Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP028101	901,169	C→T	pseudogene (478/1276 nt)	C7Y58_04430 ←	ISL3 family transposase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP028101	901,169	0	C	T	100.0%	31.8 / NA	19	pseudogene (478/1276 nt)	C7Y58_04430	ISL3 family transposase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (8/11);  total (8/11)

ATTTTTAACAGACTTAAATTCATCAATACAAATAGCTTCAGGTAAATGTTCTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATCCTTACAAATATATCTTTGTACAGTAAGCTCAAGTTCAATATTGTAA  >  CP028101/901119‑901413                                                   |                                                                                                                                                                                                                                                     atTTTTAACAGACTTAAATTCATCAATACAAATAGCTTCAGGTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGTGCAATAGCATACTTACGATTATTAGATATACTAGAGTTATCACTCACAATATTAGTGGCAGGTGAACAGTTTTTTTTACactc                                                >  2:312550/1‑246 (MQ=11) atTTTTAACAGACTTAAATTCATCAATACAAATAGCTTCAGGTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATc                                                >  2:638966/1‑249 (MQ=14)       aaCAGACTTAAATTCATCAATACAAATAGCTTCAGGTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATCCTTACaaa                                        <  2:172389/251‑1 (MQ=14)           gACTTAAGTTCATCAATACAAATAGCTTCAGGTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATCCTTACAAatata                                    >  1:696438/1‑251 (MQ=14)           gACTTAAATTCATCAATACAAATAGCTTCAGGTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATCCTTACAAatata                                    >  1:275093/1‑251 (MQ=14)           gACTTAAATTCATCAATACAAATAGCTTCAGGTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATCCTTACAAatata                                    >  2:60356/1‑251 (MQ=14)             cTTAAATTCATCAATACAAATAGCTTCAGGTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATCCTTACAAATATATc                                  <  1:220797/251‑1 (MQ=14)               tAAATTCATCAATACAAATAGCTTCAGGTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATCCTTACAAATATATCtt                                <  1:462902/251‑1 (MQ=14)                      atcaATACAAATAGCTTCAGTTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAGGGAATGGAAATATTGTATCTTTTAGCAATAGATATAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATCCTTACAAATATATCTTTGTACAg                         <  1:593214/251‑1 (MQ=9)                      atcaATACAAATAGCTTCAGGTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATCCTTACAAATATATCTTTGTACAg                         <  1:638966/251‑1 (MQ=14)                         aaTACAAATAGCTTCAGGTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATCCTTACAAATATATCTTTGTACAGTaa                      <  2:696438/251‑1 (MQ=14)                          aTACAAATAGCTTCAGGTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATCCTTACAAATATATCTTTGTACAGTAAg                     >  1:685843/1‑251 (MQ=14)                          aTACAAATAGCTTCAGGTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATCCTTACAAATATATCTTTGTACAGTAAg                     >  1:397226/1‑251 (MQ=14)                              aaaTAGCTTCAGGTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATCCTTACAAATATATCTTTGTACAGTAAGCTCa                 <  2:437017/251‑1 (MQ=14)                                    cTTCAGGTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATCCTTACAAATATATCTTTGTACAGTAAGCTCAAGTTCa           >  1:699215/1‑251 (MQ=14)                                      tCAGGTAAATGTTTTTTATTAACTTTAAAATCATAATAGCAGTTATCCATAATTCTTTGGACAGAAAGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATCCTTACAAATATATCTTTGTACAGTAAGCTCAAGTTCAat         <  2:505657/251‑1 (MQ=9)                                          gTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATCCTTACAAATATATCTTTGTACAGTAAGCTCAAGTTCAatat       <  2:685843/249‑1 (MQ=14)                                             aaTGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATCCTTACAAATATATCTTTGTACAGTAAGCTCAAGTTCAATATTGTaa  <  2:413541/251‑1 (MQ=17)                                             aaTGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATCCTTACAAATATATCTTTGTACAGTAAGCTCAAGTTCAATATTGTaa  <  1:119345/251‑1 (MQ=17)                                                   |                                                                                                                                                                                                                                                     ATTTTTAACAGACTTAAATTCATCAATACAAATAGCTTCAGGTAAATGTTCTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATCCTTACAAATATATCTTTGTACAGTAAGCTCAAGTTCAATATTGTAA  >  CP028101/901119‑901413

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑