Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,419,403	C→T	pseudogene (297/960 nt)	yhdW →	pseudogene, ABC transporter periplasmic binding protein family,putative transport, Not classified, putative periplasmic binding transport protein, periplasmic‑binding component of ABC superfamily

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,419,403	0	C	T	100.0%	196.2 / NA	62	pseudogene (297/960 nt)	yhdW	pseudogene, ABC transporter periplasmic binding protein family,putative transport, Not classified, putative periplasmic binding transport protein, periplasmic‑binding component of ABC superfamily
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (34/28);  total (34/28)

CCCCGCTCACTGCAAAAGAACGCTTCACCGCTTTACAGTCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGCGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTCAGGCGGGTACTGATACCGAACTCAACGTCGCCGACTACTTC  >  NC_000913/3419285‑3419535                                                                                                                       |                                                                                                                                     ccccGCTCACTGCAAAAGAACGCTTCACCGCTTTACAGTCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCa                                                                                                                   <  1:1151877/138‑1 (MQ=255) ccccGCTCACTGCAAAAGAACGCTTCACCGCTTTACAGTCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCa                                                                                                                   >  2:1151877/1‑138 (MQ=255) ccccGCTCACTGCAAAAGAACGCTTCACCGCTTTACAGTCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCAt                                                                                                                  >  2:1027494/1‑139 (MQ=255)       tCACTGCAAAAGAACGCTTCACCGCTTTACAGTCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCtt                                                                                                            >  2:460935/1‑139 (MQ=255)              aaaaGAACGCTTCACCGCTTTACAGTCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACg                                                                                                     <  2:288552/139‑1 (MQ=255)                       cTTCACCGCTTTACAGTCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATaaa                                                                                            >  1:7061/1‑139 (MQ=255)                        ttCACCGCTTTACAGTCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAg                                                                                           <  1:521145/139‑1 (MQ=255)                                tttACAGTCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTa                                                                                   >  1:781370/1‑139 (MQ=255)                                         aGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGcgcg                                                                          >  2:333356/1‑139 (MQ=255)                                           gggAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGaa                                                                        >  2:245023/1‑139 (MQ=255)                                               ggTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGaa                                                                    <  1:1027494/139‑1 (MQ=255)                                               ggTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGaa                                                                    <  2:513062/139‑1 (MQ=255)                                                gTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCg                                                                                         <  1:619963/117‑1 (MQ=255)                                                gTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCg                                                                                         >  2:619963/1‑117 (MQ=255)                                                gTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAAc                                                                   >  1:787570/1‑139 (MQ=255)                                                 tGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAg                                                                                           <  2:1286931/114‑1 (MQ=255)                                                 tGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAg                                                                                           >  1:1286931/1‑114 (MQ=255)                                                 tGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACt                                                                  >  1:98917/1‑139 (MQ=255)                                                 tGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACt                                                                  >  2:1093900/1‑139 (MQ=255)                                                   gATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTgg                                                                >  1:205881/1‑139 (MQ=255)                                                     tttGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGAt                                                              >  2:269901/1‑139 (MQ=255)                                                          tctcCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGgcgc                                                         >  1:1223626/1‑139 (MQ=255)                                                           ctcCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAg                                                                                           >  1:766928/1‑104 (MQ=255)                                                           ctcCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAg                                                                                           <  2:766928/104‑1 (MQ=255)                                                             cccGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCt                                                        <  2:1110846/137‑1 (MQ=255)                                                             cccGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCt                                                        >  1:1110846/1‑137 (MQ=255)                                                             cccGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTAc                                                      <  1:931509/139‑1 (MQ=255)                                                                        aCCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACttatta                                                                                                                           <  2:1129126/59‑1 (MQ=255)                                                                        aCCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACttatta                                                                                                                           >  1:1129126/1‑59 (MQ=255)                                                                        aCCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACttat                                                                                                                             <  2:1014113/57‑1 (MQ=255)                                                                        aCCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACttat                                                                                                                             >  1:1014113/1‑57 (MQ=255)                                                                        aCCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACg                                                                                                     <  1:6069/81‑1 (MQ=255)                                                                        aCCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTAtt                                            <  1:1337912/138‑1 (MQ=255)                                                                        aCCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTAtt                                            >  2:1337912/1‑138 (MQ=255)                                                                        aCCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTc                                           >  1:261/1‑139 (MQ=255)                                                                        aCCTGGACTTCATCTCCCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACg                                                                                                     >  2:6069/1‑81 (MQ=255)                                                                         ccTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTaaa                                                                                 >  2:330372/1‑100 (MQ=255)                                                                         ccTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTaaa                                                                                 <  1:330372/100‑1 (MQ=255)                                                                         ccTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTCa                                          >  1:1055732/1‑139 (MQ=255)                                                                           tGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTCAgg                                        <  2:781370/139‑1 (MQ=255)                                                                                  cATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTCAGGCGGGTAc                                 >  2:836882/1‑139 (MQ=255)                                                                                   aTCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTAc                                                      >  2:281950/1‑117 (MQ=255)                                                                                   aTCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTAc                                                      <  1:281950/117‑1 (MQ=255)                                                                                   aTCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTCAGGCGGGTACt                                >  2:1051328/1‑139 (MQ=255)                                                                                   aTCTCGCGATGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTCAGGCGGGTACt                                >  2:377800/1‑139 (MQ=255)                                                                                            tGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTCAGGCg                                      >  2:1171926/1‑124 (MQ=255)                                                                                            tGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTCAGGCg                                      <  1:1171926/124‑1 (MQ=255)                                                                                            tGCCGGGATGGGAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTCAGGCGGGTACTGATACCGaa                       <  1:377800/139‑1 (MQ=255)                                                                                                      ggAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAg                                                                                           <  2:1004713/61‑1 (MQ=255)                                                                                                      ggAATGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAg                                                                                           >  1:1004713/1‑61 (MQ=255)                                                                                                          tGGCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTCAGGCGGGTACTGATACCGAACTCAACGTCGCCGa         <  2:7061/139‑1 (MQ=255)                                                                                                           ggCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTCAGGCGGGTACTGATACCGAACTCAACGTCGCCGac        <  1:333356/139‑1 (MQ=255)                                                                                                           ggCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTCAGGCGGGTACTGATACCGAACTCAACGTCGCCGac        <  1:1093900/139‑1 (MQ=255)                                                                                                            gCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTaaa                                                                                 <  2:508240/65‑1 (MQ=255)                                                                                                            gCATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTaaa                                                                                 >  1:508240/1‑65 (MQ=255)                                                                                                             cATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAg                                                                                           <  1:236329/54‑1 (MQ=255)                                                                                                             cATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAg                                                                                           >  2:236329/1‑54 (MQ=255)                                                                                                             cATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAg                                                                              <  2:400592/67‑1 (MQ=255)                                                                                                             cATTTACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAg                                                                              >  1:400592/1‑67 (MQ=255)                                                                                                                ttACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTCAGGCGGGTACTGATACCGAACTCAACg                >  1:745527/1‑126 (MQ=255)                                                                                                                ttACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTCAGGCGGGTACTGATACCGAACTCAACg                <  2:745527/126‑1 (MQ=255)                                                                                                                 tACCGGTGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTCAGGCGGGTACTGATACCGAACTCAACGTCGCCGACTACTTc  <  1:269901/139‑1 (MQ=255)                                                                                                                       |                                                                                                                                     CCCCGCTCACTGCAAAAGAACGCTTCACCGCTTTACAGTCAGGGGAGGTGGATTTGCTCTCCCGTAATACGACCTGGACTTCATCTCGCGATGCCGGGATGGGAATGGCATTTACCGGCGTCACTTATTACGACGGCATTGGCTTCCTGACGCACGATAAAGCGGGGCTAAAAAGCGCGAAAGAACTGGATGGCGCTACCGTCTGTATTCAGGCGGGTACTGATACCGAACTCAACGTCGCCGACTACTTC  >  NC_000913/3419285‑3419535

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: ‑