Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	3,824,410	T→A	pseudogene (543/687 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	3,824,410	0	T	A	100.0%	302.7 / NA	100	pseudogene (543/687 nt)	rph	ECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (57/43);  total (57/43)

GTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGC  >  W3110S.gb/3824342‑3824468                                                                     |                                                           gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                                                          >  1:495670/1‑71 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                                                          >  1:3059277/1‑71 (MQ=255) gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                                                          >  1:3157648/1‑71 (MQ=255)    gCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCg                                                        >  1:3132795/1‑70 (MQ=255)     ccGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa                                                      <  1:3732452/71‑1 (MQ=255)     ccGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa                                                      <  1:2423685/71‑1 (MQ=255)     ccGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa                                                      <  1:3530933/71‑1 (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)            ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc                                                >  1:379853/1‑70 (MQ=255)            ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc                                                >  1:4490468/1‑70 (MQ=255)             tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCg                                               >  1:2850981/1‑70 (MQ=255)             tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCg                                               >  1:3639917/1‑70 (MQ=255)             tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                                              >  1:2845399/1‑71 (MQ=255)             tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                                              >  1:2907315/1‑71 (MQ=255)             tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                                              >  1:2624888/1‑71 (MQ=255)             tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                                              >  1:2501239/1‑71 (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                                        >  1:2777468/4‑71 (MQ=255)                   ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa                                        >  1:2772078/4‑71 (MQ=255)                   ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa                                        >  1:4458177/4‑71 (MQ=255)                   ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa                                        >  1:2044421/4‑71 (MQ=255)                   ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGa                                         >  1:1174008/4‑70 (MQ=255)                     taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg                                      <  1:3440421/70‑1 (MQ=255)                     taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg                                      <  1:440197/70‑1 (MQ=255)                       ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGt                                     <  1:2077118/70‑1 (MQ=255)                       ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGt                                     <  1:1323603/70‑1 (MQ=255)                       ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa                                    <  1:3421674/71‑1 (MQ=255)                         gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa                                        >  1:3720899/4‑65 (MQ=255)                         gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                  >  1:3946541/4‑71 (MQ=255)                         gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                  >  1:3381653/4‑71 (MQ=255)                         gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                  >  1:3571105/4‑71 (MQ=255)                         gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                  >  1:3747809/4‑71 (MQ=255)                         gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                  >  1:3823341/4‑71 (MQ=255)                         gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                  >  1:37226/4‑71 (MQ=255)                         gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                  >  1:4179528/4‑71 (MQ=255)                         gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                  >  1:4467858/4‑71 (MQ=255)                         gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                  >  1:1220899/4‑71 (MQ=255)                         gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                  >  1:957182/4‑71 (MQ=255)                         gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                  >  1:998875/4‑71 (MQ=255)                         gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                  >  1:2412023/4‑71 (MQ=255)                         gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                  >  1:2306363/4‑71 (MQ=255)                         gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                  >  1:296240/4‑71 (MQ=255)                          taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtg                                 <  1:2356716/69‑1 (MQ=255)                          taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                  <  1:980197/68‑1 (MQ=255)                          taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                  <  1:843255/68‑1 (MQ=255)                          taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                  <  1:1995950/68‑1 (MQ=255)                          taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                  <  1:448834/68‑1 (MQ=255)                          taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                  <  1:3888530/68‑1 (MQ=255)                          taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                  <  1:1656432/68‑1 (MQ=255)                          taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                  <  1:376189/68‑1 (MQ=255)                          taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                  <  1:3460668/68‑1 (MQ=255)                           aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtga                                >  1:3891179/2‑71 (MQ=255)                                 tgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGATACCGACATGAACGTAGt                                  <  1:4670746/62‑1 (MQ=255)                                  gAAGCAATTTGCGTTCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACa                                            >  1:217674/1‑52 (MQ=255)                                      caatttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtga                                >  1:3293755/4‑60 (MQ=255)                                      caatttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtga                                >  1:3215696/4‑60 (MQ=255)                                      caatttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtga                                >  1:4281545/4‑60 (MQ=255)                                       aatttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGaa                        <  1:3276750/65‑1 (MQ=255)                                       aatttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGaa                        <  1:1467728/65‑1 (MQ=255)                                         tttGCGATCTTGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                  <  1:1353390/55‑1 (MQ=255)                                          ttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAg                                   >  1:3106790/1‑53 (MQ=255)                                          ttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAg                                   >  1:119590/1‑53 (MQ=255)                                          ttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAg                                   >  1:305100/1‑53 (MQ=255)                                           tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa                                    >  1:3058814/1‑51 (MQ=255)                                           tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgatga                             >  1:2725606/1‑58 (MQ=255)                                           tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtga                                >  1:2078083/1‑55 (MQ=255)                                           tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtga                                >  1:2175090/1‑55 (MQ=255)                                           tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtga                                >  1:472496/1‑55 (MQ=255)                                           tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGgcg                >  1:825121/1‑71 (MQ=255)                                           tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGgcg                >  1:3380655/1‑71 (MQ=255)                                           tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGgcg                >  1:1952102/1‑71 (MQ=255)                                           tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGgcg                >  1:4372429/1‑71 (MQ=255)                                                    gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGaa                        <  1:654316/54‑1 (MQ=255)                                                    gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcatc            <  1:3734446/66‑1 (MQ=255)                                                    gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcat             <  1:2179890/65‑1 (MQ=255)                                                    gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcat             <  1:2207907/65‑1 (MQ=255)                                                    gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTg        <  1:4408779/70‑1 (MQ=255)                                                    gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGa       <  1:729287/71‑1 (MQ=255)                                                    gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGa       <  1:3579954/71‑1 (MQ=255)                                                    gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGa       <  1:282736/71‑1 (MQ=255)                                                    gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGa       <  1:1916014/71‑1 (MQ=255)                                                    gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAACACGGGCGCATCATTGa       <  1:2879127/71‑1 (MQ=255)                                                       tACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgatga                             <  1:2102963/46‑1 (MQ=255)                                                       tACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgatga                             <  1:1894864/46‑1 (MQ=255)                                                         cGTTGAAGACTCAGCCGCAGAGACCGACATGTACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTg   <  1:441856/70‑1 (MQ=255)                                                         cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcat             >  1:1165343/1‑60 (MQ=255)                                                         cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTg   >  1:4348000/1‑70 (MQ=255)                                                         cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTg   <  1:3884316/70‑1 (MQ=255)                                                         cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTg   <  1:248252/70‑1 (MQ=255)                                                         cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTg   >  1:2966570/1‑70 (MQ=255)                                                         cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGc  <  1:3088413/71‑1 (MQ=255)                                                                     |                                                           GTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGC  >  W3110S.gb/3824342‑3824468

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: ‑