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%	155.9 / NA	48	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 (25/23);  total (25/23)

GCCGATGTTCAACTGATAGTGAGTCGCGTCATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATCTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATGTTGTAGTTTGTCTGCTCCTCACGATCC  >  NC_000913/2453130‑2453397                                                                                                                                        |                                                                                                                                     gCCGATGTTCAACTGATAGTGAGTCGCGTCATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTAc                                                                                                                                   <  1:374937/139‑1 (MQ=255) gCCGATGTTCAACTGATAGTGAGTCGCGTCATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTAc                                                                                                                                   <  1:639720/139‑1 (MQ=255)                  aGTGAGTCGCGTCATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCg                                                                                                                  <  2:648125/139‑1 (MQ=255)                    tGAGTCGCGTCATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTAc                                                                                                                                   >  2:793834/1‑120 (MQ=255)                    tGAGTCGCGTCATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTAc                                                                                                                                   <  1:793834/120‑1 (MQ=255)                       gTCGCGTCATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGt                                                                                                             >  2:154583/1‑139 (MQ=255)                           cgTCATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATa                                                                                                         <  2:721062/139‑1 (MQ=255)                           cgTCATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATa                                                                                                         >  1:751028/1‑139 (MQ=255)                              cATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTc                                                                                                      >  1:560904/1‑139 (MQ=255)                              cATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCACTTATCCGCCCGGTTGTCATACTc                                                                                                      >  2:142490/1‑139 (MQ=255)                                tCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGt                                                                                                    >  2:315678/1‑139 (MQ=255)                                        gCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAg                                                                                            <  1:154583/139‑1 (MQ=255)                                           aaaaTAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCa                                                                                         >  2:779051/1‑139 (MQ=255)                                                 aCCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAgg                                                                                   <  1:586829/139‑1 (MQ=255)                                                   cGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGa                                                                                 <  2:550923/139‑1 (MQ=255)                                                   cGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGa                                                                                 <  1:779051/139‑1 (MQ=255)                                                         ggCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCt                                                                           <  2:472816/139‑1 (MQ=255)                                                         ggCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCt                                                                           >  1:184007/1‑139 (MQ=255)                                                             gctgTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCAt                                                                                                          <  2:552812/104‑1 (MQ=255)                                                             gctgTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCAt                                                                                                          >  1:552812/1‑104 (MQ=255)                                                                          cTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGcc                                                                                                                    >  1:670546/1‑81 (MQ=255)                                                                          cTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGcc                                                                                                                    <  2:670546/81‑1 (MQ=255)                                                                             ccATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCa                                                       >  1:693377/1‑139 (MQ=255)                                                                                       cGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATa                                             >  2:74210/1‑139 (MQ=255)                                                                                           ataGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTgg                                         >  2:485941/1‑139 (MQ=255)                                                                                            taGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTggg                                        >  2:721124/1‑139 (MQ=255)                                                                                                   cGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCat                                 >  1:764131/1‑139 (MQ=255)                                                                                                           ttgtCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCat                                                                        >  1:726359/1‑92 (MQ=255)                                                                                                           ttgtCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCat                                                                        <  2:726359/92‑1 (MQ=255)                                                                                                              tCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCATGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATGTTGTAGt                      <  1:142490/139‑1 (MQ=255)                                                                                                              tCGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATATTGTAGt                      >  1:85314/1‑139 (MQ=255)                                                                                                               cGCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATGTTGTAGtt                     >  2:354718/1‑139 (MQ=255)                                                                                                                gCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCat                                                                        >  2:609687/1‑87 (MQ=255)                                                                                                                gCCCCACGGCATACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCat                                                                        <  1:609687/87‑1 (MQ=255)                                                                                                                           tACTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATATTGTAGTTTGTCTGctcctc         <  2:85314/139‑1 (MQ=255)                                                                                                                            aCTGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATGTTGTAGTTTGTCTGCTCCTCa        <  2:647349/139‑1 (MQ=255)                                                                                                                              tGAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATCCTGCCCATATTGAAATAGTGGGAGAGCATGATGTTGTAGTTTGTCTGCTCCTCACg      <  1:598497/139‑1 (MQ=255)                                                                                                                               gAGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATGTTGTAGTTTGTCTGCTCCTCACGa     <  1:448549/139‑1 (MQ=255)                                                                                                                                aGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATGTTGTAGTTTGTCTGCTCCTCa        <  2:648764/135‑1 (MQ=255)                                                                                                                                aGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATGTTGTAGTTTGTCTGCTCCTCa        >  1:648764/1‑135 (MQ=255)                                                                                                                                aGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATGTTGTAGTTTGTCTGCTCCTCACGAt    <  2:560904/139‑1 (MQ=255)                                                                                                                                aGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATGTTGTAGTTTGTCTGCTCCTCACGAt    >  2:363154/1‑139 (MQ=255)                                                                                                                                aGCGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATGTTGTAGTTTGTCTGCTCCTCACGAt    >  2:360666/1‑139 (MQ=255)                                                                                                                                  cGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTa                                                                                             <  2:595720/48‑1 (MQ=255)                                                                                                                                  cGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTa                                                                                             >  1:595720/1‑48 (MQ=255)                                                                                                                                  cGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGga                                       <  1:436794/102‑1 (MQ=255)                                                                                                                                  cGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGga                                       >  2:436794/1‑102 (MQ=255)                                                                                                                                  cGAAATTTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATGTTGTAGTTTGTCTGCTCCTCACGATcc  >  1:491296/1‑139 (MQ=255)                                                                                                                                        |                                                                                                                                     GCCGATGTTCAACTGATAGTGAGTCGCGTCATCGACACGGCTAAAATAACCGACCTGGCTGCTGTCCGTCCCACTGCCATAGTTGCCGTTATAGCTAACGGTACTGTTGTCGCCCCACGGCATACTGAGCGAAATCTACATGCCCTTATCCGCCCGGTTGTCATACTCGTAGCGGTAGCCAGTCAGGGAAACGCTCATATTACGAATGCTGCCCATATTGAAATAGTGGGAGAGCATGATGTTGTAGTTTGTCTGCTCCTCACGATCC  >  NC_000913/2453130‑2453397

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑