Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	1	1,453,226	2 bp→GC	coding (429‑430/1737 nt)	unknown →	Coupling protein VirD4, ATPase required for T‑DNA transfer

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	1	1,453,226	0	A	G	100.0%	50.0 / NA	16	L143L (TTA→TTG)	unknown	Coupling protein VirD4, ATPase required for T‑DNA transfer
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (3/13);  total (3/13)
*	1	1,453,227	0	T	C	100.0%	53.1 / NA	16	L144M (TTA→CTG)	unknown	Coupling protein VirD4, ATPase required for T‑DNA transfer
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (3/13);  total (3/13)

CCTAAAAAATCCCTTTATGGTAACGCTGAATTTGCCACAAAATCAGAAGTACAAAAAATGGGTTTATTGGAAGAAAAAAACGGGATTATTGTCGGCAAACTTGGTAATAAACTTCTTCGCTTTATCGGTGCACAATTCGTTTCGTTGGCCGCACCGACCCGAGGTGGGAAAGGAATAGGGATTGTCATACCGAATTTATTAGAGTGGCAACAATCAGTTGTTGTGAAAGATGTTAAAAACGAATGTTATCGCATTACCAGTAAATACCGTCAAAAAATATTGGGGCAAAAAGTCTATCG  >  1/1453029‑1453327                                                                                                                                                                                                      ||                                                                                                     ccTAAAAAATCCCTTTATGGTAACGCTGAATTTGCCACAAAATCAGAAGTACAAAAAATGGGTTTATTGGAAGAAAAAAACGGGATTATTGTCGGCAAACTCGGTAATAAACTGCTCCGTTTTATCGGTGCGCAATTTGTTTCACTGGCAGCGCCGACACGGGGAGGTAAAAGCGTAGGGATTGTTATTCCAAATTTGCTGGCATGGGAACAATCTGTGGTTGTGAAGGACATTAAAAACGAATGCTATCg                                                  <  1:251483/251‑1 (MQ=255)        aaTCCCTTTATGGTAACGCTGAATTTGCCACAAAATCAGAAGTACAAAAAATGGGTTTATTGGAAGAAAAAAACGGGATTATTGTCGGCAAACTCGGTAATAAACTGCTCCGTTTTATCGGTGCGCAATTTGTTTCACTGGCAGCGCCGACACGGGGAGGTAAAAGCGTAGGGATTGTTATTCCAAATTTGCTGGCATGGGAACAATCTGTGGTTGTGAAGGACATTAAAAACGAATGCTATCgtatcacc                                           <  1:673060/251‑8 (MQ=255)        aaTCCCTTTATGGTAACGCTGAATTTGCCACAAAATCAGAAGTACAAAAAATGGGTTTATTGGAAGAAAAAAACGGGATTATTGTCGGCAAACTCGGTAATAAACTGCTCCGTTTTATCGGTGCGCAATTTGTTTCACTGGCAGCGCCGACACGGGGAGGTAAAAGCGTAGGGATTGTTATTCCAAATTTGCTGGCATGGGAACAATCTGTGGTTGTGAAGGACATTAAAAACGAATGCTATCgtatcacc                                           <  1:690776/251‑8 (MQ=255)        aaTCCCTTTATGGTAACGCTGAATTTGCCACAAAATCAGAAGTACAAAAAATGGGTTTATTGGAAGAAAAAAACGGGATTATTGTCGGCAAACTCGGTAATAAACTGCTCCGTTTTATCGGTGCGCAATTTGTTTCACTGGCAGCGCCGACACGGGGAGGTAAAAGCGTAGGGATTGTTATTCCAAATTTGCTGGCATGGGAACAATCTGTGGTTGTGAAGGACATTAAAAACGAATGCTATCgtatcacc                                           <  1:819439/251‑8 (MQ=255)             cTTTATGGTAACGCTGAATTTGCCACAAAATCAGAAGTACAAAAAATGGGTTTATTGGAAGAAAAAAACGGGATTATTGTCGGCAAACTCGGTAATAAACTGCTCCGTTTTATCGGTGCGCAATTTGTTTCACTGGCAGCGCCGACACGGGGAGGTAAAAGCGTAGGGATTGTTATTCCAAATTTGCTGGCATGGGAACAATCTGTGGTTGTGAAGGACATTAAAAACGAATgc                                                       <  1:681836/234‑2 (MQ=255)             cTTTATGGTAACGCTGAATTTGCCACAAAATCAGAAGTACAAAAAATGGGTTTATTGGAAGAAAAAAACGGGATTATTGTCGGCAAACTCGGTAATAAACTGCTCCGTTTTATCGGTGCGCAATTTGTTTCACTGGCAGCGCCGACACGGGGAGGTAAAAGCGTAGGGATTGTTATTCCAAATTTGCTGGCATGGGAACAATCTGTGGTTGTGAAGGACATTAAAAACGAATGCTATCGTATCACCAGTaa                                      <  1:207452/251‑1 (MQ=255)             cTTTATGGTAACGCTGAATTTGCCACAAAATCAGAAGTACAAAAAATGGGTTTATTGGAAGAAAAAAACGGGATTATTGTCGGCAAACTCGGTAATAAACTGCTCCGTTTTATCGGTGCGCAATTTGTTTCACTGGCAGCGCCGACACGGGGAGGTAAAAGCGTAGGGATTGTTATTCCAAATTTGCTGGCATGGGAACAATCTGTGGTTGTGAAGGACATTAAAAACGAATGCTATCGTATCACCAGTaa                                      >  1:431897/1‑251 (MQ=255)             cTTTATGGTAACGCTGAATTTGCCACAAAATCAGAAGTACAAAAAATGGGTTTATTGGAAGAAAAAAACGGGATTATTGTCGGCAAACTCGGTAATAAACTGCTCCGTTTTATCGGTGCGCAATTTGTTTCACTGGCAGCGCCGACACGGGGAGGTAAAAGCGTAGGGATTGTTATTCCAAATTTGCTGGCATGGGAACAATCTGTGGTTGTGAAGGACATTAAAAACGAATGCTATCGTATCACCAGTaa                                      <  1:81259/251‑1 (MQ=255)                 aTGGTAACGCTGAATTTGCCACAAAATCAGAAGTACAAAAAATGGGTTTATTGGAAGAAAAAAACGGGATTATTGTCGGCAAACTCGGTAATAAACTGCTCCGTTTTATCGGTGCGCAATTTGTTTCACTGGCAGCGCCGACACGGGGAGGTAAAAGCGTAGGGATTGTTATTCCAAATTTGCTGGCATGGGAACAATCTGTGGTTGTGAAGGACATTAAAAACGAATGCTATCGTATCACCAGTAAAt                                    <  1:40726/249‑1 (MQ=255)                 aTGGTAACGCTGAATTTGCCACAAAATCAGAAGTACAAAAAATGGGTTTATTGGAAGAAAAAAACGGGATTATTGTCGGCAAACTCGGTAATAAACTGCTCCGTTTTATCGGTGCGCAATTTGTTTCACTGGCAGCGCCGACACGGGGAGGTAAAAGCGTAGGGATTGTTATTCCAAATTTGCTGGCATGGGAACAATCTGTGGTTGTGAAGGACATTAAAAACGAATGCTATCGTATCACCAGTAAATat                                  <  1:86244/251‑2 (MQ=255)                     tAACGCTGAATTTGCCACAAAATCAGAAGTACAAAAAATGGGTTTATTGGAAGAAAAAAACGGGATTATTGTCGGCAAACTCGGTAATAAACTGCTCCGTTTTATCGGTGCGCAATTTGTTTCACTGGCAGCGCCGACACGGGGAGGTAAAAGCGTAGGGATTGTTATTCCAAATTTGCTGGCATGGGAACAATCTGTGGTTGTGAAGGACATTAAAAACGAATGCTATCGTATCACCAGTAAATatcgac                              <  1:201076/251‑6 (MQ=255)                                   ccACAAAATCAGAAGTACAAAAAATGGGTTTATTGGAAGAAAAAAACGGGATTATTGTCGGCAAACTCGGTAATAAACTGCTCCGTTTTATCGGTGCGCAATTTGTTTCACTGGCAGCGCCGACACGGGGAGGTAAAAGCGTAGGGATTGTTATTCCAAATTTGCTGGCATGGGAACAATCTGTGGTTGTGAAGGACATTAAAAACGAATGCTATCGTATCACCAGTAAAt                                    <  1:761182/231‑1 (MQ=255)                                          aTCAGAAGTACAAAAAATGGGTTTATTGGAAGAAAAAAACGGGATTATTGTCGGCAAACTCGGTAATAAACTGCTCCGTTTTATCGGTGCGCAATTTGTTTCACTGGCAGCGCCGACACGGGGAGGTAAAAGCGTAGGGATTGTTATTCCAAATTTGCTGGCATGGGAACAATCTGTGGTTGTGAAGGACATTAAAAACGAATGCTATCGTATCACCAGTAAATATCGACAAAAAATATTAGGGCaaaagg         >  1:163853/1‑249 (MQ=255)                                               aaGTACAAAAAATGGGTTTATTGGAAGAAAAAAACGGGATTATTGTCGGCAAACTCGGTAATAAACTGCTCCGTTTTATCGGTGCGCAATTTGTTTCACTGGCAGCGCCGACACGGGGAGGTAAAAGCGTAGGGATTGTTATTCCAAATTTGCTGGCATGGGAACAATCTGTGGTTGTGAAGGACATTAAAAACGAATGCTATCGTATCACCAGTAAATATCGACAAAAAATATTAGGGCaaaaggtatat    <  1:877799/251‑8 (MQ=255)                                                 gTACAAAAAATGGGTTTATTGGAAGAAAAAAACGGGATTATTGTCGGCAAACTCGGTAATAAACTGCTCCGTTTTATCGGTGCGCAATTTGTTTCACTGGCAGCGCCGACACGGGGAGGTAAAAGCGTAGGGATTGTTATTCCAAATTTGCTGGCATGGGAACAATCTGTGGTTGTGAAGGACATTAAAAACGAATGCTATCGTATCACCAGTAAATATCGACAAAAAATATTAGGGCAAAAGGTATATCg  >  1:410405/1‑251 (MQ=255)                                                  tACAAAAAATGGGTTTATTGGAAGAAAAAAACGGGATTATTGTCGGCAAACTCGGTAATAAACTGCTCCGTTTTATCGGTGCGCAATTTGTTTCACTGGCAGCGCCGACACGGGGAGGTAAAAGCGTAGGGATTGTTATTCCAAATTTGCTGGCATGGGAACAATCTGTGGTTGTGAAGGACATTAAAAACGAATGCTATCGTATCACCAGTAAATATCGACAAAAAATATTAGGGCAAAAGGTATATCg  <  1:71111/250‑1 (MQ=255)                                                                                                                                                                                                      ||                                                                                                     CCTAAAAAATCCCTTTATGGTAACGCTGAATTTGCCACAAAATCAGAAGTACAAAAAATGGGTTTATTGGAAGAAAAAAACGGGATTATTGTCGGCAAACTTGGTAATAAACTTCTTCGCTTTATCGGTGCACAATTCGTTTCGTTGGCCGCACCGACCCGAGGTGGGAAAGGAATAGGGATTGTCATACCGAATTTATTAGAGTGGCAACAATCAGTTGTTGTGAAAGATGTTAAAAACGAATGTTATCGCATTACCAGTAAATACCGTCAAAAAATATTGGGGCAAAAAGTCTATCG  >  1/1453029‑1453327

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑