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	97.0%	88.5 / ‑6.0	33	D70A (GAT→GCT)	thiE	thiamine phosphate synthase
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base G (17/15);  total (17/16)
Fisher's exact test for biased strand distribution p-value = 4.85e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.34e-01

ATGCCGTGCCAGCTGTTCCAGCCCCTGCGGTGCAGAAGGCATCTGTTTGGTTTGCGTCGGGAACACATGTCCCAGCGCGATATAAGAGGGGCGTGCTGCCAGCGCGACGTCGATTTCCATATCGTCATGTGTCGAAACGCCCAGCCGCAGGCCTGCCGCGCGGATGGCATTGAGATCGGTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAATCGTTGATAAA‑CAATCGCGCGTT‑ATAGCGGCGGCCCAGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCGATCTTTGATGCGTAGCTGGAGAGTACGTACGCCTGCATCCAACAGACGTTCGATCCACTGTACGCTGTCCACCACCGGGTACAGTCCTGAACGAAAAGGTACAGGAGGAAAATCAGGCTGATACATCACGCTTCCTCCTTACGCAGGTAGATTTCTCCGCCTCTGG  >  NC_000913/4193749‑4194244                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                                           aTGCCGTGCCAGCTGTTCCAGCCCCTGCGGTGCAGAAGGCATCTGTTTGGTTTGCGTCGGGAACACATGTCCCAGCGCGATATAAGAGGGGCGTGCTGCCAGCGCGACGTCGATTTCCATATCGTCATGTGTCGAAACGCCCAGCCGCAGGCCTGCCGCGCGGATGGCATGGATATCGGTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGt                                                                                                                                                                                                                                                         <  1:257458/251‑1 (MQ=255)           aGCTGTTCCAGCCCCTGCGGTGCAGAAGGCATCTGTTTGGTTTGCGTCGGGAACACATGTCCCAGCGCGATATAAGAGGGGCGTGCTGCCAGCGCGACGTCGATTTCCATATCGTCATGTGTCGAAACGCCCAGCCGCAGGCCTGCCGCGCGGATGGCATTGAGATCGGTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAA‑Ca                                                                                                                                                                                                                                               >  2:17388/1‑250 (MQ=255)             cggttcccggcccTGCGGTGCAGAAGGCATCTGTGTGGTTTGCGTCGGGAACACATGTCCCAGCGCGATATAAGAGGGGCGTGCTGCCAGCGGGACGTCGATTTCCATATCGTCATGTGTCGAAACGCCCAGCCGCAGGCCTGCCGCGCGGATGGCATTGAGATCGGTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCGTGATCGCCAGCCGCCAGTAAGCGTTGATAAA‑CAATc                                                                                                                                                                                                                                            <  2:52001/241‑1 (MQ=255)              tGTTCCAGCCCCTGCGGTGCAGAAGGCATCTGTTTGGTTTGCGTCGGGAACACATGTCCCAGCGCGATATAAGAGGGGCGTGCTGCCAGCGCGACGTCGATTTCCATATCGTCATGTGTCGAAACGCCCAGCCGCAGGCCTGCCGCGCGGATGGCATTGAGATCGGTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAA‑CAATcg                                                                                                                                                                                                                                           >  2:242428/1‑251 (MQ=255)                                           cTGTTTGGTTTGCGTCGGGAACACATGTCCCAGCGCGATATAAGAGGGGCGTGCTGCCAGCGCGACGTCGATTTCCATATCGTCATGTGTCGAAACGCCCAGCCGCAGGCCTGCCGCGCGGATGGCATTGAGATCGGTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAA‑CAATCGCGCGTT‑ATAGCGGCGGCCCAGCGCAATTg                                                                                                                                                                                                             >  1:229444/1‑251 (MQ=255)                                             gtttggtttgCGTCGGGAACACATGTCCCAGCGCGATATAAGAGGGGCGTGCTGCCAGCGCGACTTCGATTTCCATATCGTCATGTGTCGAAACGCCCAGCCGCAGGCCGGCCGCGCGGATGGCATTGAGATCGGGGGCTGGCAAATCTGCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAA‑CAATCGCGCGTT‑ATAGCGGCGGCCCAGCGCAATTgcc                                                                                                                                                                                                           <  2:24142/251‑1 (MQ=255)                                                  gtttgCGTCGGGAACACATGTCCCAGCGCGATATAAGAGGGGCGTGCTGCCAGCGCGACGTCGATTTCCATATCGTCATGTGTCGAAACGCCCAGCCGCAGGCCTGCCGCGCGGATGGCATTGAGATCGGTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAC‑CAATCGCGCGTT‑ATAGCGGCGGCCCAGCGCAATTGCCGCCAc                                                                                                                                                                                                      >  1:225583/1‑251 (MQ=255)                                                     tgCGTCGGGAACACATGTCCCAGCGCGATATAAGAGGGGCGTGCTGCCAGCGCGACGTCGATTTCCATATCGTCATGTGTCGAAACGCCCAGCCGCAGGCCTGCCGCGCGGATGGCATTGAGATCGGTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAA‑CACTCGCGCGTT‑ATAGCGGCGGCCCAGCGCAATTGCCGCCACGAc                                                                                                                                                                                                   >  1:141933/1‑251 (MQ=255)                                                        gTCGGGAACACATGTCCCAGCGCGATATAAGAGGGGCGTGCTGGCAGCGCGACGTCGATT‑CCCTTTCGTCAGGCGTAGGACAGCCCAGCCGCAGGCCTGCAGCGCGGATGGGATTGAGATCGGGGGCTTGCAAATCTTCCTGCCCAAAATGGGCGGCATCAGCCCGATGCCTGGTCGCCAGCCGCCGGTAAGCGGTGATAAAACAA‑CCCGCGTT‑ATAGCGGAGGCGCAgcgaaaatagctgccagcgacac                                                                                                                                                                                               >  2:18343/1‑231 (MQ=255)                                                           gggAACACATGCCCCAGGGAGATTTAAGGGGGGGGTGCTGCCAGCGCGACGTCGATTCCCATACCGTCATGGGCCGAAACGCCCAGCCGCAGGCCTGCCGCGCGGAGGGCATTGAGATCGGTGGTTGGCAAATCTTCCTGCCCAAAATGGACGCAATACGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAA‑CAATCGCGCGTT‑ATAGCGGCGGCCCAGCGCAAGTGCCGCCACGACATCGGc                                                                                                                                                                                             <  2:215999/251‑1 (MQ=255)                                                                cacaTGTCCCAGCGCGATATAAGAGGGGCGTGCTGCAAGCGCGACGTCGCTTTCCATATCGTCATGTGTAGAAACGCCCAGCCGCAGGCCTGCCGCGCGGATGGCATTGAGATCGGTGGCTTGCAAATCTTCCTGCCCCACATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAA‑CAATCGCGCGTT‑ATAGCGGCGGCCCAGCGCAAGTgacgcccatacttcggcttccc                                                                                                                                                                                        >  2:220620/1‑235 (MQ=255)                                                                               gATATAAGGGGGGCGGGCGGCCAGCGCGACGTGGATTTCCATATCGTCATGTGTCGAAACGCCCAGCCGCAGGCCGGCCGCGCGGATGGCATTGAGATCGGTGGCTGGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCGGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAA‑CAATCGCGCGTT‑ATAGCGGCGGCCCAGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGcc                                                                                                                                                                         <  2:79649/251‑1 (MQ=255)                                                                                              ggctgcCAGCGCGACTTCGATTTCCATATCGACAGGTGTCGAAACCCCCAGCCCCAGGCCTGCCGCGCGGATGGCATTGAGATCGGTGGCTTGCAAATCTTCCGGCCCCAAATGGACGCCATACGCCTGATGCTTTATCGCCAGCCGCCAGTAAGCGTTGATAAA‑CAATCGCGCGTT‑ATAGCGGCGGCCCAGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCGATCTTTGATGCGTa                                                                                                                                                          <  2:113538/250‑1 (MQ=255)                                                                                                             gTCGATTTCCATATCGTCATGTGTCGAAACGCCCAGCCGCAGGCCTGCCGCGCGGATGGCATTGAGATCGGTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAA‑CAATCGCGCGTT‑ATAGCGGCGGCCCAGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCGATCTTTGATGCGTAGCTGGAGAgtacgt                                                                                                                                            >  1:53531/1‑250 (MQ=255)                                                                                                             gTCGATTTCCATATCGTCAGGTGTCGAACCGCCCAGCCGCAGGCCGGCCGCTCGGATGGCATGGAGATCTGTGGCTTGCAAATCTTCCTCCCCCAAAGGGAGGCCATACGCCGGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAA‑CAATCGCGCGTT‑AGATCGGCGGCCCAGGGCAATGGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCGATCTTTGATGCGTAGCTGGAGAgtacgta                                                                                                                                           <  1:163935/251‑1 (MQ=255)                                                                                                                   ttcaatatCTTCATGTTTCGAAACGCCCAGCCGAAGCCCGGCCGCGCGGATGGCATTGAGACCGGTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGTTTGATCGCCAGCCGCCAGTAAGCGTTGATAAA‑CAATCGCGCGTT‑ATATCGGCGGCCCAGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTGCAGCGCGCCGATCTTTGATGCGTAGCCGGAGAGTACGTACGCCt                                                                                                                                      <  1:73883/246‑1 (MQ=255)                                                                                                                                  tgtCGAAACACCCAGCCGCAGGCCTGCCGCGCGGATGGCATTGAAATCGGTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCACCAGCCGCCAGTAAGCGTTGATAAA‑CAAGCGCGCGTT‑ATAGCGGCGGCCCAGCGCAGTTGCCGCAACGACATCCGCTTACACCTCTTCATCACGCCGATATTTGGTGCGTAGCTCAACAGTACGTACGCCTGCATCCacaagacgat                                                                                                                      >  2:162100/1‑242 (MQ=255)                                                                                                                                                     aGGCCTGCCGCGCGGATGGCATTGAGATCGGTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATACA‑CAATCGCGCGTT‑ATAGCGGCGGCCCAGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCGATCTTTGATGCGTAGCTGGAGAGTACGTACGCCTGCATCCCACAGACGTTCGATCCACTGTACGCTGTc                                                                                                   >  1:47943/1‑251 (MQ=255)                                                                                                                                                                 cgGATGGCATTGAGATCGGTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAA‑CAATCGCGCGTT‑ATAGCGGCGGCCCAGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCGATCTTTGATGCGTAGCTGGAGAGTACGTACGCCTGCATCCAACAGACGTTCGATCCACTGTACGCTGTCCACCACCGGGt                                                                                        >  1:221023/1‑250 (MQ=255)                                                                                                                                                                   gATGGCATTGAGATCGGTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGTTTGATCGCCAGCCGCCAGTAAGCGTTGATAAA‑CAATCGCGCGTT‑ATAGCGGCGGCCCAGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCGATCTTTGATGCGTAGCTGGAGAGTACGTACGCCTGCATCCAACAGACGTTCGATCCACTGTACGCTGTCCACCACCGGGTACa                                                                                     <  1:25519/251‑1 (MQ=255)                                                                                                                                                                         atgaagaTCGGGTGCTTGAAAAGCTTCCTGCCCCAATGGGACGCCATCCGCCTGATGCTTGAGCGCCAGCCGCCAGTAAGCGTTGATAAA‑CAATCGCGCGTT‑ATAGCGGCGGCCCAGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCGATCTTTGATGCGTAGCTGGAGAGTACGTACGCCTGCATCCAACAGACGTTCGATCCACTGTACGCTGTCCACCACCGGGTACAGTCCTg                                                                               <  2:229444/247‑1 (MQ=255)                                                                                                                                                                                 cGGTGGCTTCAAAACCTTCCGCCCCCAAAGGGACGCCATCCGCCTGATTCTTGATCGCCACCCGCCAGTAAGCGTTGATAAA‑CATGCGCGCGTT‑ATAGCGGCGGCCCAGTGCAATTGCCGCCACGACAGCGGCTGCTACCGCTTCATCGCGCCGATCTTTGATGCGTAGCTGGAGAGTACTGACGCCTGCATCCAACATACGTTCGATCCACTGTACGCTGTCCACCATCGGGTACAGTCCTGAGCGaaa                                                                        <  2:263714/250‑1 (MQ=255)                                                                                                                                                                                      gCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAA‑CAATCGCGCGTT‑ATAGCGGCGGCCCAGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCGATCTTTGATGCGTAGCTGGAGAGTACGTACGCCTGCATCCAACAGACGTTCGATCCACTGTACGCTGTCCACCACCGGGTACAGTCCTGAACGAAAAGGTAc                                                                  >  1:252547/1‑251 (MQ=255)                                                                                                                                                                                            aaaTCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAA‑CAATCGCGCGTT‑ATAGCGGCGGCCCAGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCGATCTTTGATGCGTAGCTGGAGAGTACGTACGCCTGCATCCAACAGACGTTCGATCCACTGTACGCTGTCCACCACCGGGTACAGTCCTGAACGAAAAGGTACaggagg                                                            <  1:48152/251‑1 (MQ=255)                                                                                                                                                                                            aaaTCTTCCTGCCCACAATGGCCGCCATACGCCTGCTGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAA‑CAATCGCGCGTT‑CTAGCGGCGGCCCAGCGCCCTTGCCGCCACGACATCCGCTTCCACCTCTTCATCCCGCCGATCTTTGATGCGTAGCTGGAGAGTACGTACGCCTGCATCCAACAGACGTTCGATCCACTGTACGCTGTCCACCACCGGGTACAGTCCTTAACGAAAAGGTAAaggagg                                                            >  2:111328/1‑251 (MQ=255)                                                                                                                                                                                                    cTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAA‑CAATCGCGCGTT‑ATAGCGGCGGCCCAGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCGATCTTTGATGCGTAGCTGGAGAGTACGTACGCCTGCATCCAACAGACGTTCGATCCACTGTACGCTGTCCACCACCGGGTACAGTCCTGAACGAAAAGGTACAGGAGGAAAATc                                                      >  1:107606/1‑249 (MQ=255)                                                                                                                                                                                                                   gCCATACGCCTGCTGCTTGATCGCCAGCCGCCAGTAAGCGTTGATACA‑CAATCGCGCGTT‑ATAGCGGCGGCCCCGCGCAATTGCCGCCCCGACATCGGCTTCCACCTCTTCATCGCGCCGCTCTTTGATGCGTAGCTGGAGAGTACGTACGCCTGCATCCAACAGACGTTCGATCCACTGTACGCTGTCCACCACCGGGTACAGTCCTGAACGAAAAGGTACAGGAGGAAAATCAGGCTGATACATCACGc                                     >  2:251800/1‑251 (MQ=255)                                                                                                                                                                                                                      aTACGCCTGACGCTTGATCGCCAGACGCCAGTAAGCGTTGATAAA‑CAATCGCGCGTT‑ATAGCGGCGGCCCAGCGCAATTGCCGCCACGCCATCGGCTTCCCCCTCTTCATCGCGCCGATCTTTGATGCGTAGCTGGAGAGTACGTAAGCCTGCATCCAACAGACGTTCGATCCACTGTACGCTGTCCAACACCGGGCACCGTCCTGAACGAACAGGAAACGGAGGAAAATCAGGATGATACCTCACGCTtc                                  >  2:174731/1‑251 (MQ=255)                                                                                                                                                                                                                        aCGCCTGATGCTTGATCGCCAGCCGCCAGTAAGCGTTGATAAA‑CAATCGCGCGTT‑ATAGCGGCGGCCCAGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCGATCTTTGATGCGTAGCTGGAGAGTACGTACGCCTGCATCCAACAGACGTTCGATCCACTGTACGCTGTCCACCACCGGGTACAGTCCTGAACGAAAAGGTACAGGAGGAAAATAAGGCTGATACATCACGCTtcct                                >  2:185418/1‑251 (MQ=255)                                                                                                                                                                                                                              gATGCTTGAGCGCCAGCCGCCAGTAAGCGTTGATAAA‑CAACCGCGCGTT‑ATAGCGGCGGCCCAGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCGATCTTTGATGCGTAGCTGGAGAGTACGTACGCCTGCATCCAACAGACGTTCGATCCACTGTACGCTGTCCACCACCGGGTACAGTCCTGAACGAAAAGGTACAGGAGGAAAATCAGGCTGATACATCACGCTTCCTCCTTa                           <  1:71811/250‑1 (MQ=255)                                                                                                                                                                                                                                     gATCGCCAGCCGCCAGTAAGCGGTGATAAA‑CAATCGCGCGT‑‑ATAGCGGCGGCCCAGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCGATCTTTGATGCGTAGCTGGAGAGTACGTACGCCTGCATCCAACAGACGTTCGATCCACTGTACGCTGTCCACCACCGGGTACAGTCCTGAACGAAAAGGTACAGGAGGAAAATCAGGCTGATACATCACGCTTCCTCCTTACGCAGGTa                   <  1:262995/250‑1 (MQ=255)                                                                                                                                                                                                                                                   aGTAAGCGTTGATAAA‑CAATCGCGCGTT‑ATAGCGGCGGCCCAGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCGATCTTTGATGCGTAGCTGGAGAGTACGTACGCCTGCATCCAACAGACGTTCGATCCACTGTACGCTGTCCACCACCGGGTACAGTCCTGAACGAAAAGGTACAGGAGGAAAATCAGGCTGATACATCACGCTTCCTCCTTACGCAGGTAGATTTCTCCGCctc     <  1:242428/251‑1 (MQ=255)                                                                                                                                                                                                                                                      aaTCGTTGATAAA‑CAATCG‑GTGTTTATGGCGGCTGCCCAGCGCATTTGCCGCCCCGTCATCGGCTGCCACCTCTGCATCGCGCCGATCTTTGATGCGTAGCTGGAGAGTACGTACGCCTGCATCCAACAGACGTTCGATCCACTGTACGCTGTCCACCCCCGGGTACAGTCCTGAACGAAAAGGTACAGGAGGAAAATCAGCCTGATCCATCACGCTTCCTCCTTACGCAGGTAAATTTCTCCGCCTCTgg  <  2:54134/251‑1 (MQ=255)                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                                           ATGCCGTGCCAGCTGTTCCAGCCCCTGCGGTGCAGAAGGCATCTGTTTGGTTTGCGTCGGGAACACATGTCCCAGCGCGATATAAGAGGGGCGTGCTGCCAGCGCGACGTCGATTTCCATATCGTCATGTGTCGAAACGCCCAGCCGCAGGCCTGCCGCGCGGATGGCATTGAGATCGGTGGCTTGCAAATCTTCCTGCCCCAAATGGACGCCATACGCCTGATGCTTGATCGCCAGCCGCCAGTAATCGTTGATAAA‑CAATCGCGCGTT‑ATAGCGGCGGCCCAGCGCAATTGCCGCCACGACATCGGCTTCCACCTCTTCATCGCGCCGATCTTTGATGCGTAGCTGGAGAGTACGTACGCCTGCATCCAACAGACGTTCGATCCACTGTACGCTGTCCACCACCGGGTACAGTCCTGAACGAAAAGGTACAGGAGGAAAATCAGGCTGATACATCACGCTTCCTCCTTACGCAGGTAGATTTCTCCGCCTCTGG  >  NC_000913/4193749‑4194244

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑