Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	3,824,368	G→A	pseudogene (501/687 nt)	rph →	ECK3633:JW3618:b3643; ribonuclease PH

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	3,824,368	0	G	A	100.0%	184.3 / NA	60	pseudogene (501/687 nt)	rph	ECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (49/11);  total (49/11)

AGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACC  >  W3110S.gb/3824313‑3824422                                                        |                                                       aGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACgg                                                   >  1:2396765/1‑61 (MQ=255) aGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACgg                                                   >  1:2451466/1‑61 (MQ=255) aGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACgg                                                   >  1:2180372/1‑61 (MQ=255) aGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACgg                                                   >  1:2965032/1‑61 (MQ=255) aGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACgg                                                   >  1:318934/1‑61 (MQ=255)                        gggATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATa                           <  1:2180705/62‑1 (MQ=255)                        gggATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATa                           <  1:2837426/62‑1 (MQ=255)                        gggATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATa                           <  1:702893/62‑1 (MQ=255)                        gggATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATa                           <  1:2028880/62‑1 (MQ=255)                        gggATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATa                           <  1:443546/62‑1 (MQ=255)                                     cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                      >  1:2447823/1‑54 (MQ=255)                                     cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                      >  1:2557722/1‑54 (MQ=255)                                     cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                      >  1:2788960/1‑54 (MQ=255)                                     cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                      >  1:2192026/1‑54 (MQ=255)                                     cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                      >  1:55672/1‑54 (MQ=255)                                     cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                      >  1:161145/1‑54 (MQ=255)                                     cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                      >  1:1452667/1‑54 (MQ=255)                                     cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                      >  1:1360138/1‑54 (MQ=255)                                     cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                      >  1:82213/1‑54 (MQ=255)                                     cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                      >  1:1269128/1‑54 (MQ=255)                                     cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                      >  1:908756/1‑54 (MQ=255)                                     cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                      >  1:940742/1‑54 (MQ=255)                                     cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATAAGTTg                      >  1:462157/1‑54 (MQ=255)                                           cTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGa                     <  1:2842257/49‑1 (MQ=25)                                           cTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGa                     <  1:799110/49‑1 (MQ=25)                                           cTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGa                     <  1:1144801/49‑1 (MQ=25)                                           cTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGa                     <  1:1150037/49‑1 (MQ=25)                                           cTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGa                     <  1:2252996/49‑1 (MQ=25)                                                 gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGcc           >  1:861439/3‑53 (MQ=255)                                                 gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc  >  1:804781/3‑62 (MQ=255)                                                 gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc  >  1:59661/3‑62 (MQ=255)                                                 gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc  >  1:60247/3‑62 (MQ=255)                                                 gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc  >  1:467215/3‑62 (MQ=255)                                                 gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc  >  1:1842153/3‑62 (MQ=255)                                                 gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc  >  1:1529918/3‑62 (MQ=255)                                                 gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc  >  1:1979953/3‑62 (MQ=255)                                                 gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc  >  1:2990635/3‑62 (MQ=255)                                                 gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc  >  1:1278225/3‑62 (MQ=255)                                                 gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc  >  1:2168159/3‑62 (MQ=255)                                                 gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc  >  1:857830/3‑62 (MQ=255)                                                 gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc  >  1:866454/3‑62 (MQ=255)                                                 gtaTTGTAAACGGTGAAGCAATTCGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGccc  >  1:2133632/3‑62 (MQ=255)                                                  taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGActca              >  1:536377/2‑48 (MQ=25)                                                  taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGActca              >  1:1676879/2‑48 (MQ=25)                                                  taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGActca              >  1:657976/2‑48 (MQ=25)                                                  taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGActca              >  1:61709/2‑48 (MQ=25)                                                  taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGActca              >  1:109904/2‑48 (MQ=25)                                                  taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGActca              >  1:580899/2‑48 (MQ=25)                                                  taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGActca              >  1:1757534/2‑48 (MQ=25)                                                  taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGActca              >  1:2365184/2‑48 (MQ=25)                                                  taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGActca              >  1:1830336/2‑48 (MQ=25)                                                  taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGActca              >  1:357957/2‑48 (MQ=25)                                                  taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGActca              >  1:2032448/2‑48 (MQ=25)                                                  taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGActca              >  1:2880747/2‑48 (MQ=25)                                                  taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGActca              >  1:272674/2‑48 (MQ=25)                                                  taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGActca              >  1:2597915/2‑48 (MQ=25)                                                  taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGActca              >  1:2597016/2‑48 (MQ=25)                                                  taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGActca              >  1:2318025/2‑48 (MQ=25)                                                  taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGActca              >  1:2515142/2‑48 (MQ=25)                                                   aTTGTAAACGGTGAAGCAATTTGCGATCTGGAATa                           <  1:739343/35‑1 (MQ=16)                                                        |                                                       AGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACC  >  W3110S.gb/3824313‑3824422

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑