCCTTTCAAAATACTATTAAAGATTGCTGGAATATCAAGATCAGTATACTATTACTATATTAATAAAAAAGATTTTGATGAGAAGAATaa                                 <  2:763970/251‑1 (MQ=14)                  tattatCTGAAAAAGAAAAAATTAAACTATTAGAAGATGAAATAATTTATCTTAAAGCTGAGAATGAATACTTAAAAAAATTGAGAGCTCTAGTTCAAGAAAGGGAGCTAAAAGAGAAGAAAAAGTAAGAGTAATAGCAGAACTTAGAGCTAAATATCCTTTCAAAATACTATTAAAGATTGCTGGAATATCAAGATCAGTATACTATTACTATATTAATAAAAAAGATTTTGATGAGAAGAATAAAGat                             <  1:455057/250‑1 (MQ=14)                                          aaCTATTAGAAGATGAAATAATTTATCTTAAAGCTGAGAATGAATACTTAAAAAAATTGAGAGCTCTAGTTCAAGAAAGGGAGCTAAAAGAGAAGAAAAAGTAAGAGTAATAGCAGAACTTAGAGCTAAATATCCTTTCAAAATACTATTAAAGATTGCTGGAATATCAAGATCAGTATACTATTACTATATTAATAAAAAAGATTTTGATGAGAAGAATAAAGATATTATTGAAAAAATTAGAGAAAttt    >  1:302686/1‑251 (MQ=14)                                            cTATTAGAAGATGAAATAATTTATCTTAAAGCTGAGAATGAATACTTAAAAAAATTGAGAGCTCTAGTTCAAGAAAGGGAGCTAAAAGAGAAGAAAAAGTAAGAGTAATAGCAGAACTTAGAGCTAAATATCCTTTCAAAATACTATTAAAGATTGCTGGAATATCAAGATCAGTATACTATTACTATATTAATAAAAAAGATTTTGATGAGAAGAATAAAGATATTATTGAAAAAATTAGAGAAATTTa   >  1:391003/1‑250 (MQ=14)                                            cTATTAGAAGATGAAATAATTTATCTTAAAGCTGAGAATGAATACTTAAAAAAATTGAGAGCTCTAGTTCAAGAAAGGGAGCTAAAAGAGAAGAAAAAGTAAGAGTAATAGCAGAACTTAGAGCTAAATATCCTTTCAAAATACTATTAAAGATTGCTGGAATATCAAGATCAGTATACTATTACTATATTAATAAAAAAGATTTTGATGAGAAGAATAAAGATATTATTGAAAAAATTAGAGAAATTTa   >  1:70916/1‑250 (MQ=14)                                            cTATTAGAAGATGAAATAATTTATCTTAAAGCTGAGAATGAATACTTAAAAAAATTGAGAGCTCTAGTTCAAGAAAGGGAGCTAAAAGAGAAGAAAAAGTAAGAGTAATAGCAGAACTTAGAGCTAAATATCCTTTCAAAATACTATTAAAGATTGCTGGAATATCAAGATCAGTATACTATTACTATATTAATAAAAAAGATTTTGATGAGAAGAATAAAGATATTATTGAAAAAATTAGAGAAATTTAc  <  2:423344/251‑1 (MQ=14)                                                                                                                                                                                                                                                   |                                                    TAAGAAAAATGATAAAGTATTATCTGAAAAAGAAAAAATTAAACTATTAGAAGATGAAATAATTTATCTTAAAGCTGAGAATGAATACTTAAAAAAATTGAGAGCTCTAGTTCAAGAAAGGGAGCTAAAAGAGAAGAAAAAGTAAGAGTAATAGCAGAACTTAGAGCTAAATATCCTTTCAAAATACTATTAAAGATTGCTGGAATATCAAGATCAGTATACTATTACTATATTAATAAAAAGGATTTTGATGAGAAGAATAAAGATATTATTGAAAAAATTAGAGAAATTTAC  >  CP028101/2123827‑2124120

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑