Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,968,916	T→C	Q21R (CAG→CGG)	rppH ←	RNA pyrophosphohydrolase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,968,916	0	T	C	100.0%	220.6 / NA	58	Q21R (CAG→CGG)	rppH	RNA pyrophosphohydrolase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (27/31);  total (27/31)

GAACGTCTTTGCGGCTTAATCCTACTTCTTCAAACAATTCACGGTACATCGCCTGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCTGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCGGACTACCTCAAAATAAAGCTTTATATACGAATGATTGTTTCATACTCCAGGAAGACGGTAAACCA  >  NC_000913/2968782‑2969044                                                                                                                                       |                                                                                                                                 taaCGCCTTTGCTGCTTAATCCTACTTCTTCAAACAATTCACGGTACATCGCCTGCTCTGCGGATTCTCCGGGGTTGAGTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAAGCGCCGGGCCCACATTACCCGccc                                                                                                                              <  1:1066453/138‑1 (MQ=255)       cTTTGCGGCTTAATCCTACTTCTTCAAACAATTCACGGTACATCGCCTGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCg                                                                                                                        >  1:848066/1‑139 (MQ=255)       cTTTGCGGCTTAATCCTACTTCTTCAAACAATTCACGGTAAATCGCCTGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTCCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCg                                                                                                                        >  2:676406/1‑139 (MQ=255)           gCGGCTTAATCCTACTTCTTCAAACAATTCACGGTACATCGCCTGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTa                                                                                                                    <  1:1061922/139‑1 (MQ=255)           gCGGCTTAATCCTACTTCTTCAAACAATGCACGGTACATCGCCTGCTCTGCGGATTCTCCCGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTa                                                                                                                    <  1:680884/139‑1 (MQ=255)                ttAATCCTACTTCTTCAAACAATTCACGGTACATCGCCTGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGccc                                                                                                                              <  2:686584/124‑1 (MQ=255)                ttAATCCTACTTCTTCAAACAATTCACGGTACATCGCCTGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGccc                                                                                                                              >  1:686584/1‑124 (MQ=255)                ttAATCCTACTTCTTCAAACAATTCACGGTACATCGCCTGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAAt                                                                                                               <  1:94522/139‑1 (MQ=255)                              tcAAACAATTCACGGTACATCGCCTGCTCTGCTGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGATTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGAGTACAAATCACGATACCTACGt                                                                                                 >  1:48914/1‑139 (MQ=255)                              tcAAACAATTCACGGTACATCGCCTGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGt                                                                                                 >  1:1030653/1‑139 (MQ=255)                                      ttCACGGTACATCGCCTGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTggg                                                                                            >  2:269090/1‑136 (MQ=255)                                      ttCACGGTACATCGCCTGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTggg                                                                                            <  1:269090/136‑1 (MQ=255)                                      ttCACGGTACATCGCCTGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCgg                                                                                         >  1:429250/1‑139 (MQ=255)                                            gTACATCGCCTGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCa                                                                                   <  1:204543/139‑1 (MQ=255)                                             tACATCGCCTGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCAt                                                                                  <  1:316460/139‑1 (MQ=255)                                                aTCGCCTGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCAt                                                                                  <  2:783640/136‑1 (MQ=255)                                                aTCGCCTGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCAt                                                                                  >  1:783640/1‑136 (MQ=255)                                                aTCGCCTGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGt                                                                               >  2:534244/1‑139 (MQ=255)                                                aTCGCCTGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGt                                                                               >  2:409898/1‑139 (MQ=255)                                                aTCGCCTGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGt                                                                               >  2:319605/1‑139 (MQ=255)                                                aTCGCCTGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGt                                                                               >  1:301409/1‑139 (MQ=255)                                                    ccTGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGtcatc                                                                           >  1:824514/1‑139 (MQ=255)                                                       gCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCatcaat                                                                        >  1:1083943/1‑139 (MQ=255)                                                       gCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCatcaat                                                                        >  2:930941/1‑139 (MQ=255)                                                        ctctGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCatcaatc                                                                       >  2:419964/1‑139 (MQ=255)                                                        ctctGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCatcaatc                                                                       >  2:1076658/1‑139 (MQ=255)                                                         tctGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCatcaatca                                                                      <  2:13520/139‑1 (MQ=255)                                                         tctGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCatcaatca                                                                      <  1:930941/139‑1 (MQ=255)                                                          ctGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCa                                                                                                             >  1:781526/1‑99 (MQ=255)                                                          ctGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCa                                                                                                             <  2:781526/99‑1 (MQ=255)                                                             cGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCgg                                                                  >  1:941358/1‑139 (MQ=255)                                                               gATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCGGAc                                                                <  1:676406/139‑1 (MQ=255)                                                               gATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCGGAc                                                                <  1:409898/139‑1 (MQ=255)                                                                     ccGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCGGACTACCTc                                                          >  1:562715/1‑139 (MQ=255)                                                                           ttGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCGGACTACCTCAAAATa                                                    <  1:430393/139‑1 (MQ=255)                                                                              aTTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACg                                                                                                           <  2:721879/81‑1 (MQ=255)                                                                              aTTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACg                                                                                                           >  1:721879/1‑81 (MQ=255)                                                                              aTTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCGGACTACCTCAAAATAAAg                                                 >  1:309865/1‑139 (MQ=255)                                                                              aTTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCGGACTACCTCAAAATAAAg                                                 >  1:850312/1‑139 (MQ=255)                                                                                tCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCGGACTACCTCAAAATAAAGCt                                               <  1:102531/139‑1 (MQ=255)                                                                                tCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCGGACTACCTCAAAATAAAGCt                                               >  1:1098882/1‑139 (MQ=255)                                                                                tCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCGGACTACCTCAAAATAAAGCt                                               <  1:703124/139‑1 (MQ=255)                                                                                tCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCGGACTACCTCAAAATAAAGCt                                               <  2:824514/139‑1 (MQ=255)                                                                                    ccTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCAc                                                                     >  1:438610/1‑113 (MQ=255)                                                                                    ccTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCAc                                                                     <  2:438610/113‑1 (MQ=255)                                                                                              aTTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCGGACTACCTCAAAATAAAGCTTTATATACGAATGa                                 <  2:941358/139‑1 (MQ=255)                                                                                              aTTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCGGACTACCTCAAAATAAAGCTTTATATACGAATGa                                 <  2:1029376/139‑1 (MQ=255)                                                                                                 gCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCGGACTACCTCAAAATAAAGCTTTATATACGAATGATTg                              <  1:160961/139‑1 (MQ=255)                                                                                                    aGGAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCGGACTACCTCAAAATAAAGCTTTATATACGAATGATTGttt                           <  2:1030653/139‑1 (MQ=255)                                                                                                      gAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCGGACTACCTCAAAATAAAGCTTTATATACGAATGATTGTTTCa                         <  2:429250/139‑1 (MQ=255)                                                                                                      gAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCGGACTACCTCAAAATAAAGCTTTATATACGAATGATTGTTTCa                         <  1:419964/139‑1 (MQ=255)                                                                                                      gAGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCGGACTACCTCAAAATAAAGCTTTATATACGAATGATTGTTTCa                         <  1:364672/139‑1 (MQ=255)                                                                                                       aGTGCTGACCAAATCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCGGACTACCTCAAAATAAAGCTTTATATACGAATGATTGTTTCAt                        <  2:1083943/139‑1 (MQ=255)                                                                                                                   aTCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCGGAc                                                                <  2:507401/87‑1 (MQ=255)                                                                                                                   aTCGCCGGGCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCGGAc                                                                >  1:507401/1‑87 (MQ=255)                                                                                                                          ggCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCGGACTACCTCAAAATAAAGCTTTATATACGAATGATTGTTTCATACTCCAGGAAGACGGTaaa     <  2:848066/139‑1 (MQ=255)                                                                                                                          ggCCCACATTACCCGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCGGACTACCTCAAAATAAAGCTTTATATACGAATGATTGTTTCATACTCCAGGAAGACGGTaaa     >  2:989699/1‑139 (MQ=255)                                                                                                                             ccACATTACCCGCCCCTGGCGATTACTAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCGGACTACCTCAAAATAAAGCTTTATATACGAATGATTGTTTCATACTCCAGGAAGACGGTAAACCa  <  2:48914/139‑1 (MQ=255)                                                                                                                                       |                                                                                                                                 GAACGTCTTTGCGGCTTAATCCTACTTCTTCAAACAATTCACGGTACATCGCCTGCTCTGCGGATTCTCCGGGGTTGATTCCGCCTTGCGGAAATTGCCAGGAGTGCTGACCAAATCGCCGGGCCCACATTACCTGCCCCTGGCGATTACAAATCACGATACCTACGTTTGGGCGGTAGCCATCGTCATCAATCACCGGACTACCTCAAAATAAAGCTTTATATACGAATGATTGTTTCATACTCCAGGAAGACGGTAAACCA  >  NC_000913/2968782‑2969044

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑