Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	3,824,410	T→A	pseudogene (543/687 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	3,824,410	0	T	A	100.0%	151.2 / NA	47	pseudogene (543/687 nt)	rph	ECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (32/15);  total (32/15)

GAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAG  >  W3110S.gb/3824361‑3824465                                                  |                                                        gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGcc                                                      >  1:861439/3‑53 (MQ=255) gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc                                             >  1:857830/3‑62 (MQ=255) gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc                                             >  1:467215/3‑62 (MQ=255) gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc                                             >  1:2168159/3‑62 (MQ=255) gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc                                             >  1:59661/3‑62 (MQ=255) gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc                                             >  1:1979953/3‑62 (MQ=255) gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc                                             >  1:60247/3‑62 (MQ=255) gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc                                             >  1:1842153/3‑62 (MQ=255) gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc                                             >  1:804781/3‑62 (MQ=255) gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc                                             >  1:1529918/3‑62 (MQ=255) gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc                                             >  1:866454/3‑62 (MQ=255) gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc                                             >  1:2990635/3‑62 (MQ=255) gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc                                             >  1:1278225/3‑62 (MQ=255) gtaTTGTAAACGGTGAAGCAATTCGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGccc                                             >  1:2133632/3‑62 (MQ=255)              tgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACa                                         <  1:1288803/52‑1 (MQ=255)              tgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACa                                         <  1:2920547/52‑1 (MQ=255)                      tttGCGATCTGGAATACGTTGAAGACTCAGCCGTAGAGACCGACATGAACGTAGTGATGAc                         >  1:1408636/1‑61 (MQ=255)                      tttGCGATCTGGAATACGTTGAAGACTCAGCCGCagag                                                >  1:574389/1‑38 (MQ=255)                      tttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGAc                         >  1:776419/1‑61 (MQ=255)                      tttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGAc                         >  1:3115215/1‑61 (MQ=255)                      tttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGAc                         >  1:3111585/1‑61 (MQ=255)                      tttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGAc                         >  1:3123285/1‑61 (MQ=255)                      tttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGAc                         >  1:1205067/1‑61 (MQ=255)                      tttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGAc                         >  1:881053/1‑61 (MQ=255)                      tttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGAc                         >  1:931397/1‑61 (MQ=255)                      tttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGAc                         >  1:962984/1‑61 (MQ=255)                      tttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGAc                         >  1:2424194/1‑61 (MQ=255)                      tttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGAc                         >  1:2072157/1‑61 (MQ=255)                      tttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGAc                         >  1:1621758/1‑61 (MQ=255)                                     aCGTTGAAGACTCAGCCGCAGAGACCGACATGAACTTAGTGATGACCGAAGTCGGGCGcatc         <  1:3090790/62‑1 (MQ=255)                                     aCGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                               >  1:2337601/1‑40 (MQ=255)                                     aCGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                               >  1:1388497/1‑40 (MQ=255)                                     aCGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcatc         <  1:1104246/62‑1 (MQ=255)                                     aCGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcatc         <  1:2896952/62‑1 (MQ=255)                                     aCGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcatc         <  1:1320189/62‑1 (MQ=255)                                     aCGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcatc         <  1:1335773/62‑1 (MQ=255)                                     aCGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcatc         <  1:86087/62‑1 (MQ=255)                                     aCGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcatc         <  1:788686/62‑1 (MQ=255)                                     aCGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcatc         <  1:1845893/62‑1 (MQ=255)                                     aCGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcatc         <  1:762130/62‑1 (MQ=255)                                     aCGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcatc         <  1:1958890/62‑1 (MQ=255)                                     aCGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcatc         <  1:457045/62‑1 (MQ=255)                                     aCGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcatc         <  1:2604052/62‑1 (MQ=255)                                          gAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGa    >  1:1625558/1‑62 (MQ=255)                                          gAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGa    >  1:2308399/1‑62 (MQ=255)                                          gAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGa    >  1:2492990/1‑62 (MQ=255)                                             gACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAg  <  1:1293639/61‑1 (MQ=255)                                                  |                                                        GAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAG  >  W3110S.gb/3824361‑3824465

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: ‑