Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,960,851	G→A	A59T (GCA→ACA)	rep →	ATP‑dependent DNA helicase Rep

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,960,851	0	G	A	100.0%	72.8 / NA	22	A59T (GCA→ACA)	rep	ATP‑dependent DNA helicase Rep
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (9/13);  total (9/13)

TTACCGGCCCCTGCCTGGTGCTGGCGGGCGCGGGTTCCGGTAAAACTCGTGTTATCACCAATAAAATCGCCCATCTGATCCGCGGTTGCGGTTATCAGGCGCGGCACATTGCGGCGGTGACCTTTACTAATAAAGCAGCGCGCGAGATGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACGTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATGAAAGCG  >  NC_000913/3960717‑3960985                                                                                                                                       |                                                                                                                                       ttACCGGCCCCTGCCTGGTGCTGGCGGGCGCGGGTTCCGGTAAAACTCGTGTTATCACCAATAAAATCGCCCATCTGATCCGCGGTTGCGGTTATCAGGCGCGGCACATTGCGGCGGTGACCTTTACTAATAAAACAgcg                                                                                                                                   <  2:250678/140‑1 (MQ=255)   aCCGGCCCCTGCCTGGTGCTGGCGGGCGCGGGTTCCGGTAAAACTCGTGTTATCACCAATAAAATCGCCCATCTGATCCGCGGTTGCGGTTATCAGGCGCGGCACATTGCGGCGGTGACCTTTACTAATAAAACAgcgcg                                                                                                                                 <  2:238444/140‑1 (MQ=255)   aCCGGCCCCTGCCTGGTGCTGGCGGGCGCGGGTTCCGGTAAAACTCGTGTTATCACCAATAAAATCGCCCATCTGATCCGCGGTTGCGGTTATCAGGCGCGGCACATTGCGGCGGTGACCTTTACTAATAAAACAgcgcg                                                                                                                                 <  2:220663/140‑1 (MQ=255)   aCCGGCCCCTGCCTGGTGCTGGCGGGCGCGGGTTCCGGTAAAACTCGTGTTATCACCAATAAAATCGCCCATCTGATCCGCGGTTGCGGTTATCAGGCGCGGCACATTGCGGCGGTGACCTTTACTAATAAAACAgcgcg                                                                                                                                 <  2:205398/140‑1 (MQ=255)                    gCTGGCGGGCGCGGGTTCCGGTAAAACTCGTGTTATCACCAATAAAATCGCCCATCTGATCCGCGGTTGCGGTTATCAGGCGCGGCACATTGCGGCGGTGACCTTTACTAATAAAACAGCGCGCGAGATGAAAGAGCgtg                                                                                                                <  1:387340/140‑1 (MQ=255)                        gcgggcgCGGGTTCCGGTAAAACTCGTGTTATCACCAATAAAATCGCCCATCTGATCCGCGGTTGCGGTTATCAGGCGCGGCACATTGCGGCGGGGGGCTTTTTTTATAAAAAAACGCGCGGGAAGAAAAAGGGGGTAgg                                                                                                            >  2:514797/1‑140 (MQ=255)                                              cTCGTGTTATCACCAATAAAATCGCCCATCTGATCCGCGGTTGCGGTTATCAGGCGCGGCACATTGCGGCGGTGACCTTTACTAATAAAACAGCGCGCGAGATGAAAGAGCGTGTAGGGCAGACGCt                                                                                                   >  2:245509/1‑127 (MQ=255)                                              cTCGTGTTATCACCAATAAAATCGCCCATCTGATCCGCGGTTGCGGTTATCAGGCGCGGCACATTGCGGCGGTGACCTTTACTAATAAAACAGCGCGCGAGATGAAAGAGCGTGTAGGGCAGACGCt                                                                                                   <  1:245509/127‑1 (MQ=255)                                                      aTCACCAATAAAATCGCCCATCTGATCCGCGGTTGCGGTTATCAGGCGCGGCACATTGCGGCGGTGACCTTTACTAATAAAACAGCGCGCGAGATGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTgg                                                                              >  1:414953/1‑140 (MQ=255)                                                            aaTAAAATCGCCCATCTGATCCGCGGTTGCGGTTATCAGGCGCGGCACATTGCGGCGGTGACCTTTACTAATAAAACAGCGCGCGAGATGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCtgat                                                                        <  1:26127/140‑1 (MQ=255)                                                            aaTAAAATCGCCCATCTGATCCGCGGTTGCGGTTATCAGGCGCGGCACATTGCGGCGGTGACCTTTACTAATAAAACAGCGCGCGAGATGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCtgat                                                                        <  2:33238/140‑1 (MQ=255)                                                                 aaTCGCCCATCTGATCCGCGGTTGCGGTTATCAGGCGCGGCACATTGCGGCGGTGAACCTTACTAAAAAAACACCGCGCGAGATGAAAGAGCGGGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTgatgatac                                                                   >  2:139813/1‑138 (MQ=255)                                                                  aTCGCCCATCTGATCCGCGGTTGCGGTTATCAGGCGCGGCACATTGCGGCGGTGACCTTTACTAATAAAACAGCGCGCGAGATGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGAtctc                                                                  <  1:376761/140‑1 (MQ=255)                                                                     gCCCATCTGATCCGCGGTTGCGGTTATCAGGCGCGGCACATTGCGGCGGTGACCTTTACTAATAAAACAGCGCGCGAGATGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCTAc                                                               >  2:47053/1‑140 (MQ=255)                                                                           cTGATCCGCGGTTGCGGTTATCAGGCGCGGCACATTGCGGCGGTGACCTTTACTAATAAAACAGCGCGCGAGATGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCa                                                         <  2:414953/140‑1 (MQ=255)                                                                                ccGCGGTTGCGGTTATCAGGCGCGGCACATTGCGGCGGTGACCTTTACTAATAAAACAGCGCGCGAGATGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACGt                                                    <  1:256815/140‑1 (MQ=255)                                                                                  gcggttgcggttATCAGGCGCGGCACATTGCGGCGGTGACCTTTACTAATAAAACAGCGCGCGAGATGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACGTTg                                                  <  1:514797/140‑1 (MQ=255)                                                                                                     gcgGCACATTGCGGCGGTGACCTTTACTAATAAAACAGCGCGCGAGATGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACGTTGGGGCTGGATATCATCAAAc                               >  2:222783/1‑140 (MQ=255)                                                                                                      cgGCACATTGCGGCGGTGACCTTTACTAATAAAACAGCGCGCGAGATGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGGGCGTGGGCTGATGATCTCCACTTTCCATACGTTGGGGCTGGATATCATCCAAcg                              >  2:433837/1‑140 (MQ=255)                                                                                                               gcggcgGTGACCTTTACTAATAAAACAGCGCGCGAGATGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACGTTGGGGCTGGATATCATCAAACGCGAGTATgc                     <  1:139813/140‑1 (MQ=255)                                                                                                                   cggTGACCTTTACTAATAAAACAGCGCGCGAGATGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACGTTGGGGCTGGATATCATCAAACGCGAGTATgcggcg                 >  2:340579/1‑140 (MQ=255)                                                                                                                                  ataaAACAGCGCGCGAGATGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACGTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATGAAAGCg  >  2:239780/1‑140 (MQ=255)                                                                                                                                  ataaAACAGCGCGCGAGATGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACGTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATGAAAGCg  >  2:200858/1‑140 (MQ=255)                                                                                                                                  ataaAACAGCGCGCGAGATGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACGTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATGAAAGCg  >  1:502699/1‑140 (MQ=255)                                                                                                                                       |                                                                                                                                       TTACCGGCCCCTGCCTGGTGCTGGCGGGCGCGGGTTCCGGTAAAACTCGTGTTATCACCAATAAAATCGCCCATCTGATCCGCGGTTGCGGTTATCAGGCGCGGCACATTGCGGCGGTGACCTTTACTAATAAAGCAGCGCGCGAGATGAAAGAGCGTGTAGGGCAGACGCTGGGGCGCAAAGAGGCGCGTGGGCTGATGATCTCCACTTTCCATACGTTGGGGCTGGATATCATCAAACGCGAGTATGCGGCGCTTGGGATGAAAGCG  >  NC_000913/3960717‑3960985

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑