Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,453,265	C→T	pseudogene (1737/2646 nt)	yfcU ←	pseudogene, FimD fimbrial export usher family,putative membrane, Not classified, putative outer membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,453,265	0	C	T	100.0%	223.9 / NA	69	pseudogene (1737/2646 nt)	yfcU	pseudogene, FimD fimbrial export usher family,putative membrane, Not classified, putative outer membrane protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (33/36);  total (33/36)

GCCGATGTTCAACTGATAGTGAGTCGCGTCATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATCTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATGTTGTAGTTTGTCTGCTCCTCACGAT  >  NC_000913/2453130‑2453395                                                                                                                                        |                                                                                                                                   gCCGATGTTCAACTGATAGTGAGTCGCGTCATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTAc                                                                                                                                 <  2:768989/139‑1 (MQ=255)       gTTCAACTGATAGTGAGTCGCGTCATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGccc                                                                                                                           <  1:536585/139‑1 (MQ=255)                  aGTGAGTCGCGTCATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCg                                                                                                                >  2:157989/1‑139 (MQ=255)                   gTGAGTCGCGTCATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCgg                                                                                                               <  1:852675/139‑1 (MQ=255)                   gTGAGTCGCGTCATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCgg                                                                                                               <  1:994265/139‑1 (MQ=255)                    tGAGTCGCGTCATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTAc                                                                                                                                 >  1:1155899/1‑120 (MQ=255)                    tGAGTCGCGTCATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTAc                                                                                                                                 <  2:1155899/120‑1 (MQ=255)                          gcgTCATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCAGTTGTCAt                                                                                                        >  1:225529/1‑139 (MQ=255)                                         cTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGc                                                                                         >  2:968034/1‑139 (MQ=255)                                                      ccTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACa                                                                                                                                >  1:1292753/1‑87 (MQ=255)                                                      ccTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACa                                                                                                                                <  2:1292753/87‑1 (MQ=255)                                                       cTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGc                                                                                         <  2:187600/125‑1 (MQ=255)                                                       cTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGc                                                                                         >  1:187600/1‑125 (MQ=255)                                                         ggCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCt                                                                         <  1:157989/139‑1 (MQ=255)                                                                   cgtccCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGa                                                               >  1:192154/1‑139 (MQ=255)                                                                           tGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGcc                                                       <  2:1202818/139‑1 (MQ=255)                                                                           tGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGcc                                                       <  1:1091780/139‑1 (MQ=255)                                                                             ccATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCa                                                     <  2:225529/139‑1 (MQ=255)                                                                                tAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTAc                                                                                                                                 <  2:119724/60‑1 (MQ=255)                                                                                tAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTAc                                                                                                                                 >  1:119724/1‑60 (MQ=255)                                                                                   ttGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGa                                               <  1:558208/139‑1 (MQ=255)                                                                                     gCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGTAAACGCTCATATTACGAATGCTGCCCa                                                     <  2:804316/131‑1 (MQ=255)                                                                                     gCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCa                                                     >  1:804316/1‑131 (MQ=255)                                                                                       cGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGcc                                                                                                                  <  2:605720/68‑1 (MQ=255)                                                                                       cGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGcc                                                                                                                  >  1:605720/1‑68 (MQ=255)                                                                                       cGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATa                                                                                                       <  2:635702/79‑1 (MQ=255)                                                                                       cGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATa                                                                                                       >  1:635702/1‑79 (MQ=255)                                                                                             aGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGga                                     <  2:192154/139‑1 (MQ=255)                                                                                                 aaCGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCa                                                                                                         >  2:1114699/1‑67 (MQ=255)                                                                                                 aaCGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCa                                                                                                         <  1:1114699/67‑1 (MQ=255)                                                                                                  aCGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCa                                <  1:968034/139‑1 (MQ=255)                                                                                                   cGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGcc                                                       <  1:988943/115‑1 (MQ=255)                                                                                                   cGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGcc                                                       >  2:988943/1‑115 (MQ=255)                                                                                                       aCTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCatg                              <  1:783603/136‑1 (MQ=255)                                                                                                       aCTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCatg                              >  2:783603/1‑136 (MQ=255)                                                                                                        cTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCgg                                                                                                               <  2:339325/54‑1 (MQ=255)                                                                                                        cTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCgg                                                                                                               >  1:339325/1‑54 (MQ=255)                                                                                                         tgttgtCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGAtgtt                         >  1:262871/1‑139 (MQ=255)                                                                                                           ttgtCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACg                                                                           <  1:801582/87‑1 (MQ=255)                                                                                                           ttgtCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACg                                                                           >  2:801582/1‑87 (MQ=255)                                                                                                              tCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGccc                                                                                                                 >  2:823776/1‑46 (MQ=255)                                                                                                              tCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGccc                                                                                                                 <  1:823776/46‑1 (MQ=255)                                                                                                              tCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCg                                                                                                   >  1:764443/1‑60 (MQ=255)                                                                                                              tCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCg                                                                                                   <  2:764443/60‑1 (MQ=255)                                                                                                              tCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGaaa                                                                             <  2:579640/82‑1 (MQ=255)                                                                                                              tCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGaaa                                                                             >  1:579640/1‑82 (MQ=255)                                                                                                                gCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCa                                >  2:1236051/1‑125 (MQ=255)                                                                                                                gCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCa                                <  1:1236051/125‑1 (MQ=255)                                                                                                                gCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATGTTGTAg                     >  1:418793/1‑136 (MQ=255)                                                                                                                gCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATGTTGTAg                     <  2:418793/136‑1 (MQ=255)                                                                                                                gCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATGTTGTAGttt                  >  1:1018472/1‑139 (MQ=255)                                                                                                                     aCGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAAtgctg                                                         <  1:452464/95‑1 (MQ=255)                                                                                                                     aCGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAAtgctg                                                         >  2:452464/1‑95 (MQ=255)                                                                                                                     aCGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCa                                                     <  2:210091/99‑1 (MQ=255)                                                                                                                     aCGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCa                                                     >  1:210091/1‑99 (MQ=255)                                                                                                                     aCGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATGTTGTAGTTTGTCTg             >  1:1330414/1‑139 (MQ=255)                                                                                                                     aCGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATGTTGTAGTTTGTCTg             >  2:703985/1‑139 (MQ=255)                                                                                                                             cTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATGTTGTAGTTTGTCTGCTCCTCAc     <  2:262871/139‑1 (MQ=255)                                                                                                                              tGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATGTTGTAg                     >  2:237565/1‑122 (MQ=255)                                                                                                                              tGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATGTTGTAg                     <  1:237565/122‑1 (MQ=255)                                                                                                                                aacGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGa                                               <  1:339750/92‑1 (MQ=255)                                                                                                                                aacGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGa                                               >  2:339750/3‑94 (MQ=255)                                                                                                                                aGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCt                                                                         >  1:201800/1‑68 (MQ=255)                                                                                                                                aGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCt                                                                         <  2:201800/68‑1 (MQ=255)                                                                                                                                aGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATGTTGTAGTTTGTCTGCTCCTCACGAt  >  2:370009/1‑139 (MQ=255)                                                                                                                                 gCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTgg                                       >  1:205159/1‑101 (MQ=255)                                                                                                                                 gCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTgg                                       <  2:205159/101‑1 (MQ=255)                                                                                                                                 gCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATGTTGTAGTTTGTCTGCTCCTCa      <  2:546835/134‑1 (MQ=255)                                                                                                                                 gCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATGTTGTAGTTTGTCTGCTCCTCa      >  1:546835/1‑134 (MQ=255)                                                                                                                                        |                                                                                                                                   GCCGATGTTCAACTGATAGTGAGTCGCGTCATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATCTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATGTTGTAGTTTGTCTGCTCCTCACGAT  >  NC_000913/2453130‑2453395

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑