Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	3,824,326	T→C	pseudogene (459/687 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	3,824,326	0	T	C	100.0%	266.2 / NA	77	pseudogene (459/687 nt)	rph	ECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (29/48);  total (29/48)

GGTGCCTGCGTGGCGCTGGTAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGG  >  W3110S.gb/3824261‑3824393                                                                  |                                                                    ggTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGAt                                                                >  1:4003532/1‑71 (MQ=255) ggTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGAt                                                                >  1:744525/1‑71 (MQ=255)   tGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATg                                                               >  1:3531970/1‑70 (MQ=255)   tGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATg                                                               >  1:500426/1‑70 (MQ=255)   tGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                              <  1:1187740/71‑1 (MQ=255)   tGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                              <  1:958890/71‑1 (MQ=255)     ccTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCACCCCGATGa                                                              >  1:2022755/1‑69 (MQ=255)     ccTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaaa                                                            <  1:905565/71‑1 (MQ=255)     ccTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                              >  1:2376945/1‑69 (MQ=255)     ccTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                              >  1:1820404/1‑69 (MQ=255)     ccTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                              >  1:830155/1‑69 (MQ=255)         cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg                                                          <  1:454243/69‑1 (MQ=255)         cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg                                                          <  1:1830383/69‑1 (MQ=255)         cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg                                                          <  1:4448093/69‑1 (MQ=255)         cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg                                                          <  1:2760232/69‑1 (MQ=255)         cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg                                                          <  1:1485458/69‑1 (MQ=255)         cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg                                                          <  1:1395024/69‑1 (MQ=255)         cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg                                                          <  1:1355794/69‑1 (MQ=255)         cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg                                                          <  1:3431187/69‑1 (MQ=255)             gcgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATgg                                                     >  1:909141/1‑70 (MQ=255)                cTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGc                                                 <  1:3307811/71‑1 (MQ=255)                    caGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGa                                                                 >  1:3019558/2‑51 (MQ=255)                      gATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGAt                                                       <  1:3003104/59‑1 (MQ=255)                      gATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGAt                                                       <  1:3416103/59‑1 (MQ=255)                      gATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGt                                           <  1:2054718/71‑1 (MQ=255)                      gATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGt                                           <  1:1763361/71‑1 (MQ=255)                       aTGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGtt                                          <  1:4286396/71‑1 (MQ=255)                       aTGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGtt                                          <  1:1635129/71‑1 (MQ=255)                        tGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaaa                                                            >  1:2078857/1‑52 (MQ=255)                        tGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaa                                                             >  1:3007500/1‑51 (MQ=255)                        tGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTa                                                   >  1:1151437/1‑61 (MQ=255)                        tGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGttt                                         >  1:3726604/1‑71 (MQ=255)                        tGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGttt                                         >  1:2569636/1‑71 (MQ=255)                        tGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGttt                                         <  1:1501565/71‑1 (MQ=255)                        tGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGtt                                          >  1:3340625/1‑70 (MQ=255)                         gcgcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTc                                        >  1:2421425/1‑71 (MQ=255)                          cgcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTc                                        <  1:969672/70‑1 (MQ=255)                             tACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg                                                          <  1:4230323/49‑1 (MQ=255)                               cAGAAGCTGGTGGAAAACGGCAAGCTGAGAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg                                  <  1:4450823/71‑1 (MQ=255)                               cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg                                  <  1:1588566/71‑1 (MQ=255)                               cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg                                  <  1:4131700/71‑1 (MQ=255)                               cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg                                  >  1:1425651/1‑71 (MQ=255)                               cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg                                  <  1:1289134/71‑1 (MQ=255)                               cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg                                  >  1:2263807/1‑71 (MQ=255)                               cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg                                  <  1:4618610/71‑1 (MQ=255)                                 gAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCggta                                >  1:1486018/1‑69 (MQ=255)                                   aGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAtt                              >  1:970099/1‑71 (MQ=255)                                   aGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAtt                              >  1:1352960/1‑71 (MQ=255)                                   aGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt                               >  1:3261811/1‑70 (MQ=255)                                   aGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt                               <  1:3062819/70‑1 (MQ=255)                                        gtggAAAACGGCAAGCTGAAAACCAACCCGATGaaa                                                            <  1:1505053/36‑1 (MQ=255)                                        gtggAAAACGGCAAGCTGAAAACCAACCCGATGaaa                                                            <  1:4653461/36‑1 (MQ=255)                                        gtggAAAACGGCAAGCTGAAAACCAACCCGATGaaa                                                            <  1:2420379/36‑1 (MQ=255)                                        gtggAAAACGGCAAGCTGAAAACCAACCCGATGaaa                                                            <  1:4395566/36‑1 (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          >  1:1362099/1‑71 (MQ=255)                                                       cTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTg          >  1:2663736/1‑71 (MQ=255)                                                       cTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTg          >  1:4238046/1‑71 (MQ=255)                                                          aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg        <  1:732871/70‑1 (MQ=255)                                                          aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg        <  1:371609/70‑1 (MQ=255)                                                          aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg        <  1:4338196/70‑1 (MQ=255)                                                              ccAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTg   >  1:2595105/1‑71 (MQ=255)                                                               cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg  <  1:680706/71‑1 (MQ=255)                                                               cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg  <  1:2091196/71‑1 (MQ=255)                                                               cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg  <  1:2372701/71‑1 (MQ=255)                                                               cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTg   >  1:4111967/1‑70 (MQ=255)                                                               cAACCCGATGAAACGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg  <  1:1132267/71‑1 (MQ=255)                                                                  |                                                                    GGTGCCTGCGTGGCGCTGGTAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGG  >  W3110S.gb/3824261‑3824393

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑