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%	61.2 / NA	29	pseudogene (856/1244 nt)	C7Y58_03400	IS3 family transposase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (20/9);  total (20/9)

AGTTATCTTCTTCTCTTTCAGTCTTTCTTGATATGAATAATGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGCTTTTCTCCTCTTAAATTAAATTCTGTTACATCTGTAAACCATTTTTGATTTGGAGCTGTTGCTTCAAAATCTCTCTTAATATGATTA  >  CP028101/693728‑694025                                                                                                                                                                                                                                                     |                                                      aGTTATCTTCTTCTCTTTCAGTCTTTCTTGATATGAATAATGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAAc                                                  <  1:73741/250‑1 (MQ=25)  gTTATCTTCTTCTCTTTCAGTCTTTCTTGATATGAATAATGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCa                                                >  1:130298/1‑251 (MQ=21)          cttctCTTTCAGTCTTTCTTGATATGAATAATGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGAt                                        <  2:123400/251‑1 (MQ=21)              tctTTCAGTCTTTCTTGATATGAATAATGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTgg                                    >  1:500974/1‑251 (MQ=21)               ctTTCAGTCTTTCTTGATATGAATAATGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGa                                   >  2:144479/1‑251 (MQ=21)                 ttCAGTCTTTCTTGATATGAATAATGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGc                                 <  2:364502/251‑1 (MQ=21)                     gTCTTTCTTGATATGAATAATGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGc                                 <  2:376658/247‑1 (MQ=18)                     gTCTTTCTTGATATGAATAATGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGc                                 >  1:376658/1‑247 (MQ=18)                       ctttcttGATATGAATAATGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATAAATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGCTGTTg                            >  2:907001/1‑250 (MQ=18)                         ttcttGATATGAATAATGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGCTGTTGCtt                         >  2:372891/1‑251 (MQ=18)                              gATATGAATAATGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGCTGTTGCTTCaaaa                    >  2:749543/1‑251 (MQ=18)                              gATATGAATAATGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGCTGTTGCTTCaaaa                    >  1:224380/1‑251 (MQ=18)                              gATATGAATAATGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCAAAATATCATACGAAACTATATATCTGCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGCTGTTGCTTCaaaa                    >  1:755467/1‑251 (MQ=16)                                   gAATAATGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGCTGTTGCTTCAAAAtct                 >  1:202005/1‑249 (MQ=17)                                   gAATAATGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGCTGTTGCTTCAAAAtct                 >  2:639825/1‑249 (MQ=17)                                   gAATAATGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGCTGTTGCTTCAAAAtct                 >  2:566973/1‑249 (MQ=17)                                   gAATAATGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGCTGTTGCTTCAAAAtct                 >  1:583429/1‑249 (MQ=17)                                     ataatGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGCTGTTGCTTCAAAAtctct               >  1:535992/1‑249 (MQ=17)                                        atGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGCTGTTGCTTCAAAATCTCTCTTaa          >  2:48025/1‑251 (MQ=14)                                         tGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGTACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGCTGTTGCTTCAAAATCTCTCTTAat         >  2:596995/1‑251 (MQ=14)                                         tGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGCTGTTGCTTCAAAATCTCTCTTAat         >  2:553352/1‑251 (MQ=14)                                         tGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGCTGTTGCTTCAAAATCTCTCTTAat         >  2:601584/1‑251 (MQ=14)                                         tGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGCTGTTGCTTCAAAATCTCTCTTAat         >  1:6185/1‑251 (MQ=14)                                         tGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGCTGTCGCTTCAAAATCTCTCTTAat         >  1:622708/1‑251 (MQ=14)                                           cTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGCTGTTGCTTCAAAATCTCTCTTAata        <  1:536439/250‑1 (MQ=14)                                           cTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGCTGTTGCTTCAAAATCTCTCTTAata        <  2:755467/250‑1 (MQ=14)                                           cTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCACTTTCTTTAAATGCTAAATTTATCATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGCTGTTGCTTCAAAATCTCTCTTAata        <  1:639825/250‑1 (MQ=9)                                              aTACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGCTGTTGCTTCAAAATCTCTCTTAATATGAt    <  2:202005/251‑1 (MQ=14)                                                aCTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGTTTTTCTCCTCTTAAATTAAATTCTGTTACATCTATAAACCATTTTTGATTTGGAGCTGTTGCTTCAAAATCTCTCTTAATATGATTa  <  1:453302/251‑1 (MQ=14)                                                                                                                                                                                                                                                     |                                                      AGTTATCTTCTTCTCTTTCAGTCTTTCTTGATATGAATAATGCTGATACTGTCATCCTTGATCACTATGAAATATCAAATTTTCATAGTTTTCATTTTCTTTAAATGCTAAATTTAACATATGATTTATCTGCTCCAAGTTAGGACTGCGCGAAATATCATACGAAACTATATATCTTCCATAAGCATCTAATATTGGAGATAAGTATAGCTTTTCTCCTCTTAAATTAAATTCTGTTACATCTGTAAACCATTTTTGATTTGGAGCTGTTGCTTCAAAATCTCTCTTAATATGATTA  >  CP028101/693728‑694025

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑