Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	461,242	G→A	*785* (TAG→TAA)	lon →	DNA‑binding ATP‑dependent protease La

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	461,242	0	G	A	98.5%	206.1 / ‑3.3	65	*785* (TAG→TAA)	lon	DNA‑binding ATP‑dependent protease La
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (31/33);  minor base C (0/1);  total (31/34)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01

GAGATTCCTGACAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAGTGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGCC‑TTTTTTTGTCTCGCTAAGTTAGATGGCGGATCGGGCTTGCCCTTATTAAGGGGTGTTGTAAGGGGATGG  >  NC_000913/461123‑461373                                                                                                                        |                                                                                                                                     gagaTTCCTGACAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCa                                                                                                                   <  2:219878/139‑1 (MQ=255)  agaTTCCTGACAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCAc                                                                                                                  <  1:477041/139‑1 (MQ=255)    aTTCCTGACAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCa                                                                                                                   <  1:591549/136‑1 (MQ=255)    aTTCCTGACAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCa                                                                                                                   >  2:591549/1‑136 (MQ=255)    aTTCCTGACAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACta                                                                                                                >  1:1054536/1‑139 (MQ=255)    aTTCCTGACAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGATATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACta                                                                                                                >  1:855018/1‑139 (MQ=255)      tCCTGACAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACtaat                                                                                                              >  2:542492/1‑139 (MQ=255)      tCCTGACAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCACTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACtaat                                                                                                              <  1:854966/139‑1 (MQ=255)           aCAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATaaaaa                                                                                                         >  1:1342661/1‑139 (MQ=255)                         gATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGc                                                                                           >  1:618329/1‑139 (MQ=255)                          aTCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATaaaaa                                                                                                         >  1:1309834/1‑124 (MQ=255)                          aTCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATaaaaa                                                                                                         <  2:1309834/124‑1 (MQ=255)                          aTCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCt                                                                                          >  1:1097010/1‑139 (MQ=255)                              ggACATTCATCCTGTGAAGCGCATTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAAtt                                                                                      >  1:919619/1‑139 (MQ=255)                                  aTTCATCCTGTGAAGCGCATTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCggg                                                                                  <  2:618329/139‑1 (MQ=255)                                    tCATCCTGTGAAGCGCATTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCa                                                                                                                   <  1:1149979/104‑1 (MQ=255)                                    tCATCCTGTGAAGCGCATTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCa                                                                                                                   >  2:1149979/1‑104 (MQ=255)                                      aTCCTGTGAAGCGCATTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTgg                                                                                                >  2:649123/1‑121 (MQ=255)                                      aTCCTGTGAAGCGCATTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTgg                                                                                                <  1:649123/121‑1 (MQ=255)                                       tCCTGTGAAGCGCATTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGc                                                                             >  1:476483/1‑139 (MQ=255)                                            tgAAGCGCATTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTgg                                                                                                >  1:1071525/1‑115 (MQ=255)                                            tgAAGCGCATTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTgg                                                                                                <  2:1071525/115‑1 (MQ=255)                                            tgAAGCGCATTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGcc                                                                        >  1:648899/1‑139 (MQ=255)                                            tgAAGCGCATTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGcc                                                                        <  2:1097010/139‑1 (MQ=255)                                              aaGCGCATTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCa                                                                                                                   >  1:1034883/1‑94 (MQ=255)                                              aaGCGCATTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCa                                                                                                                   <  2:1034883/94‑1 (MQ=255)                                                 cgcATTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATaaaa                                                                                                          >  1:780997/1‑100 (MQ=255)                                                 cgcATTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATaaaa                                                                                                          <  2:780997/100‑1 (MQ=255)                                                     ttGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCGAATTCGGGCTTGCCAGCC‑TTTTTTTGt                                                              <  2:855018/139‑1 (MQ=255)                                                      tGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGAGTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCTGCC‑TTTTTTTAtc                                                             >  2:945420/1‑139 (MQ=255)                                                      tGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGCC‑TTTTTTTGtc                                                             >  1:1100990/1‑139 (MQ=255)                                                             gTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGCC‑TTTTTTTGt                                                              <  1:742653/131‑1 (MQ=255)                                                             gTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGCC‑TTTTTTTGt                                                              >  2:742653/1‑131 (MQ=255)                                                             gTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGCC‑TTTTTTTGTCTCGCTaa                                                      >  2:1420769/1‑139 (MQ=255)                                                                cTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGCCTTTTTTTTGTCTCGCTAAGt                                                    <  2:1342661/139‑1 (MQ=255)                                                                cTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGCC‑TTTTTTTGTCTCGCTAAGtt                                                   <  1:143490/139‑1 (MQ=255)                                                                  gACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGCC‑TTTTTTTGTCTCGCTAAGTTAg                                                 >  2:96585/1‑139 (MQ=255)                                                                    ctctGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGCC‑TTTTTTTGTCTCGCTAAGTTAGAt                                               <  1:96585/139‑1 (MQ=255)                                                                        ggCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTgg                                                                                                <  2:1326493/87‑1 (MQ=255)                                                                        ggCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTgg                                                                                                >  1:1326493/1‑87 (MQ=255)                                                                        ggCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGCC‑TTTTTTTGTCTCGCTAAGTTAGATGGCg                                           >  1:182000/1‑139 (MQ=255)                                                                          cgcTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGCC‑TTTTTTTGTCTCGCTAAGTTAGATGGCGGa                                         <  1:1420769/139‑1 (MQ=255)                                                                           gcTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATACTGACCTCGCGCAAAATGGACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGCC‑TTTTTTTGTCTCGCTAAGTTAGATGGCAGAt                                        <  2:919619/139‑1 (MQ=255)                                                                           gcTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGCC‑TTTTTTTGTCTCGCTAAGTTAGATGGCGGAt                                        <  2:1100990/139‑1 (MQ=255)                                                                           gcTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGCC‑TTTTTTTGTCTCGCTAAGTTAGATGGCGGAt                                        <  2:648899/139‑1 (MQ=255)                                                                           gcTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGACAGCC‑TTTTTTTGTCTCGCTAAGTTAGATGGCGGAt                                        <  2:182000/139‑1 (MQ=255)                                                                                           tCTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGCC‑TTTTTTTGTCTCGCTAAGTTAGATGGCGGATCGGGCTTGCCCttatt                        >  2:557975/1‑139 (MQ=255)                                                                                            cTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGCC‑TTTTTTTGTCTCGCTAAGTTAGATGGCGGATCGGGCTTGc                               <  2:114042/131‑1 (MQ=255)                                                                                            cTGGTATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGCC‑TTTTTTTGTCTCGCTAAGTTAGATGGCGGATCGGGCTTGc                               >  1:114042/1‑131 (MQ=255)                                                                                                tATGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGCC‑TTTTTTTGTCTCGCTAAGTTAGATGGCGGATCGGGCTTGCCCTTATTAAggg                   <  2:185660/139‑1 (MQ=255)                                                                                                 aTGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGCC‑TTTTTTTGTCTCGCTAAGTTAGATGGCGGATCGGGCTTGCCCTTATTAAgggg                  <  2:476483/139‑1 (MQ=255)                                                                                                  tGCAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGCC‑TTTTTTTGTCTCGCTAAGTTAGATGGCGGATCGGGCTTGCCCTTATTAAGGGgt                 <  1:945420/139‑1 (MQ=255)                                                                                                    cAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTgg                                                                                                >  1:1190342/1‑59 (MQ=255)                                                                                                    cAGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTgg                                                                                                <  2:1190342/59‑1 (MQ=255)                                                                                                     aGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAggg                                                                                                    <  1:905457/54‑1 (MQ=255)                                                                                                     aGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAggg                                                                                                    >  2:905457/1‑54 (MQ=255)                                                                                                     aGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGc                                                                             >  2:1103491/1‑77 (MQ=255)                                                                                                     aGGTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGc                                                                             <  1:1103491/77‑1 (MQ=255)                                                                                                      ggTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAg                                                                                             >  1:682939/1‑60 (MQ=255)                                                                                                      ggTTGTGACTGCAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAg                                                                                             <  2:682939/60‑1 (MQ=255)                                                                                                         tgtgACTGCAAAATAATGACCTCGCGCAAAATGCa                                                                                                                   >  1:81020/1‑35 (MQ=255)                                                                                                         tgtgACTGCAAAATAATGACCTCGCGCAAAATGCa                                                                                                                   <  2:81020/35‑1 (MQ=255)                                                                                                                 cAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAg                                                                          >  2:463999/1‑68 (MQ=255)                                                                                                                 cAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAg                                                                          <  1:463999/68‑1 (MQ=255)                                                                                                                 cAAAATAATGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGCC‑TTTTTTTGTCTCGCTAAGTTAGATGGCGGATCGGGCTTGCCCTTATTAAGGGGTGTTGTAAGGGGAtgg  <  1:1065142/139‑1 (MQ=255)                                                                                                                        |                                                                                                                                     GAGATTCCTGACAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAGTGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGCC‑TTTTTTTGTCTCGCTAAGTTAGATGGCGGATCGGGCTTGCCCTTATTAAGGGGTGTTGTAAGGGGATGG  >  NC_000913/461123‑461373

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑