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%	210.9 / NA	71	pseudogene (501/687 nt)	rph	ECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (35/36);  total (35/36)

GTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTA  >  W3110S.gb/3824300‑3824434                                                                     |                                                                   gtggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtgtg                                                                    <  1:3552810/69‑1 (MQ=255)          ggCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGc                                                         <  1:376730/71‑1 (MQ=255)           gCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGca                                                        <  1:52484/71‑2 (MQ=255)           gCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGc                                                         <  1:2055959/70‑1 (MQ=255)                cTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTg                                                   >  1:4238046/1‑71 (MQ=255)                cTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTg                                                   >  1:1362099/1‑71 (MQ=255)                cTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTg                                                   >  1:3352708/1‑71 (MQ=255)                cTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTg                                                   >  1:2663736/1‑71 (MQ=255)                   aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg                                                 <  1:732871/70‑1 (MQ=255)                   aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg                                                 <  1:4338196/70‑1 (MQ=255)                   aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg                                                 <  1:371609/70‑1 (MQ=255)                       ccAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTg                                            >  1:2595105/1‑71 (MQ=255)                        cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                           <  1:2091196/71‑1 (MQ=255)                        cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                           <  1:2372701/71‑1 (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                        >  1:3157648/1‑71 (MQ=255)                                           gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                        >  1:495670/1‑71 (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                    <  1:3732452/71‑1 (MQ=255)                                               ccGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa                    <  1:2423685/71‑1 (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              >  1:4490468/1‑70 (MQ=255)                                                      ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc              >  1:379853/1‑70 (MQ=255)                                                       tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                         >  1:493077/1‑42 (MQ=19)                                                       tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                         >  1:2765330/1‑42 (MQ=19)                                                       tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                         >  1:3473472/1‑42 (MQ=19)                                                       tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCg             >  1:3639917/1‑70 (MQ=255)                                                       tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCg             >  1:2850981/1‑70 (MQ=255)                                                       tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa            >  1:2845399/1‑71 (MQ=255)                                                       tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa            >  1:2624888/1‑71 (MQ=255)                                                       tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa            >  1:2501239/1‑71 (MQ=255)                                                       tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa            >  1:2907315/1‑71 (MQ=255)                                                       tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa            >  1:3286638/1‑71 (MQ=255)                                                       tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa            >  1:1696233/1‑71 (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)                                                             ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa      >  1:4458177/4‑71 (MQ=255)                                                             ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa      >  1:2044421/4‑71 (MQ=255)                                                             ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa      >  1:2777468/4‑71 (MQ=255)                                                             ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa      >  1:2772078/4‑71 (MQ=255)                                                             ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGa       >  1:1174008/4‑70 (MQ=255)                                                               taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg    <  1:440197/70‑1 (MQ=255)                                                               taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg    <  1:3440421/70‑1 (MQ=255)                                                                 ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                <  1:3154823/41‑1 (MQ=25)                                                                 ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                <  1:3460994/41‑1 (MQ=25)                                                                 ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGt   <  1:1323603/70‑1 (MQ=255)                                                                 ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGt   <  1:2077118/70‑1 (MQ=255)                                                                 ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa  <  1:3421674/71‑1 (MQ=255)                                                                  tgtaAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                                  <  1:1326767/38‑1 (MQ=21)                                                                     |                                                                   GTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTA  >  W3110S.gb/3824300‑3824434

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: ‑