Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	2,452,436	C→A	9.1%	pseudogene (2566/2646 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	2,452,436	0	C	A	9.1%	193.6 / 5.5	55	pseudogene (2566/2646 nt)	yfcU	pseudogene, FimD fimbrial export usher family;putative membrane; Not classified; putative outer membrane protein
Reads supporting (aligned to +/- strand):  ref base C (31/19);  new base A (3/2);  total (34/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CACCCAATTTGGCAGAGCAAAGTAAATCAGACATGGATCATTCCTTAATCACGTTATTGGTTAGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAAGCCGTTAAACAGATCGGCAGGCAGCGGGTCCGGCAGGTTGATATCGCAATGCGCAACACCACTCCAGAACACACTCATATGTTCGCC  >  NC_000913/2452303‑2452574                                                                                                                                      |                                                                                                                                           cACCCAATTTGGCAGAGCAAAGTAAATCAGACATGGATCATTCCTTAATCACGTTATTGGTTAGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAgg                                                                                                                                      <  1:1680521/140‑1 (MQ=255)   cccAATTTGGCAGAGCAAAGTAAATCAGACATGGATCATTCCTTAATCACGTTATTGGTTAGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGaa                                                                                                                                    >  2:266042/1‑140 (MQ=255)            gCAGAGCAAAGTAAATCAGACATGGATCATTCCTTAATCACGTTATTGGTTAGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGgcg                                                                                                                           <  1:879943/140‑1 (MQ=255)             cAGAGCAAAGTAAATCAGACATGGATCATTCCTTAATCACGTTATTGGTTAGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGgcgc                                                                                                                          <  1:1373190/140‑1 (MQ=255)                  cAAAGTAAATCAGACATGGATCATTCCTTAATCACGTTATTGGTTAGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGt                                                                                                                     <  1:1547919/140‑1 (MQ=255)                          aTCAGACATGGATCATTCCTTAATCACGTTATTGGTTAGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTa                                                                                                             >  1:254800/1‑140 (MQ=255)                          aTCAGACATGGATCATTCCTTAATCACGTTATTGGTTAGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTa                                                                                                             >  1:1511711/1‑140 (MQ=255)                          aTCAGACATGGATCATTCCTTAATCACGTTATTGGGTAGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTa                                                                                                             >  1:43847/1‑140 (MQ=255)                           tCAGACATGGATCATTCCTTAATCACGTTATTGGTTAGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTAt                                                                                                            <  2:1569943/140‑1 (MQ=255)                            cAGACATGGATCATTCCTTAATCACGTTATTGGTTAGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATg                                                                                                           >  2:263140/1‑140 (MQ=255)                            cAGACATGGATCATTCCTTAATCACGTTATTGGTTAGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATg                                                                                                           >  2:263211/1‑140 (MQ=255)                             aGACATGGATCATTCCTTAATCACGTTATTGGTTAGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTAATCAGGAACAACCGGCGCGACGTTGCCTTTATGc                                                                                                          >  2:122414/1‑140 (MQ=255)                                   ggATCATTCCTTAATCACGTTATTGGTTAGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCtggcat                                                                                                    >  1:998694/1‑140 (MQ=255)                                   ggATCATTCCTTAATCACGTTATTGGTTAGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCtggcat                                                                                                    >  1:998699/1‑140 (MQ=255)                                    gATCATTCCTTAATCACGTTATTGGTTAGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCtggcatg                                                                                                   >  1:135726/1‑140 (MQ=255)                                    gATCATTCCTTAATCACGTTATTGGTTAGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCtggcatg                                                                                                   >  1:472643/1‑140 (MQ=255)                                    gATCATTCCTTAATCACGTTATTGGTTAGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCtggcatg                                                                                                   >  1:135239/1‑140 (MQ=255)                                     aTCATTCCTTAATCACGTTATTGGTTAGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCtggcatgg                                                                                                  <  1:1374041/140‑1 (MQ=255)                                     aTCATTCCTTAATCACGTTATTGGTTAGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCtggcatgg                                                                                                  <  1:801330/140‑1 (MQ=255)                                         ttCCTTAATCACGTTATTGGTTAGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGt                                                                                              >  2:712035/1‑140 (MQ=255)                                         ttCCTTAATCACGTTATTGGTTAGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGt                                                                                              >  2:711822/1‑140 (MQ=255)                                             ttAATCACGTTATTGGTTAGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACa                                                                                          <  2:1231486/140‑1 (MQ=255)                                             ttAATCACGTTATTGGTTAGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACa                                                                                          <  1:328775/140‑1 (MQ=255)                                               aaTCACGTTATTGGTTAGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAAg                                                                                        >  1:1339436/1‑140 (MQ=255)                                               aaTCACGTTATTGGTTAGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAAg                                                                                        >  1:870471/1‑140 (MQ=255)                                               aaTCACGTTATTGGTTAGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAAg                                                                                        >  1:870630/1‑140 (MQ=255)                                                 tCACGTTATTGGTTAGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAAGcc                                                                                      >  1:839651/1‑140 (MQ=255)                                                    cGTTATTGGTTAGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAAGCCGtt                                                                                   >  2:78657/1‑140 (MQ=255)                                                               aGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACTAGCCGTTAAACAGATCgg                                                                        >  2:1623302/1‑140 (MQ=255)                                                               aGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAAGCCGTTAAACAGATCgg                                                                        >  2:54203/1‑140 (MQ=255)                                                               aGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAAGCCGTTAAACAGATCgg                                                                        >  2:1071062/1‑140 (MQ=255)                                                               aGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAAGCCGTTAAACAGATCgg                                                                        >  2:1071018/1‑140 (MQ=255)                                                                 cTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAAGCCGTTAAACAGATCggca                                                                      >  2:1388515/1‑140 (MQ=255)                                                                 cTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAAGCCGTTAAACAGATCggca                                                                      >  2:1389337/1‑140 (MQ=255)                                                                 aaaaaacaaaaaaagTGGGATCGGTGGGAGTCACCTTATTATTCTGCTAATTAATTACAGGCTTAATGAAATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAAGCCGTTAAACAGATCggca                                                                      >  1:678390/4‑140 (MQ=255)                                                                 aaaaaacaaaaaaagTGGGAACGGTGGGATTCACATTTTTCTACATCTAATTAATTACATGCATTATGAAAACAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAAGCCGTTAAACAGATCggca                                                                      >  1:678340/4‑140 (MQ=255)                                                                      acagaaacagGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAAGCCGTTAAACAGATCGgcaggcag                                                                 <  2:946152/140‑1 (MQ=255)                                                                      acagaaacagGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAAGCCGTTAAACAGATCGgcaggcag                                                                 <  2:946200/140‑1 (MQ=255)                                                                           aacagGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAAGCCGTTAAACAGATCGGCAGGCAGCGGGt                                                            >  2:706207/1‑140 (MQ=255)                                                                             cagGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAAGCCGTTAAACAGATCGGCAGGCAGCGGGTcc                                                          >  1:62878/1‑140 (MQ=255)                                                                               gggggATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAAGCCGTTAAACAGATCGGCAGGCAGCGGGTCCgg                                                        <  2:1359095/140‑1 (MQ=255)                                                                                              gtCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAAGCCGTTAAACAGATCGGCAGGCAGCGGGTCCGGCAGGTTGATATCGCa                                         <  1:1092980/140‑1 (MQ=255)                                                                                              gtCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAAGCCGTTAAACAGATCGGCAGGCAGCGGGTCCGGCAGGTTGATATCGCa                                         <  1:1093051/140‑1 (MQ=255)                                                                                              gtCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAAGCCGTTAAACAGATCGGCAGGCAGCGGGTCCGGCAGGTTGATATCGCa                                         >  1:1125043/1‑140 (MQ=255)                                                                                              gtCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAAGCCGTTAAACAGATCGGCAGGCAGCGGGTCCGGCAGGTTGATATCGCa                                         <  1:1449907/140‑1 (MQ=255)                                                                                                      ttGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAATCCGTTAAACAGATCGGCAGGCAGAGGGTCCGGCAGGTTGATATCGCAATGCGCaa                                 <  1:524753/140‑1 (MQ=255)                                                                                                       tGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAAGCCGTTAAACAGATCGGCAGGCAGCGGGTCCGGCAGGTTGATATCGCAATGCGCAac                                >  2:1076857/1‑140 (MQ=255)                                                                                                                tCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAAGCCGTTAAACAGATCGGCAGGCAGCGGGTCCGGCAGGTTGATATCGCAATGCGCAACACCACTCCa                       >  2:1547026/1‑140 (MQ=255)                                                                                                                     aaTGACTGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTTACAAGCCGTTAAACAGATCGGCAGGCTGCGGGTCCGGCAGGTTGATATCGCAATGCGCAACACCACTCCAGAaca                  <  2:180924/140‑1 (MQ=255)                                                                                                                     aaTGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAAGCCGTTAAACAGATCGGCAGGCAGCGGGTCCGGCAGGTTGATATCGCAATGCGCAACACCACTCCAGAaca                  >  1:553481/1‑140 (MQ=255)                                                                                                                     aaTGACAGGCTTTATGTAATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAAGCCGTTAAACAGATCGGCAGGCAGCGGGTCCGGCAGGTTGATATCGCAATGCGCAACACCACTCCAGAaca                  <  2:678340/140‑1 (MQ=255)                                                                                                                     aaTGACAGGCTTTATGTAATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAAGCCGTTAAACAGATCGGCAGGCAGCGGGTCCGGCAGGTTGATATCGCAATGCGCAACACCACTCCAGAaca                  <  2:678390/140‑1 (MQ=255)                                                                                                                         aCAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAAGCCGTTAAACAGATCGGCAGGCAGCGGGTCCGGCAGGTTGATATCGCAATGCGCAACACCACACCAGAACACACt              >  2:1569837/1‑140 (MQ=255)                                                                                                                             gCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAAGCCGTTAAACAGATCGGCAGGCAGCGGGTCCGGCAGGTTGATATCGCAATGCGCAACACCACTCCAGAACACACTCata          <  1:404677/140‑1 (MQ=255)                                                                                                                                    gTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAAGCCGTTAAACAGATCGGCAGGCAGCGGGTCCGGCAGGTTGATATCGCAATGCGCAACACCACTCCAGAACACACTCATATGTTCGc   <  2:1344726/140‑1 (MQ=255)                                                                                                                                     tcatcaGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAAGCCGTTAAACAGATCGGCAGGCAGCGGGTCCGGCAGGTTGATATCGCAATGCGCAACACCACTCCAGAACACACTCATATGTTCGcc  <  2:1080141/140‑1 (MQ=255)                                                                                                                                      |                                                                                                                                           CACCCAATTTGGCAGAGCAAAGTAAATCAGACATGGATCATTCCTTAATCACGTTATTGGTTAGCTGAAACAGAAACAGGGGGATCGGTGGGTGTCACCTGTTGCGTCTGCTCCTGAATGACAGGCTTTATGTCATCAGGAACAACCGGCGCGACGTTGCCTTTATGCTGGCATGGCAGTAACAAGCCGTTAAACAGATCGGCAGGCAGCGGGTCCGGCAGGTTGATATCGCAATGCGCAACACCACTCCAGAACACACTCATATGTTCGCC  >  NC_000913/2452303‑2452574

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑