Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,193,996	T→G	D70A (GAT→GCT)	thiE ←	thiamine phosphate synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,193,996	0	T	G	90.9%	90.5 / ‑1.8	34	D70A (GAT→GCT)	thiE	thiamine phosphate synthase
Reads supporting (aligned to +/- strand):  ref base T (2/1);  new base G (21/9);  total (24/10)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.76e-01

CAGCTGTTCCAGCCCCTGCGGTGCAGAAGGCATCTGTTTGGTTTGCGTCGGGAACACATGTCCCAGCGCGATATAAGAGGGGCGTG‑CTGCCAGCGCGACGTCGATTTCCATATCGTCATGTGTCGAAACGCCCAGCCGCAGGCCTGCCGCGCGGATGGCATTGAGATCGGTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAATCGTTGATAAACAATCGCGCGTTATAGCGGCGGCCC‑AGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCGATCTTTGATGCGTAGCTGGAGAGTACGTACGCCTGCATCCA‑ACAGACGTTCGATCCACTGTACGCTGTCCACCACCGGGTACAGTCCTGAACGAAAAGGTACAGGAGGAAAATCAGGCTGATACATCACGCTTCCTCCTTACGCAGGTAGATTTCTCCGCC  >  NC_000913/4193758‑4194239                                                                                                                                                                                                                                                |                                                                                                                                                                                                                                                      cAGCTGTTCCAGCCCCTGCGGTGCAGAAGGCATCTGTTTGGTTTGCGTCGGGAACACATGTCCCAGCGCGATATAAGAGGGGCGTG‑CTGCCAGCGCGACGTCGATTTCCATATCGTCATGTGTCGAAACGCCCAGCCGCAGGCCTGCCGCGCGGATGGCATTGAGATCGGTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAAc                                                                                                                                                                                                                                            >  1:209798/1‑250 (MQ=255)              cccTGCGGTGCAGAAGGCATCTGTTTGGTTTGCGTCGGGAACACATGTCCCAGCGCGATATAAGAGGGGCGTG‑CTGCCAGCGCGACGTCGATTTCCATATCGTCATGTGTCGAAACGCCCAGCCGCAGGCCTGCCGCGCGGATGGCATTGAGATCGGTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATACACAATCGCGCGatat                                                                                                                                                                                                                               >  1:243543/1‑250 (MQ=255)                cTGCGGTGCAGAAGGCATCTGTTTGGTTGGCGTCGGGAACACATGTCCCAGCGCGATATAAGAGGGGCGTG‑CTGCCAGCGAGACGTCGATTTCCATATCGTCATGGGTCGACAAGCCCAGCCGCAGGCCTGCCGCGCGGATGGCATTGAGATCGGGGGCTTGCAAAACTTCCTGCCCCAAATGGAAGCCATACTCCTGATTCTTAATCGCCAGCCGCCAGTAATCGTTGATacaataacgcgagtttcacg                                                                                                                                                                                                                            >  2:231709/1‑232 (MQ=255)                          gAAGGCATCTGTTTGGTTTGCGTCGGGAACACATGTCCCAGCGCGATATAAGAGGGGCGTG‑CTGCCAGCGCGACGTCGATTTCCATATCGTCATGTGTCGAAACGCCCAGCCGCAGTCCTGCCGCGCGGATGGCATTGAGATCGGTGGCTTGCAAATCTTCCTGCCCCAAATGCACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAACCAATCGCGCGTTATAGCggcggctc                                                                                                                                                                                                                    >  1:26057/1‑247 (MQ=255)                                             gCGTCGGGATCACATGTCCCAGCGCGATATAAGAGGGGC‑TGATTGCCAGCGCGACGTCGTTTTCCATATCGTCATGTGTCGAAACGCCCAGCCGCAGGCCTGCCGCGCGGATGGCATTGAGATCGTTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATCCGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAACAATCGCGCGTTATAGCGGCGGCCC‑AGCGCAATTGCCGCCACGAc                                                                                                                                                                                               <  1:221921/250‑1 (MQ=255)                                                     aaCACATGTCCCAGAGCGATATAAGAGGGGCGTG‑CTGCCAGCGCGACGTCGATTTCCATATCGTCATGTGTCGAAACGCCCAGCCGCCGGCCTGCCGCGCGGATGGCATTGAGATCGGTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAACAATCGCGCGTTTAAGACGCGGCCCCAGC‑CAATTgccgcacccacatcgggctc                                                                                                                                                                                      >  2:24563/1‑236 (MQ=255)                                                         caTGTCCCAGCGCGATATAAGAGGGGCGTG‑CTGCCAGCGCGACGTCGATTTCCATATCGTCATGTGTCGAAACGCCCAGCCGCAGGCCTGCCGCGCGGATGGCATTGAGATCGGTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAACAATCGCGCGTTATAGCGGCGGCCC‑AGCGCAATTGCCGCCACGACATCGGCTTCCAcc                                                                                                                                                                                  >  1:206584/1‑251 (MQ=255)                                                          aTGTCCCAGCGCGATATAAGAGGGGCGTG‑CTGCCAGCGCGACGTCGATTTCCATATCGTCATGTGTCGAAACGCCCAGCCGCAGGCCTGCCGCGCGGATGGCATTGAGATCGGTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAACAATCGCGCGTTATAGCGGCGGCCC‑AGCGCAATTGCCGCCACGACATCGGCTTCCAccc                                                                                                                                                                                 >  1:198736/1‑250 (MQ=255)                                                          aTGTCCCAGCGCGATATAAGAGGGGCGTG‑CTGCCAGCGCGACGTCGATTTCCATATCGTCATGTGTCGAAACGCCCAGCCGCAGGCCTGCCGCGCGGATGGCATTGAGATCGGTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAACAATCGCGCGTTATAGCGGCGGCCC‑AGCGCAATTGCCGCCACGACAACGGCTTCCAccc                                                                                                                                                                                 >  1:153960/1‑250 (MQ=255)                                                            gTCCCAGCGCGATATAAGAGGGGCGTG‑CTGCCAGCGCGACTTCGATTTCCATATCGTCATGTGTCGAAACGCCCAGCCGCAGGCCTGCCGCGCGGATGGCATTGAGATCGGTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAACAATCGCGCGTTATAGCGGCGGCCC‑AGCGCAATTGCCGCCACGACATCGGCTTCCACctct                                                                                                                                                                               <  1:1753/251‑1 (MQ=255)                                                               ccAGCGCGATATAAGAGGGGCGTG‑CTGCCAGCGCGACGTCGATTTCCATATCGTCATGTGTCGAAACGCCCAGCCGCAGGCCTGCCGCGCGGATGGCATTGAGATCGGTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAACAATCGCGCGTTATAGCGGCGGCCC‑AGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTc                                                                                                                                                                             >  1:215145/1‑250 (MQ=255)                                                                        gataAGAGGGGCGTG‑CTGCCAGCGCGACGTCGATTTCCATATCATCATGTGTCGAAACGCCCAGCCGAAGGCATGCCGCGCGGGTGGCATTGTGATCGGAGGCATGCAAATCTACCTGCCCCAAATGGACGCCATCCGCCTGAATCTTGATCACCTGCCGCCATTAAACGTTGATCAACAATCTAGCGTAATAGCGACGGCCC‑AACGCAATTGCCGCCAAGACATCgtgcacccccaccacatctccacc                                                                                                                                                                    >  2:226989/2‑227 (MQ=255)                                                                                  ggcggcctgccagcgggggatCGATTTCATTATCGTCATGTGCCAAACCCCCCAGCCCAAGGCCTCCCGCGCGGATGGCATTGAGATCGGTGGCGGGCAAATCGCCCGTCCCCAAATGGACGCCATACGCCTGATGCTTGACCGCCAGCCGCCAGTAAGCGGTGATAAACAATCGCGCGTTATAGCGGCGGCCC‑AGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCGATCTTTGATg                                                                                                                                                          <  2:62164/231‑1 (MQ=255)                                                                                   cggg‑ctgcCAGCGCGACGTCGATTTCCATATCGTCATGTGTCGAAACGCCCAGCCGCAGGCCTGCCGCGCGGATGGCATTGAGATCGGTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAACAATCGCGCGTTATAGCGGCGGCCC‑AGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCGATCTTTGATGCg                                                                                                                                                        <  1:104664/248‑1 (MQ=255)                                                                                      g‑ctgcCAGCGCGACGTCGATTTCCATACCGTCATGTGTCGAAACGCCCAGCCGCAGGCCTGCCGCGCGGATGGCATTGAGATCGGTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAACAATCGCGCGTTATAGCGGCGGCCC‑AGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCGATCTTTGATGCGTAg                                                                                                                                                     <  1:18532/251‑1 (MQ=255)                                                                                                  gACGTCGATTTCCATATCGTCATGTGTCGAAACGCCCAGCCGCAGGCCTGCCGCGCGGATGGCATTGAGATCGGTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAACAATCGCGCGTTATAGCGGCGGCCC‑AGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCCCCGATCTTTGATGCGTAGCTTGagagaac                                                                                                                                          >  2:260107/1‑248 (MQ=255)                                                                                                          tgtCCATATCGCTATGTGTCGAAACGCCAAGCCGAAGGCCTGCCTCGAGGATGTCATGGGGATCGGTGGCTTGCAATGCTTCCTGCTCCAAATGGCTGCCATCCGCCTGTGGCTTGATCTCCAGCCGCCAGTAAGCGTTGATAAACAATCGCGCGTTATAGCGGCGGCCC‑AGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCTATCTTTGATGCGTAGCTGGAGAGTACGTACGcc                                                                                                                                   <  1:126727/248‑1 (MQ=255)                                                                                                           ttCCATATCGTCATGTGTCGAAACGCCCAGCCGCAGGCCTGCCGCGCGGATGGCATTGAGATCGGTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAACAATCGCGCGTTATAGCGGCGGCCC‑AGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCGATCTTTGATGCGTAGCTGGAGAGTACGTACGCCTg                                                                                                                                 >  1:7794/1‑251 (MQ=255)                                                                                                            cccacatctacagttgacGAACCGCCCGGCCGCATCCCTGCCGCGGGAATGGACTTGGGATCGTTGGCTTGCAAATCTTCCTTCCCCAAAGGGTCGCCATCCGCCTGATGCGTGACCGCCAGCCGCCAGTAAGCGTTGATAAACAATCGCGCGTTATAGCGGCGGCCC‑AGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCTCCGATCTTTGATGCGTAGCTGGGGATTACGTACGCCTGc                                                                                                                                <  2:21858/234‑1 (MQ=255)                                                                                                                                  cGCCCAGCCGCAGGCCTGCCGCGCGGATGGCATTGAGATCGGTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAATCGTTGATAAACAATCGCGCGTTATCGCGGCGGCCC‑AGCGCCATTGCCGCCCCGACATCGGCTTCCACCTCTTCATCCCGCCGACCCTTTATGCGTAGCTGGCGAGTAAGTACGCACGCTTCCA‑ACAGACCTTCGATCCa                                                                                                          >  2:157674/1‑250 (MQ=255)                                                                                                                                           gCAGGCCTGCCGCGCGGATGGCATTGAGATCGGTAGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCACGTAAGCGTTGATAAACAATCGCGCGTTATAGCGGCGGCCC‑AGCGCAATTGACGCCCCGACATCGGCTTCCACCCCTTCATCGCGCCGCTCTTTGATGCGTAGCTGGAGAGTACGTGAGCATGCA‑CCACACAGACGTTcactcaacagtaagctc                                                                                                >  2:284577/1‑235 (MQ=255)                                                                                                                                             aGGCCTGCCGCGCGGATGGCATTGAGATCGGTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAACAATCGCGCGTTATAGCGGCGGCCC‑AGCGCAATTGCCGCCACGACATCGGCTTCCCCCTCTTCATCGCGCCGATCTTTGATGCGTAGCTGGAGAGTACGTACGCCTGCATCCA‑ACAGACGTTCGATCCACTGTACGCTGTc                                                                                              >  1:244516/1‑251 (MQ=255)                                                                                                                                                                       aTCGGTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAACAATCGCGCGTTATAGCGGCGGCCC‑AGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCGATCTTTGATGCGTAGCTGGAGAGTACGTACGCCTGCATCCA‑ACAGACGTTCGATCCACTGTACGCTGTCCACCACCGGGTACAGTCCTGAACGa                                                                     >  1:262626/1‑250 (MQ=255)                                                                                                                                                                                               ccccAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAACAATCGCGCGTTATAGCGGCGGCCC‑AGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCGATCTTTGCTGCGTAGCTGGAGAGTACGTACGCCTGCATCCA‑ACAGACGTTCGATCCACTGTACGCTGTCCACCACCGGGTACAGTCCTGAACGAAAAGGTACAGGCGGAAAATCAAGCt                                            >  1:286560/1‑251 (MQ=255)                                                                                                                                                                                               ccccAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAACAATCGCGCGTTATAGCGGCGGCCC‑AGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCGATCTTTGATGCGTAGCTGGAGAGTACGTACGCCTGCATCCA‑ACAGACGTTCGATCCACTGTACGCTGTCCACCACCGGGAACAGTCCTGAACGAAAAGGTACAGGAGGAAAATCAGGCt                                            >  1:170236/1‑251 (MQ=255)                                                                                                                                                                                                              aTACGCCCAATGCTTGATCGCCAGCCGCCAGTAATCGTTGATAAACAAGCGCGCGTTATAGCGGCGGCCC‑AGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCGATCTTTGATGCGTAGCTGGAGAGTACGTACGCCTGCATCCA‑ACAGACGTTCGATCCACTGTACGCTGTCCACCACCGGGTACAGTCCTGAACGAAAAGGTAGAGGAGGAAAATCAGGCTGATACATCACGCTtc                             <  1:118971/251‑1 (MQ=255)                                                                                                                                                                                                                  cccgtacgcttgcccgcccgccGCCAGTAAGCGTTGATAAACAATCGGGCGTTATAGCGGCTGCCC‑AGCGCAATTGCCTCCACGACATCGGCTTCCACCTCTTCATCGCGCCGATCTCTGATGCGTAGCTGGAGAGTACGTACGCCTGCATCCA‑ACAGACGTTCGATCCACTGTACGCTGTCCACCACCGGGTACAGTCCTGAACGAAAAGGTACAGGAGGAAAATCAGGCTGATGCATCACGCTtcctcc                         <  2:15179/237‑1 (MQ=255)                                                                                                                                                                                                                             gATCGCCAGCCGCCAGTAAGCGTTGATAAACAATCGCGCGTTATAGCGGCGGCCC‑AGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCGATCTTTGATGCGTAGCTGGAGAGTACGAACGCCTGCATCCA‑ACAGACGTTCGATCCACTGTACGCTGTCCCCCACAGGGTACAGTCCTGAACGAAAAGGTACAGGGGGAAAAACAGGCTGATACATCACGCTTCCTCCTTACGCAggg               >  2:147497/1‑249 (MQ=255)                                                                                                                                                                                                                              aTCGCCAGCCGCCAGTAAGCGTTGATAAACAATCGCGCGTTATAGCGGCGGCCC‑AGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCGATCTTTGATGCGTAGCTGGAGAGTACGTACGCCTGCATCCA‑ACAGACGTTCGATCCACTGTACGCTGTCCACCACCGGGTACAGTCCTGAACGAAAAGGTACAGGAGGAAAATCAGGCTGATACATCACGCTTCCTCCTTACGCAggc               >  1:52896/1‑248 (MQ=255)                                                                                                                                                                                                                                cGCCAGCCGCCCGTAAGCGTTGATAAACAATCGCGCGTTATAGCGGCTGCCC‑AGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCGTTCCTTGATGCGTAGCTGGAGAGTACGTTCGCCTGCAACCA‑ACAGACGCTCGATCCCCTGTAAGCTGTCCACCCCCGGGCACAGTCCTTAACGAAAAGGGTCAGGAGGAAAATCAGGCTGCTACATTCCGCCTCCTCCTTACCCAGGt               >  2:133747/1‑247 (MQ=255)                                                                                                                                                                                                                                cGCCAGCCGCCAGTAAGCGTTGATAAACAATCGCGCGTTATAGCGGCGGCCC‑AGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTCCATCGCGCCGATCTTTGATGCGTAGCTGGAGAGTACGTACGCCTGCATCCA‑ACAGACGTTCGATCCACTGTACGCTGTCCACCACCGGGTACAGTCCTGAACGAAAAGGTACAGGAGGAAAATCAGGCTGATACATCACGCTTCCTCCTTACGCAGGt               >  1:233392/1‑247 (MQ=255)                                                                                                                                                                                                                                  ccatctgccAGTAAGCGGTGCTAAACAATCGCTCGTTTGAGCGGCGGCCC‑ATCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCTATCTTTGATGCGTAGCTGGAGATTACGTACGCCTGCATCCA‑ACAGACGTTCGATCCACTGTACGCTGTCCACCACCGGGTACAGTCCTGAACGAAAAGGTACAGGAGGAAAATCAGGCTGATACATCACGCTTCCTCCTTACTCAGGTAGAt           <  2:109314/243‑1 (MQ=255)                                                                                                                                                                                                                                  ccAGCCGCCAGTAAGCGTTGATAAACAATCGCGCGTTATAGCGGCGGCCC‑AGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCGATCTTTGATGCGTAGCTGGAGAGTACGTACGCCTGCATCCA‑ACAGACGTTCGATCCACTGTACGCTGTCCACCACCGGGGACAGTCCTGAACGAAAAGGAACAGGAGGAAAATCAGGCTGATACATCACGCTTCCTCCTTACGCAGGTAGAttt         >  1:285320/1‑251 (MQ=255)                                                                                                                                                                                                                                         ccAGTAAGCGTTGATAAACAATCGCGCGTTATAGCGGCGGCCC‑AGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCGATCTGTGCTGCGTAGCTGGAGAGGACGCACGCCTGCATCCA‑ACAGACGTTCGATCCACTGTACGCTGTCCACCACCGGGTACAGTCCTGAACGAAAAGGGACAGGAGGGCAATCAGGCTGATACATCACGCTTCCTCCTTACGCAGGGAGATTTCTccccc  >  2:217550/1‑248 (MQ=255)                                                                                                                                                                                                                                                |                                                                                                                                                                                                                                                      CAGCTGTTCCAGCCCCTGCGGTGCAGAAGGCATCTGTTTGGTTTGCGTCGGGAACACATGTCCCAGCGCGATATAAGAGGGGCGTG‑CTGCCAGCGCGACGTCGATTTCCATATCGTCATGTGTCGAAACGCCCAGCCGCAGGCCTGCCGCGCGGATGGCATTGAGATCGGTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAATCGTTGATAAACAATCGCGCGTTATAGCGGCGGCCC‑AGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCGATCTTTGATGCGTAGCTGGAGAGTACGTACGCCTGCATCCA‑ACAGACGTTCGATCCACTGTACGCTGTCCACCACCGGGTACAGTCCTGAACGAAAAGGTACAGGAGGAAAATCAGGCTGATACATCACGCTTCCTCCTTACGCAGGTAGATTTCTCCGCC  >  NC_000913/4193758‑4194239

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑