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%	35.2 / NA	19	pseudogene (478/1276 nt)	C7Y58_04430	ISL3 family transposase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (7/12);  total (7/12)

ATCAATATTTTTAACAGACTTAAATTCATCAATACAAATAGCTTCAGGTAAATGTTCTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATCCTTACAAATATATCTTTGTACAGTAAGCTCAAGTTCAATATTGTAA  >  CP028101/901113‑901413                                                         |                                                                                                                                                                                                                                                     aTCAATATTTTTAACAGACTTAAATTCATCAATACAAATAGCTTCAGGTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTAc                                                    <  2:788013/251‑1 (MQ=14)      tatTTTTAACAGACTTAAATTCATCAATACAAATAGCTTCAGGTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTATATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATc                                                >  1:640055/1‑250 (MQ=14)      tatTTTTAACAGACTTAAATTCATCAATACAAATAGCTTCAGGTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATc                                                >  1:347170/1‑250 (MQ=14)       atTTTTAACAGACTTAAATTCATCAATACAAATAGCTTCAGGTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGAGGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATc                                                >  1:826460/1‑249 (MQ=14)       atTTTTAACAGACTTAAATTCATCAATACAAATAGCTTCAGGTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGACGTAAGAGAAATAGTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATc                                                >  1:819877/1‑249 (MQ=14)                  aCTTAAATTCATCAATACAAATAGCTTCAGGTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATCCTTACAAat                                       <  1:212877/247‑1 (MQ=14)                   cTTAAATTCATCAATACAAATAGCTTCAGGTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATCCTTACAAATATATc                                  <  2:265730/251‑1 (MQ=14)                   cTTAAATTCATCAATACAAATAGCTTCAGGTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATCCTTACAAATATATc                                  <  2:107356/251‑1 (MQ=14)                     tAAATTCATCAATACAAATAGCTTCAGGTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATCCTTACAAATATATCtt                                <  1:198085/251‑1 (MQ=14)                      aaaTTCATCAATACAAATAGCTTCAGGTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATCCTTACAAATATATCttt                               >  1:593387/1‑251 (MQ=14)                          tcatcaATACAAATAGCTTCAGGTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGTAAAGTTTTTTTTACAATCCTTACAAATATATCTTTGTAc                           <  2:292231/251‑1 (MQ=14)                          tcatcaATACAAATAGCTTCAGGTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATCCTTACAAATATATCTTTGTAc                           <  1:64146/251‑1 (MQ=14)                          tcatcaATACAAATAGCTTCAGGTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATCCTTACAAATATATCTTTGTAc                           <  1:156514/251‑1 (MQ=14)                            atcaATACAAATAGCTTCAGGTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATCCTTACAAATATATCTTTGTACAg                         <  2:313490/251‑1 (MQ=14)                                aTACAAATAGCTTCAGGTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTAGAAGGTGAAAAGTTTTTTTTACAATCCTTACAGATATATCTTTGTACAGTAAg                     >  1:613038/1‑251 (MQ=14)                                    aaaTAGCTTCAGGTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGTAATATTGTATCTTTTAGCAATAGATGTAAGAGACATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATCCTTACAAATATATCTTTGTACAGTAAGCTCa                 <  1:771800/251‑1 (MQ=14)                                     aaTAGCTTCAGGTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTATAGTTAGCACTAACAATATTAGAGGAAGGTGAAAAGTTTTTTTGACAATCCTTACAAat                                       >  1:672024/1‑228 (MQ=255)                                     aaTAGCTTCAGGTAAATGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATCCTTACAAat                                       <  2:672024/228‑1 (MQ=14)                                                   aaTGTTTTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATCCTTACAAATATATCTTTGTACAGTAAGCTCAAGTTCAATATTGTaa  <  2:707255/251‑1 (MQ=17)                                                         |                                                                                                                                                                                                                                                     ATCAATATTTTTAACAGACTTAAATTCATCAATACAAATAGCTTCAGGTAAATGTTCTTTATTAACTTTAAAATCAGAATAGCAGTTATCCATAATTCTTTGAACAGAAGGAATGGAAATATTGTATCTTTTAGCAATAGATGTAAGAGAAATATTTTTTTGAAGCTCAAGCGCAATAGCATACTTAAGATTATTAGATATACTAGAGTTATCACTAACAATATTAGTGGAAGGTGAAAAGTTTTTTTTACAATCCTTACAAATATATCTTTGTACAGTAAGCTCAAGTTCAATATTGTAA  >  CP028101/901113‑901413

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑