Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	3,824,374	C→T	pseudogene (507/687 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	3,824,374	0	C	T	100.0%	284.4 / NA	97	pseudogene (507/687 nt)	rph	ECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (51/46);  total (51/46)

GGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGA  >  W3110S.gb/3824309‑3824438                                                                  |                                                                 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                                                       >  1:3352708/1‑71 (MQ=255)       cTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTg                                                       >  1:1362099/1‑71 (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                                               <  1:680706/71‑1 (MQ=255)               cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                               <  1:2372701/71‑1 (MQ=255)               cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                               <  1:2091196/71‑1 (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                                    <  1:3755794/71‑1 (MQ=255)                          aaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                    <  1:3906999/71‑1 (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                        <  1:3732452/71‑1 (MQ=255)                                      ccGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa                        <  1:3530933/71‑1 (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                                             >  1:3473472/1‑42 (MQ=19)                                              tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                             >  1:2765330/1‑42 (MQ=19)                                              tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                             >  1:493077/1‑42 (MQ=19)                                              tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCg                 >  1:2850981/1‑70 (MQ=255)                                              tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCg                 >  1:3639917/1‑70 (MQ=255)                                              tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                >  1:2501239/1‑71 (MQ=255)                                              tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                >  1:1696233/1‑71 (MQ=255)                                              tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                >  1:3286638/1‑71 (MQ=255)                                              tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                >  1:2624888/1‑71 (MQ=255)                                              tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                >  1:2907315/1‑71 (MQ=255)                                              tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                >  1:2845399/1‑71 (MQ=255)                                               cTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                <  1:1348653/70‑1 (MQ=255)                                               cTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                <  1:1881387/70‑1 (MQ=255)                                                tGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                <  1:1634207/69‑1 (MQ=255)                                                tGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACa              >  1:4186139/1‑71 (MQ=255)                                                    ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa          >  1:4458177/4‑71 (MQ=255)                                                    ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa          >  1:2777468/4‑71 (MQ=255)                                                    ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa          >  1:2044421/4‑71 (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       <  1:2077118/70‑1 (MQ=255)                                                        ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGt       <  1:1323603/70‑1 (MQ=255)                                                        ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa      <  1:3421674/71‑1 (MQ=255)                                                         tgtaAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                                      <  1:1326767/38‑1 (MQ=21)                                                          gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa          >  1:3720899/4‑65 (MQ=255)                                                          gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt    >  1:296240/4‑71 (MQ=255)                                                          gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt    >  1:1220899/4‑71 (MQ=255)                                                          gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt    >  1:3381653/4‑71 (MQ=255)                                                          gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt    >  1:4467858/4‑71 (MQ=255)                                                          gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt    >  1:957182/4‑71 (MQ=255)                                                          gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt    >  1:998875/4‑71 (MQ=255)                                                          gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt    >  1:2306363/4‑71 (MQ=255)                                                          gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt    >  1:3747809/4‑71 (MQ=255)                                                          gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt    >  1:2412023/4‑71 (MQ=255)                                                          gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt    >  1:3823341/4‑71 (MQ=255)                                                          gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt    >  1:3946541/4‑71 (MQ=255)                                                          gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt    >  1:3571105/4‑71 (MQ=255)                                                          gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt    >  1:4179528/4‑71 (MQ=255)                                                          gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt    >  1:37226/4‑71 (MQ=255)                                                           taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtg   <  1:2356716/69‑1 (MQ=255)                                                           taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt    <  1:3460668/68‑1 (MQ=255)                                                           taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt    <  1:448834/68‑1 (MQ=255)                                                           taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt    <  1:1656432/68‑1 (MQ=255)                                                           taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt    <  1:3888530/68‑1 (MQ=255)                                                           taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt    <  1:843255/68‑1 (MQ=255)                                                           taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt    <  1:376189/68‑1 (MQ=255)                                                           taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt    <  1:1995950/68‑1 (MQ=255)                                                           taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt    <  1:980197/68‑1 (MQ=255)                                                            aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtga  >  1:3891179/2‑71 (MQ=255)                                                                  |                                                                 GGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGA  >  W3110S.gb/3824309‑3824438

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: ‑