Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	1	1,453,322	C→A	V175V (GTC→GTA)	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	1,453,322	0	C	A	100.0%	126.8 / NA	37	V175V (GTC→GTA)	unknown	Coupling protein VirD4, ATPase required for T‑DNA transfer
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (16/21);  total (16/21)

GTACAAAAAATGGGTTTATTGGAAGAAAAAAACGGGATTATTGTCGGCAAACTTGGTAATAAACTTCTTCGCTTTATCGGTGCACAATTCGTTTCGTTGGCCGCACCGACCCGAGGTGGGAAAGGAATAGGGATTGTCATACCGAATTTATTAGAGTGGCAACAATCAGTTGTTGTGAAAGATGTTAAAAACGAATGTTATCGCATTACCAGTAAATACCGTCAAAAAATATTGGGGCAAAAAGTCTATCGCTTTGCCCCATTTGACCGTAACACGCACCGATTTAATCCATTGGATTGTATTGATATGCGCGACCGAGCACGCGCCGAACTCGATTTAAAAAATCAGGCAATGGGCTTATATCCGCTCACCGGCGACCCGGATAAAGACTTTTGGCAGCACCAGGCACAAAATCTTTTTGTGGCAACCACTTTTTTACTGTGGGATATGCGCCAAAAAAGCCTTACTGATATGACACTGACTTACGC  >  1/1453077‑1453564                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                   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)                                                                                                                                                                                                          cgtatcaCCAGTAAATATCGACAAAAAATATTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTatat                                                                                                                               <  1:40005/156‑1 (MQ=255)                                                                                                                                                                                                          cgtatcaCCAGTAAATATCGACAAAAAATATTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTATATCCGCTCACCGGCGACCCGGATAAAGACTTTTGGCAGCACCAGGCACAGAATCTTTTTGTAGCAACCACTTTTTTAc                                                   <  1:864890/232‑1 (MQ=255)                                                                                                                                                                                                          cgtatcaCCAGTAAATATCGACAAAAAATATTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTATATCCGCTCACCGGCGACCCGGATAAAGACTTTTGGCAGCACCAGGCACAGAATCTTTTTGTAGCAACCACTTTTTTACTGTGGGATATgcg                                      >  1:170613/7‑251 (MQ=255)                                                                                                                                                                                                            tatcaCCAGTAAATATCGACAAAAAATATTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTATATCCGCTCACCGGCGACCCGGATAAAGACTTTTGGCAGCACCAGGCACAGAATCTTTTTGTAGCAACCACTTTTTTACTGTGGGATATgcgc                                     <  1:796497/246‑1 (MQ=255)                                                                                                                                                                                                                    gTAAATATCGACAAAAAATATTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTAAATCCGCTCACCGGCGACCCGGATAAAGACTTTTGGCAGCACCAGGCACAGAATCTTTTTGTAGCAACCACTTTTTTACTGTGGGATATGCGCCAAAAAAg                             >  1:119774/1‑250 (MQ=255)                                                                                                                                                                                                                      aaaTATCGACAAAAAATATTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTATATCCGCTCACCGGCGACCCGGATAAAGACTTTTGGCAGCACCAGGCACAGAATCTTTTTGTAGCAACCACTTTTTTACTGTGGGATATGCGCCAAAAAAGc                            >  1:356409/1‑249 (MQ=255)                                                                                                                                                                                                                       aatatcgacAAAAAATATTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCt                                                                                                                                    <  1:63099/136‑1 (MQ=255)                                                                                                                                                                                                                           tcgacAAAAAATATTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTATATCCGCTCACCGGCGACCCGGATAAAGACTTTTGGCAGCACCAGGCACAGAATCTTTTTGTAGCAACCACTTTTTTACTGTGGGATATGCGCCAAAAAAGCCTTAccg                     <  1:84567/247‑3 (MQ=255)                                                                                                                                                                                                                                   aaaTATTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTATATCCGCTCACCGGCGACTCGGATAAAGACTTTTGGCAGCACCAGGCACAGAATCTTTTTGTAGCAACCACTTTTTTAc                                                   <  1:157528/213‑1 (MQ=255)                                                                                                                                                                                                                                   aaaTATTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTATATCCGCTCACCGGCGACCCGGATAAAGACTTTTGGCAGCACCAGGCACAGAATCTTTTTGTAGCAACCACTTTTTTACTGTGGGATATGCGCCAAAAAAGCCTTACCGATATGata             >  1:286276/1‑249 (MQ=255)                                                                                                                                                                                                                                    aaTATTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTATATCCGCTCACCGGCGACCCGGATAAAGACTTTTGGCAGCACCAGGCACAGAATCTTTTTGTAGCAACCACTTTTTTACTGTGGGATATGCGCCAAAAAAGCCTTACCGATATGatac            <  1:300752/251‑4 (MQ=255)                                                                                                                                                                                                                                    aaTATTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTATATCCGCTCACCGGCGACCCGGATAAAGACTTTTGGCAGCACCAGGCACAGAATCTTTTTGTAGCAACCACTTTTTTACTGTGGGATATGCGCCAAAAAAGCCTTACCGATATGatac            <  1:897884/251‑4 (MQ=255)                                                                                                                                                                                                                                     atatTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTATATCCGCTCACCGGCGACCCGGATAAAGACTTTTGGCAGCACCAGGCACAGAATCTTTTTGTAGCAACCACTTTTTTACTGTGGGATATGCGCCAAAAAAGCCTTACCGATATGatac            <  1:411677/250‑4 (MQ=255)                                                                                                                                                                                                                                     atatTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTATATCCGCTCACCGGCGACCCGGATAAAGACTTTTGGCAGCACCAGGCACAGAATCTTTTTGTAGCAACCACTTTTTTACTGTGGGATATGCGCCAAAAAAGCCTTACCGATATGata             >  1:858618/1‑247 (MQ=255)                                                                                                                                                                                                                                      tatTAGGGCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTATATCCGCTCACCGGCGACCCGGATAAAGACTTTTGGCAGCACCAGGCACAGAATCTTTTTGTAGCAACCACTTTTTTACTGTGGGATATGCGCCAAAAAAGCCTTACCGATATGatac            <  1:772374/249‑4 (MQ=255)                                                                                                                                                                                                                                         tagggCAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTATATCCGCTCACCGGCGACCCGGATAAAGACTTTTGGCAGCACCAGGCACAGAATCTTTTTGTAGCAACCACTTTTTTACTGTGGGATATGCGCCAAAAAAGCCTTACCGATATGATACTGAcc       <  1:368887/249‑2 (MQ=255)                                                                                                                                                                                                                                              cAAAAGGTATATCGCTTTGCCCCGTTTGACCGTAATACGCACCGGTTTAATCCGCTGGATTGTATTGATATGCGCGACCGGGCGCGCGCCGAACTCGATTTAAAAAATCAGGCTATGGGCTTATATCCGCTCACCGGCGACCCGGATAAAGACTTTTGGCAGCACCAGGCACAGAATCTTTTTGTAGCAACCACTTTTTTACTGTGGGATATGCGCCAAAAAAGCCTTACCGATATGATACTGAcctatgc  <  1:158817/251‑7 (MQ=255)                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                   GTACAAAAAATGGGTTTATTGGAAGAAAAAAACGGGATTATTGTCGGCAAACTTGGTAATAAACTTCTTCGCTTTATCGGTGCACAATTCGTTTCGTTGGCCGCACCGACCCGAGGTGGGAAAGGAATAGGGATTGTCATACCGAATTTATTAGAGTGGCAACAATCAGTTGTTGTGAAAGATGTTAAAAACGAATGTTATCGCATTACCAGTAAATACCGTCAAAAAATATTGGGGCAAAAAGTCTATCGCTTTGCCCCATTTGACCGTAACACGCACCGATTTAATCCATTGGATTGTATTGATATGCGCGACCGAGCACGCGCCGAACTCGATTTAAAAAATCAGGCAATGGGCTTATATCCGCTCACCGGCGACCCGGATAAAGACTTTTGGCAGCACCAGGCACAAAATCTTTTTGTGGCAACCACTTTTTTACTGTGGGATATGCGCCAAAAAAGCCTTACTGATATGACACTGACTTACGC  >  1/1453077‑1453564

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑