Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	3,824,362	A→T	pseudogene (495/687 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	3,824,362	0	A	T	100.0%	205.2 / NA	70	pseudogene (495/687 nt)	rph	ECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (33/37);  total (33/37)

AGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACA  >  W3110S.gb/3824295‑3824426                                                                    |                                                                 aGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAtt                                                               >  1:970099/1‑71 (MQ=255) aGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAtt                                                               >  1:1352960/1‑71 (MQ=255) aGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt                                                                <  1:3062819/70‑1 (MQ=255) aGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt                                                                >  1:3261811/1‑70 (MQ=255)      gtggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtgtg                                                            <  1:3552810/69‑1 (MQ=255)      gtggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtgta                                                            <  1:1057807/69‑2 (MQ=255)      gtggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtgta                                                            <  1:1401298/69‑2 (MQ=255)      gtggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtgta                                                            <  1:1552664/69‑2 (MQ=255)      gtggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtgta                                                            <  1:1570888/69‑2 (MQ=255)      gtggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtgta                                                            <  1:249483/69‑2 (MQ=255)      gtggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtgta                                                            <  1:4072104/69‑2 (MQ=255)               ggCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGc                                                 <  1:376730/71‑1 (MQ=255)                gCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGca                                                <  1:52484/71‑2 (MQ=255)                gCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGc                                                 <  1:2055959/70‑1 (MQ=255)                     cTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTg                                           >  1:3352708/1‑71 (MQ=255)                     cTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTg                                           >  1:2663736/1‑71 (MQ=255)                     cTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTg                                           >  1:1362099/1‑71 (MQ=255)                     cTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTg                                           >  1:4238046/1‑71 (MQ=255)                        aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg                                         <  1:371609/70‑1 (MQ=255)                        aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg                                         <  1:4338196/70‑1 (MQ=255)                        aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg                                         <  1:732871/70‑1 (MQ=255)                            ccAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTg                                    >  1:2595105/1‑71 (MQ=255)                             cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                   <  1:2372701/71‑1 (MQ=255)                             cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                   <  1:2091196/71‑1 (MQ=255)                             cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                   <  1:680706/71‑1 (MQ=255)                             cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTg                                    >  1:4111967/1‑70 (MQ=255)                             cAACCCGATGAAACGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                   <  1:1132267/71‑1 (MQ=255)                               acccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                 <  1:2579831/69‑1 (MQ=255)                               acccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                 <  1:946062/69‑1 (MQ=255)                                        aaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                        <  1:3906999/71‑1 (MQ=255)                                        aaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                        <  1:3755794/71‑1 (MQ=255)                                         aGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                          >  1:2180764/1‑68 (MQ=255)                                          gggATGGTAGCCTCAGTTTCTGTCGGTATTGTAAACGGTGAAGca                                                <  1:522257/45‑2 (MQ=255)                                          gggATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGca                                                <  1:2029631/45‑2 (MQ=255)                                          gggATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                        <  1:1277838/69‑1 (MQ=255)                                              tGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                   <  1:3477828/54‑1 (MQ=255)                                               ggTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGActcag                 >  1:1113474/1‑69 (MQ=255)                                                gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                >  1:495670/1‑71 (MQ=255)                                                gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                >  1:3157648/1‑71 (MQ=255)                                                gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                >  1:3059277/1‑71 (MQ=255)                                                 tAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                          <  1:4105893/60‑1 (MQ=255)                                                   gCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                   <  1:3268323/49‑1 (MQ=25)                                                   gCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                 >  1:2691192/1‑51 (MQ=255)                                                   gCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCg              >  1:3132795/1‑70 (MQ=255)                                                    ccGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa            <  1:3530933/71‑1 (MQ=255)                                                    ccGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa            <  1:2423685/71‑1 (MQ=255)                                                    ccGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa            <  1:3732452/71‑1 (MQ=255)                                                      gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCaga          <  1:1213481/71‑1 (MQ=255)                                                      gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa            >  1:1390594/1‑69 (MQ=255)                                                       cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCagag         <  1:522305/71‑1 (MQ=255)                                                       cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCaga          <  1:4144715/70‑1 (MQ=255)                                                         gTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAc       >  1:1325749/1‑71 (MQ=255)                                                           ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATa                               >  1:2850356/1‑45 (MQ=25)                                                           ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc      >  1:379853/1‑70 (MQ=255)                                                           ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc      >  1:4490468/1‑70 (MQ=255)                                                            tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                 >  1:493077/1‑42 (MQ=19)                                                            tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                 >  1:3473472/1‑42 (MQ=19)                                                            tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                 >  1:2765330/1‑42 (MQ=19)                                                            tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCg     >  1:2850981/1‑70 (MQ=255)                                                            tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCg     >  1:3639917/1‑70 (MQ=255)                                                            tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa    >  1:2501239/1‑71 (MQ=255)                                                            tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa    >  1:2624888/1‑71 (MQ=255)                                                            tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa    >  1:1696233/1‑71 (MQ=255)                                                            tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa    >  1:2907315/1‑71 (MQ=255)                                                            tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa    >  1:2845399/1‑71 (MQ=255)                                                            tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa    >  1:3286638/1‑71 (MQ=255)                                                             cTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa    <  1:1881387/70‑1 (MQ=255)                                                             cTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa    <  1:1348653/70‑1 (MQ=255)                                                              tGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa    <  1:1634207/69‑1 (MQ=255)                                                              tGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACa  >  1:4186139/1‑71 (MQ=255)                                                                    |                                                                 AGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACA  >  W3110S.gb/3824295‑3824426

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: ‑