Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,696,452	(A)5→4	intergenic (‑381/+10)	uidA ← / ← uidR	beta‑D‑glucuronidase/transcriptional repressor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,696,448	0	A	.	100.0%	235.8 / NA	58	intergenic (‑377/+14)	uidA/uidR	beta‑D‑glucuronidase/transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (32/26);  total (32/26)

GTATTGGGAACGATAAACTCTCATGACATATGGCTACAGTGAATATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCGAAAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATCGGCCAGTACACCGTAGGTCAGATCCAGCAGTAAA  >  NC_000913/1696311‑1696582                                                                                                                                          |                                                                                                                                       gTATTGGGAACGATAAACTCTCATGACATATGGCTACAGTGAATATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCGaa                                                                                                                                       <  1:1442152/139‑1 (MQ=255)         aaCGATAAACTCTCATGACATATGGCTACAGTGAATATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAagagaga                                                                                                                              >  2:308316/1‑139 (MQ=255)            gATAAACTCTCATGACATATGGCTACAGTGAATATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCGaaaa                                                                                                                                     <  2:35755/130‑1 (MQ=255)            gATAAACTCTCATGACATATGGCTACAGTGAATATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCGaaaa                                                                                                                                     >  1:35755/1‑130 (MQ=255)            gATAAACTCTCATGACATATGGCTACAGTGAATATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGaa                                                                                                                           >  2:186980/1‑139 (MQ=255)             aTAAACTCTCATGACATATGGCTACAGTGAATATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAAt                                                                                                                          >  1:755510/1‑139 (MQ=255)                        tGACATATGGCTACAGTGAATATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGAt                                                                                                                    <  1:1212254/134‑1 (MQ=255)                        tGACATATGGCTACAGTGAATATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGAt                                                                                                                    >  2:1212254/1‑134 (MQ=255)                                     cAGTGAATATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAgg                                                                                                                      <  2:1621568/119‑1 (MQ=255)                                     cAGTGAATATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAgg                                                                                                                      >  1:1621568/1‑119 (MQ=255)                                      aGTGAATATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCaa                                                                                                 >  2:574642/1‑139 (MQ=255)                                          aaTATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGAt                                                                                                                    <  2:774351/116‑1 (MQ=255)                                          aaTATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGAt                                                                                                                    >  1:774351/1‑116 (MQ=255)                                          aaTATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGAt                                                                                                                    <  2:485506/116‑1 (MQ=255)                                          aaTATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGAt                                                                                                                    >  1:485506/1‑116 (MQ=255)                                          aaTATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAatcat                                                                                             <  2:1341464/139‑1 (MQ=255)                                          aaTATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTCCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAatcat                                                                                             <  1:574642/139‑1 (MQ=255)                                                 tGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGt                                                                                      <  1:186980/139‑1 (MQ=255)                                                  ggggggAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTa                                                                                     >  2:881896/1‑139 (MQ=255)                                                                  aGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAatcat                                                                                             >  1:977580/1‑115 (MQ=255)                                                                  aGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAatcat                                                                                             <  2:977580/115‑1 (MQ=255)                                                                             aTAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCAcgcg                                                          >  1:406073/1‑139 (MQ=255)                                                                               aaTTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGcc                                                        <  2:406073/139‑1 (MQ=255)                                                                               aaTTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGcc                                                        <  2:1526133/139‑1 (MQ=255)                                                                                           gagaAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCGaaaagaga                                                                                                                                 >  1:1191156/1‑51 (MQ=255)                                                                                           gagaAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCGaaaagaga                                                                                                                                 <  2:1191156/55‑5 (MQ=255)                                                                                            agaAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCGaaaagaga                                                                                                                                 >  1:1312743/1‑50 (MQ=255)                                                                                            agaAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCGaaaagaga                                                                                                                                 <  2:1312743/54‑5 (MQ=255)                                                                                            agaAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAacgacg                                                                   >  1:1587225/1‑115 (MQ=255)                                                                                            agaAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAacgacg                                                                   <  2:1587225/115‑1 (MQ=255)                                                                                                 ttACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCGaaaagag                                                                                                                                  <  1:429528/48‑4 (MQ=255)                                                                                                 ttACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCGaaaagag                                                                                                                                  >  2:429528/1‑45 (MQ=255)                                                                                                 ttACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGata                                      <  2:780983/139‑1 (MQ=255)                                                                                                      atatGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGt                                                                                      <  2:1094917/86‑1 (MQ=255)                                                                                                      atatGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGt                                                                                      >  1:1094917/1‑86 (MQ=255)                                                                                                       tatGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGAt                                                                                                                    >  1:1444816/1‑55 (MQ=255)                                                                                                       tatGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGAt                                                                                                                    <  2:1444816/55‑1 (MQ=255)                                                                                                          gAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGTCAATCATCGCGCGTAATCCCTGAGCAAACGACGCtt                                                                >  2:1012893/1‑104 (MQ=255)                                                                                                          gAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCtt                                                                <  1:1012893/104‑1 (MQ=255)                                                                                                           aaaCGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGa                                                                                                                     <  2:1063342/50‑1 (MQ=255)                                                                                                           aaaCGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGa                                                                                                                     >  1:1063342/1‑50 (MQ=255)                                                                                                               gcgGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGAt                                                                                                                    <  2:509526/47‑1 (MQ=39)                                                                                                               gcgGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGAt                                                                                                                    >  1:509526/1‑47 (MQ=39)                                                                                                               gcgGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGACACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGata                                      >  1:869086/1‑125 (MQ=255)                                                                                                               gcgGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGACACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGata                                      <  2:869086/125‑1 (MQ=255)                                                                                                                  ggCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTc                                                <  1:859165/112‑1 (MQ=255)                                                                                                                  ggCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTc                                                >  2:859165/1‑112 (MQ=255)                                                                                                                       aGTTATCACCAGCCCGCCG‑CAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATCGGCCAGTACACCGTAGGTCa                >  2:1387715/1‑139 (MQ=255)                                                                                                                         ttATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCAc                                                             <  2:1286039/92‑1 (MQ=255)                                                                                                                         ttATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCAc                                                             >  1:1286039/1‑92 (MQ=255)                                                                                                                           aTCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATCGGCCAGTACACCGTAGGTCAGATc            >  1:467832/1‑139 (MQ=255)                                                                                                                               ccAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATCGGCCAGTACACCGTAGGTCAGATCcagc        <  2:951278/139‑1 (MQ=255)                                                                                                                                 aGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATCGGc                                 <  1:1623150/112‑1 (MQ=255)                                                                                                                                 aGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATCGGc                                 >  2:1623150/1‑112 (MQ=255)                                                                                                                                  gCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATCGGc                                 <  2:219871/111‑1 (MQ=255)                                                                                                                                  gCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATCGGc                                 >  1:219871/1‑111 (MQ=255)                                                                                                                                   cccGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATc                                    <  1:964408/107‑1 (MQ=255)                                                                                                                                   cccGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATc                                    >  2:964408/1‑107 (MQ=255)                                                                                                                                   cccGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATCGGCCAGTACACCGTAGGTCAGATCCAGCAGTa    >  1:284347/1‑139 (MQ=255)                                                                                                                                   cccGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATCGGCCAGTACACCGTAGGTCAGATCCAGCAGTa    >  1:1699765/1‑139 (MQ=255)                                                                                                                                   cccGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATCGGCCAGTACACCGTAGGTCAGATCCAGCAGTa    >  1:589240/1‑139 (MQ=255)                                                                                                                                   cccGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATCGGCCAGTACACCGTAGGTCAGATCCAGCAGTa    >  1:103125/1‑139 (MQ=255)                                                                                                                                     cgccg‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGata                                      <  2:1099769/103‑1 (MQ=255)                                                                                                                                     cgccg‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGata                                      >  1:1099769/1‑103 (MQ=255)                                                                                                                                     cgccg‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATc                                    <  2:831184/105‑1 (MQ=255)                                                                                                                                     cgccg‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATc                                    >  1:831184/1‑105 (MQ=255)                                                                                                                                     cgccg‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATCGGCCAGTACACCGTAGGTCAGATCCAGCAGTaaa  >  2:1602298/1‑139 (MQ=255)                                                                                                                                          |                                                                                                                                       GTATTGGGAACGATAAACTCTCATGACATATGGCTACAGTGAATATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCGAAAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATCGGCCAGTACACCGTAGGTCAGATCCAGCAGTAAA  >  NC_000913/1696311‑1696582

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑