Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	1	1,453,280	C→T	R161R (CGC→CGT)	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	1,453,280	0	C	T	100.0%	97.3 / NA	29	R161R (CGC→CGT)	unknown	Coupling protein VirD4, ATPase required for T‑DNA transfer
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (13/16);  total (13/16)

CTTTATGGTAACGCTGAATTTGCCACAAAATCAGAAGTACAAAAAATGGGTTTATTGGAAGAAAAAAACGGGATTATTGTCGGCAAACTTGGTAATAAACTTCTTCGCTTTATCGGTGCACAATTCGTTTCGTTGGCCGCACCGACCCGAGGTGGGAAAGGAATAGGGATTGTCATACCGAATTTATTAGAGTGGCAACAATCAGTTGTTGTGAAAGATGTTAAAAACGAATGTTATCGCATTACCAGTAAATACCGTCAAAAAATATTGGGGCAAAAAGTCTATCGCTTTGCCCCATTTGACCGTAACACGCACCGATTTAATCCATTGGATTGTATTGATATGCGCGACCGAGCACGCGCCGAACTCGATTTAAAAAATCAGGCAATGGGCTTATATCCGCTCACCGGCGACCCGGATAAAGACTTTTGGCAGCACCAGGCACAAAATCTTTTTGTGGCAACCACTTTTTTACTGTGGGATA  >  1/1453041‑1453524                                                                                                                                                                                                                                                |                                                                                                                                                                                                                                                     cTTTATGGTAACGCTGAATTTGCCACAAAATCAGAAGTACAAAAAATGGGTTTATTGGAAGAAAAAAACGGGATTATTGTCGGCAAACTCGGTAATAAACTGCTCCGTTTTATCGGTGCGCAATTTGTTTCACTGGCAGCGCCGACACGGGGAGGTAAAAGCGTAGGGATTGTTATTCCAAATTTGCTGGCATGGGAACAATCTGTGGTTGTGAAGGACATTAAAAACGAATGCTATCGTATCACCAGTaa                                                                                                                                                                                                                                           <  1:81259/251‑1 (MQ=255) cTTTATGGTAACGCTGAATTTGCCACAAAATCAGAAGTACAAAAAATGGGTTTATTGGAAGAAAAAAACGGGATTATTGTCGGCAAACTCGGTAATAAACTGCTCCGTTTTATCGGTGCGCAATTTGTTTCACTGGCAGCGCCGACACGGGGAGGTAAAAGCGTAGGGATTGTTATTCCAAATTTGCTGGCATGGGAACAATCTGTGGTTGTGAAGGACATTAAAAACGAATGCTATCGTATCACCAGTaa                                                                                                                                                                                                                                           <  1:207452/251‑1 (MQ=255) cTTTATGGTAACGCTGAATTTGCCACAAAATCAGAAGTACAAAAAATGGGTTTATTGGAAGAAAAAAACGGGATTATTGTCGGCAAACTCGGTAATAAACTGCTCCGTTTTATCGGTGCGCAATTTGTTTCACTGGCAGCGCCGACACGGGGAGGTAAAAGCGTAGGGATTGTTATTCCAAATTTGCTGGCATGGGAACAATCTGTGGTTGTGAAGGACATTAAAAACGAATGCTATCGTATCACCAGTaa                                                                                                                                                                                                                                           >  1:431897/1‑251 (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)                                                                                                                                                                                ttccaaatttgctggcatgggaacaaTCTGTGGTTGTGAAGGACATTAAAAACGAATGCTATCGTATCACCAGTAAATATCGACAAAAAATATTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTATATCCGCTCACCGGCGACCCGGATAAAGAc                                                            <  1:658709/230‑1 (MQ=255)                                                                                                                                                                                               catgggaacaaTCTGTGGTTGTGAAGGACATTAAAAACGAATGCTATCGTATCACCAGTAAATATCGACAAAAAATATTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTATATc                                                                                      >  1:761916/7‑210 (MQ=255)                                                                                                                                                                                                    gaacaaTCTGTGGTTGTGAAGGACATTAAAAACGAATGCTATCGTATCACCAGTAAATATCGACAAAAAATATTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTATATCCGCTCACCGGCGACCCGGATAAAGACTTTTGGCAGCACCAGGcac                                         <  1:601535/249‑1 (MQ=255)                                                                                                                                                                                                         atctgtggttgtGAAGGACATTAAAAACGAATGCTATCGTATCACCAGTAAATATCGACAAAAAATATTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTatat                                                                                       >  1:709998/8‑199 (MQ=255)                                                                                                                                                                                                         atctgtggttgtGAAGGACATTAAAAACGAATGCTATCGTATCACCAGTAAATATCGACAAAAAATATTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTATATCCGCTCACCGGCGACCCGGATAAAGACTTTTGGCAGCACCAGGCACAGAAt                                    >  1:407013/8‑250 (MQ=255)                                                                                                                                                                                                             gtggttgtGAAGGACATTAAAAACGAATGCTATCGTATCACCAGTAAATATCGACAAAAAATATTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTATATCCGCTCACCGGCGACCCGGATAAAGACTTTTGGCAGCACCAGGCACAGAATCtttt                               >  1:222724/4‑251 (MQ=255)                                                                                                                                                                                                                gttgtGAAGGACATTAAAAACGAATGCTATCGTATCACCAGTAAATATCGACAAAAAATATTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTATATCCGCTCACCGGCGACCCGGAt                                                                  <  1:489360/213‑1 (MQ=255)                                                                                                                                                                                                                gttgtGAAGGACATTAAAAACGAATGCTATCGTATCACCAGTAAATATCGACAAAAAATATTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTATATCCGCTCACCGGCGACCCGGATAAAGACTTTTGGCAGCACCAGGCACAGAATCTTTTtgt                            >  1:463565/1‑251 (MQ=255)                                                                                                                                                                                                                  tgtgaaggacattAAAAACGAATGCTATCGTATCACCAGTAAATATCGACAAAAAATATTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTATATCCGCTCACCGGCGACCCGGATAAAGACTTTTGGCAGCACCAGGCACAGAATCTTTTtgtag                          <  1:636583/240‑3 (MQ=255)                                                                                                                                                                                                                   gtgaaggacattAAAAACGAATGCTATCGTATCACCAGTAAATATCGACAAAAAATATTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTATATc                                                                                      >  1:177614/11‑190 (MQ=255)                                                                                                                                                                                                                           cattAAAAACGAATGCTATCGTATCACCAGTAAATATCGACAAAAAATATTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGc                                                                                             >  1:630866/3‑175 (MQ=255)                                                                                                                                                                                                                           cattAAAAACGAATGCTATCGTATCACCAGTAAATATCGACAAAAAATATTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTATATc                                                                                      >  1:353291/3‑182 (MQ=255)                                                                                                                                                                                                                           cattAAAAACGAATGCTATCGTATCACCAGTAAATATCGACAAAAAATATTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTATATCCGCTCACCGGCGACCCGGATAAAGACTTTTGGCAGCACCAGGCACAGAATCTTTTTGTAGCAACCACtt                 >  1:795126/3‑251 (MQ=255)                                                                                                                                                                                                                                 aaaCGAATGCTATCGTATCACCAGTAAATATCGACAAAAAATATTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTATATCCGCTCACCGGCGACCCGGATAAAGACTTTTGGCAGCACCAGGCACAGAATCTTTTTGTAGCAACCACTTTTTTAc           <  1:779473/251‑1 (MQ=255)                                                                                                                                                                                                                                 aaaCGAATGCTATCGTATCACCAGTAAATATCGACAAAAAATATTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTATATCCGCTCACCGGCGACCCGGATAAAGACTTTTGGCAGCACCAGGCACAGAATCTTTTTGTAGCAACCACTTTTTTAc           <  1:806529/251‑1 (MQ=255)                                                                                                                                                                                                                                 aaaCGAATGCTATCGTATCACCAGTAAATATCGACAAAAAATATTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTATATCCGCTCACCGGCGACCCGGATAAAGACTTTTGGCAGCACCAGGCACAGAATCTTTTTGTAGCAACCACTTTTTTAc           <  1:241414/251‑1 (MQ=255)                                                                                                                                                                                                                                       atgctATCGTATCACCAGTAAATATCGACAAAAAATATTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTatat                                                                                       <  1:715876/165‑1 (MQ=255)                                                                                                                                                                                                                                          ctATCGTATCACCAGTAAATATCGACAAAAAATATTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTATATCCGCTCACCGGCGACCCGGATAAAGACTTTTGGCAGCACCAGGCACAGAATCTTTTTGTAGCAACCACTTTTTTACTGTGGGata  >  1:876069/2‑251 (MQ=255)                                                                                                                                                                                                                                                |                                                                                                                                                                                                                                                     CTTTATGGTAACGCTGAATTTGCCACAAAATCAGAAGTACAAAAAATGGGTTTATTGGAAGAAAAAAACGGGATTATTGTCGGCAAACTTGGTAATAAACTTCTTCGCTTTATCGGTGCACAATTCGTTTCGTTGGCCGCACCGACCCGAGGTGGGAAAGGAATAGGGATTGTCATACCGAATTTATTAGAGTGGCAACAATCAGTTGTTGTGAAAGATGTTAAAAACGAATGTTATCGCATTACCAGTAAATACCGTCAAAAAATATTGGGGCAAAAAGTCTATCGCTTTGCCCCATTTGACCGTAACACGCACCGATTTAATCCATTGGATTGTATTGATATGCGCGACCGAGCACGCGCCGAACTCGATTTAAAAAATCAGGCAATGGGCTTATATCCGCTCACCGGCGACCCGGATAAAGACTTTTGGCAGCACCAGGCACAAAATCTTTTTGTGGCAACCACTTTTTTACTGTGGGATA  >  1/1453041‑1453524

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: ‑