Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP028101	693,972	G→A	pseudogene (856/1244 nt)	C7Y58_03400 ←	IS3 family transposase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP028101	693,972	0	G	A	100.0%	41.2 / NA	20	pseudogene (856/1244 nt)	C7Y58_03400	IS3 family transposase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (12/8);  total (12/8)

GAGTTATCTTCTTCTCTTTCAGTCTTTCTTGATATGAATAATGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGCTTTTCTCCTCTTAAATTAAATTCTGTTACATCTGTAAACCATTTTTGATTTGGAGCTGTTGCTTCAAAATCTCTCTTAATATGATTATCA  >  CP028101/693727‑694028                                                                                                                                                                                                                                                      |                                                         gAGTTATCTTCTTCTCTTTCAGTCTTTCTTGATATGAATAATGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATaaa                                                      >  1:379523/1‑250 (MQ=25)  aGTTATCTTCTTCTCTTTCAGTCTTTCTTGATATGAATAATGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAAc                                                     <  2:330989/250‑1 (MQ=25)    ttATCTTCTTCTCTTTCAGTCTTTCTTGATATGAATAATGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAAcc                                                    <  2:75181/249‑1 (MQ=25)      aTCTTCTTCTCTTTCAGTCTTTCTTGATATGAATAATGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCAttt                                                >  2:143167/1‑251 (MQ=21)        cttcttctCTTTCAGTCTTTCTTGATATGAATAATGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCAttttt                                              >  2:219413/1‑251 (MQ=21)                       tctttcttGATATGAATAATGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGCTGTTg                               <  1:115719/251‑1 (MQ=18)                          ttcttGATATGAATAATGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGCTGTTGCtt                            >  2:705546/1‑251 (MQ=18)                               gatctgactactacTGATACTGTCCTCCTTGATCACTATGAAATATCACATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGAATTATCTGCTCTATGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAATATAGTTTTTCTCCTCTTAAATTAACTTCTGTTACATCTATAAACTATTTTTGCTTTGGTGCTGTTGCTTCaaaa                       >  2:268796/14‑251 (MQ=11)                               gATATGAATAATGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGCTGTTGCTTCaaaa                       >  2:529396/1‑251 (MQ=18)                                     aataatGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATAATGGAGATAAGTATAGATTTTCTCCTCTTAAAGTAAATTCTGTTACATCTATAGACCATTTTTGATTTGGAGCTGTTGCTTCAAAAtctct                  >  1:532961/1‑250 (MQ=255)                                         atGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGCTGTTGCTTCAAAATCTCTCTTaa             >  1:125834/1‑251 (MQ=14)                                          tGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAGTTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGc                                    >  1:594419/1‑227 (MQ=9)                                          tGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGc                                    <  2:594419/227‑1 (MQ=14)                                          tGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGCTGTTGCTTCAAAATCTCTCTTAat            >  2:250399/1‑251 (MQ=14)                                          tGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGCTGTTGCTTCAAAATCTCTCTTAat            >  1:290364/1‑251 (MQ=14)                                            cTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGCTGTTGCTTCAAAATCTCTCTTAata           <  1:307749/250‑1 (MQ=14)                                               aTACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGCTGTTGCTTCAAAATCTCTCTTAATATGAt       <  1:250399/251‑1 (MQ=14)                                                 aCTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGCTGTTGCTTCAAAATCTCTCTTAATATGATTa     <  2:16853/251‑1 (MQ=14)                                                   tGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGCTGTTGCTTCAAAATCTCTCTTAATATGATTATc   <  2:228608/251‑1 (MQ=14)                                                    gTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGCTGTTGCTTCAAAATCTCTCTTAATATGATTATCa  >  1:374484/1‑251 (MQ=11)                                                                                                                                                                                                                                                      |                                                         GAGTTATCTTCTTCTCTTTCAGTCTTTCTTGATATGAATAATGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGCTTTTCTCCTCTTAAATTAAATTCTGTTACATCTGTAAACCATTTTTGATTTGGAGCTGTTGCTTCAAAATCTCTCTTAATATGATTATCA  >  CP028101/693727‑694028

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑