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%	168.7 / NA	55	pseudogene (501/687 nt)	rph	ECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (35/20);  total (35/20)

AAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACG  >  W3110S.gb/3824318‑3824432                                                   |                                                                 aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc                                                <  1:3145416/69‑1 (MQ=255) aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg                                               <  1:1529465/70‑1 (MQ=255) aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg                                               <  1:3906090/70‑1 (MQ=255)    aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCTGTATTGTAAACGGTGAAGCAATTTGCGATCt                                           >  1:4001186/1‑71 (MQ=255)    aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTaaa                                                                >  1:2981635/1‑50 (MQ=255)    aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATc                                            >  1:569867/1‑70 (MQ=255)    aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCt                                           >  1:3045409/1‑71 (MQ=255)    aCCAACCCGATGAAAGGGATGGTAGCCGAAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCt                                           >  1:3262449/1‑71 (MQ=255)        acccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                       <  1:838538/69‑1 (MQ=255)        acccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                       <  1:3228940/69‑1 (MQ=255)        acccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                       <  1:1955239/69‑1 (MQ=255)        acccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                       <  1:2176847/69‑1 (MQ=255)        acccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                       <  1:3584757/69‑1 (MQ=255)         cccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                       <  1:154754/69‑1 (MQ=255)            gATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACg                                   <  1:2215413/71‑1 (MQ=255)            gATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACg                                   <  1:3075801/71‑1 (MQ=255)            gATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACg                                   <  1:764257/71‑1 (MQ=255)               gAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGaa                                                         >  1:792651/1‑46 (MQ=255)               gAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                 >  1:3656858/1‑70 (MQ=255)               gAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                 >  1:2905889/1‑70 (MQ=255)               gAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                 >  1:1067936/1‑70 (MQ=255)               gAAAGGGATGGTAGCCGCAGTTTCTGTCGGGATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                 >  1:3806210/1‑70 (MQ=255)                aaaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                                <  1:2534711/70‑1 (MQ=255)                aaaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                                <  1:2667950/70‑1 (MQ=255)                aaaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                                <  1:3519229/70‑1 (MQ=255)                aaaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                                <  1:3860395/70‑1 (MQ=255)                 aaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                                <  1:1148967/69‑1 (MQ=255)                         gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                      >  1:939555/1‑71 (MQ=255)                         gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                      >  1:345405/1‑71 (MQ=255)                         gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                      >  1:560493/1‑71 (MQ=255)                         gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                      >  1:1435717/1‑71 (MQ=255)                         gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                      >  1:3849542/1‑71 (MQ=255)                           aGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                       <  1:1172387/52‑1 (MQ=255)                              cGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCTATCTGGaa                                       >  1:3992993/1‑49 (MQ=255)                              cGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                       >  1:827531/1‑49 (MQ=25)                              cGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                       >  1:3339105/1‑49 (MQ=25)                              cGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                       >  1:1501502/1‑49 (MQ=25)                              cGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTAGCGATCTGGaa                                       >  1:2921406/1‑49 (MQ=255)                                           ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGa     <  1:707680/67‑1 (MQ=255)                                           ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGa     <  1:702508/67‑1 (MQ=255)                                             taatgtaAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAAc   >  1:3130143/4‑70 (MQ=255)                                             taTTGTAAACGGTGAAGGAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg  >  1:431391/2‑71 (MQ=255)                                             taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATAc                                    >  1:123897/2‑37 (MQ=16)                                             taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg  >  1:705347/2‑71 (MQ=255)                                             taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg  >  1:3998004/2‑71 (MQ=255)                                             taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg  >  1:4127433/2‑71 (MQ=255)                                             taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg  >  1:1567349/2‑71 (MQ=255)                                             taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg  >  1:1974322/2‑71 (MQ=255)                                             taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg  >  1:2091871/2‑71 (MQ=255)                                             taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg  >  1:2453036/2‑71 (MQ=255)                                             taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg  >  1:2489307/2‑71 (MQ=255)                                             taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg  >  1:258543/2‑71 (MQ=255)                                             taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg  >  1:270667/2‑71 (MQ=255)                                             taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg  >  1:3294788/2‑71 (MQ=255)                                             taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg  >  1:3286862/2‑71 (MQ=255)                                             taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg  >  1:307375/2‑71 (MQ=255)                                             taTTGTAAACGG‑TAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg  >  1:744917/2‑70 (MQ=255)                                                   |                                                                 AAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACG  >  W3110S.gb/3824318‑3824432

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑