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%	154.4 / NA	37	intergenic (‑377/+14)	uidA/uidR	beta‑D‑glucuronidase/transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (19/18);  total (19/18)

ATAAACTCTCATGACATATGGCTACAGTGAATATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCGAAAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATCGGCCAGTACACCGTAGGTCAGATCCAGCAGTAAA  >  NC_000913/1696323‑1696582                                                                                                                              |                                                                                                                                       aTAAACTCTCATGACATATGGCTACAGTGAATATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCGaaaagaga                                                                                                                                 >  1:853591/1‑129 (MQ=255) aTAAACTCTCATGACATATGGCTACAGTGAATATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCGaaaagaga                                                                                                                                 <  2:853591/133‑5 (MQ=255)       tctcATGACATATGGCTACAGTGAATATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGAt                                                                                                                    <  1:212095/139‑1 (MQ=255)       tctcATGACATATGGCTACAGTGAATATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGAt                                                                                                                    <  2:693868/139‑1 (MQ=255)       tctcATGACATATGGCTACAGTGAATATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGAt                                                                                                                    >  1:990106/1‑139 (MQ=255)         tcATGACATATGGCTACAGTGAATATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGc                                                                                                                  <  2:679813/139‑1 (MQ=255)            tGACATATGGCTACAGTGAATATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGt                                                                                                               <  2:990106/139‑1 (MQ=255)                   tGGCTACAGTGAATATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATa                                                                                                        >  1:616067/1‑139 (MQ=255)                   tGGCTACAGTGAATATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATa                                                                                                        >  1:1014229/1‑139 (MQ=255)                         cAGTGAATATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCa                                                                                                  >  1:364607/1‑139 (MQ=255)                              aaTATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATc                                                                                                                         >  2:808708/1‑111 (MQ=255)                              aaTATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGAt                                                                                                                    >  2:917077/1‑116 (MQ=255)                              aaTATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGAt                                                                                                                    <  1:917077/116‑1 (MQ=255)                              aaTATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTGAAGATACCGCCAatcat                                                                                             <  2:616067/139‑1 (MQ=255)                              aaTATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATGTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATc                                                                                                                         <  1:808708/111‑1 (MQ=255)                                    ttGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATcgcgcg                                                                                       >  1:781436/1‑139 (MQ=255)                                      ggggggAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTa                                                                                     >  2:995894/1‑139 (MQ=255)                                           gAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATccc                                                                                >  1:862760/1‑139 (MQ=255)                                            aaTTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGTAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGt                                                                                      >  2:499834/1‑132 (MQ=255)                                            aaTTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGt                                                                                      <  1:499834/132‑1 (MQ=255)                                                                                agaAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCtt                                           >  2:729437/1‑139 (MQ=255)                                                                                          atatGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATCGGc                                 <  1:995894/139‑1 (MQ=255)                                                                                          atatGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATCGGc                                 <  2:554286/139‑1 (MQ=255)                                                                                          atatGAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTGCCGCTTCGATATCGGc                                 <  2:749210/139‑1 (MQ=255)                                                                                              gAAACGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATCGGCCAGt                             >  2:505055/1‑139 (MQ=255)                                                                                               aaaCGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATCGGCCAGTa                            <  2:161757/139‑1 (MQ=255)                                                                                               aaaCGCGGGCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATCGGCCAGTa                            <  1:405123/139‑1 (MQ=255)                                                                                                     gggCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTc                                                               >  1:820952/1‑98 (MQ=255)                                                                                                     gggCACAGTTATCACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTc                                                               <  2:820952/98‑1 (MQ=255)                                                                                                      ggCACAGTTATCACAAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATCGGCCAGTACACCGTa                     >  1:653082/1‑139 (MQ=255)                                                                                                                 cACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATCGGCCAGTacac                         <  2:724011/124‑1 (MQ=255)                                                                                                                 cACCAGCCCGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATCGGCCAGTacac                         >  1:724011/1‑124 (MQ=255)                                                                                                                       cccGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATc                                    >  2:5912/1‑107 (MQ=255)                                                                                                                       cccGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATc                                    <  1:5912/107‑1 (MQ=255)                                                                                                                       cccGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATCGGCCAGTACACCGTAGGTCAGATCcag         <  2:1060526/134‑1 (MQ=255)                                                                                                                       cccGCCG‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATCGGCCAGTACACCGTAGGTCAGATCcag         >  1:1060526/1‑134 (MQ=255)                                                                                                                         cgccg‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGcc                                                        >  1:485819/1‑85 (MQ=255)                                                                                                                         cgccg‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATCGGCCAGTACACCGTAGGTCAGATCCAGCAGTaaa  >  1:883033/1‑139 (MQ=255)                                                                                                                         cgccg‑AAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGGAATCCCTGAGCAAACGACGCTTCACGCGcc                                                        <  2:485819/85‑1 (MQ=255)                                                                                                                              |                                                                                                                                       ATAAACTCTCATGACATATGGCTACAGTGAATATTTTGGGGGGAATTCTCCGAAGCCGGGAAGGATAATTTTTGCACAGAGAAATTACGATATGAAACGCGGGCACAGTTATCACCAGCCCGCCGAAAAAGAGAGAGAATCAGGATGCGGTTAAGATACCGCCAATCATCGCGCGTAATCCCTGAGCAAACGACGCTTCACGCGCCAGGTCTTCCGCTTCGATATCGGCCAGTACACCGTAGGTCAGATCCAGCAGTAAA  >  NC_000913/1696323‑1696582

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑