Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,400,615	(T)7→8	intergenic (+19/‑57)	hfq → / → hflX	global sRNA chaperone, HF‑I, host factor for RNA phage Q beta replication/GTPase, stimulated by 50S subunit binding, Mn(2+) homeostasis regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,400,608	1	.	T	100.0%	152.6 / NA	49	intergenic (+12/‑64)	hfq/hflX	global sRNA chaperone, HF‑I, host factor for RNA phage Q beta replication/GTPase, stimulated by 50S subunit binding, Mn(2+) homeostasis regulator
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base T (24/25);  total (24/25)

GTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTG‑TTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCGGTACTGGTACACATCTATTTTACGCAAGA  >  NC_000913/4400471‑4400733                                                                                                                                           |                                                                                                                              gttgtCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTG‑t                                                                                                                              <  2:346397/139‑1 (MQ=255)                  ggTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGATTCGGGCTGTTTTTTTTACACGGGGAg                                                                                                              >  1:818079/1‑139 (MQ=255)                   gTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGc                                                                                                             <  2:9261/139‑1 (MQ=255)                                  aacaacGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGtt                                                                                              <  1:697794/139‑1 (MQ=255)                                     aacGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTccc                                                                                           <  2:818079/139‑1 (MQ=255)                                       cGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCg                                                                                         <  2:785831/139‑1 (MQ=255)                                       cGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCg                                                                                         <  2:277678/139‑1 (MQ=255)                                       cGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCg                                                                                         <  1:59437/139‑1 (MQ=255)                                         ccGGTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCt                                                                                       >  2:111204/1‑139 (MQ=255)                                         ccGGTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCt                                                                                       >  1:800336/1‑139 (MQ=255)                                                  gTACCAGCAGTAACTACCATCATGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTAttt                                                                              >  2:331869/1‑139 (MQ=255)                                                       agcagTAACTACCATCATGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAgg                                                                         >  1:706716/1‑139 (MQ=255)                                                                   catcatGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTg                                                             >  1:87793/1‑139 (MQ=255)                                                                      catGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACggg                                                                                                                 <  2:457904/84‑1 (MQ=255)                                                                      catGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACggg                                                                                                                 >  1:457904/1‑84 (MQ=255)                                                                       atGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTg                                                         >  1:226608/1‑139 (MQ=255)                                                                            agcagcGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGttt                                                          >  2:825212/1‑133 (MQ=255)                                                                            agcagcGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGttt                                                          <  1:825212/133‑1 (MQ=255)                                                                            agcagcGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAACAAGGGTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGt                                                    >  2:195026/1‑139 (MQ=255)                                                                             gcagcGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTaga                                                                           <  1:317117/115‑1 (MQ=255)                                                                             gcagcGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTaga                                                                           >  2:317117/1‑115 (MQ=255)                                                                             gcagcGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGtt                                                   >  2:152325/1‑139 (MQ=255)                                                                                gcgcgcAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTatg                                                >  2:524601/1‑139 (MQ=255)                                                                                 cgcgcAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTag                                                                            <  1:202263/110‑1 (MQ=255)                                                                                 cgcgcAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTag                                                                            >  2:202263/1‑110 (MQ=255)                                                                                 cgcgcAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTatga                                               >  1:151067/1‑139 (MQ=255)                                                                                   cgcAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTatgatg                                             <  2:800336/139‑1 (MQ=255)                                                                                           aCTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAg                                     <  2:442339/139‑1 (MQ=255)                                                                                           aCTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAg                                     <  2:706716/139‑1 (MQ=255)                                                                                             ttCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCa                                   >  1:378107/1‑139 (MQ=255)                                                                                               ccGCGCAACAGGACGGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAgg                                 <  2:379441/139‑1 (MQ=255)                                                                                               ccGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAgg                                 <  2:340123/139‑1 (MQ=255)                                                                                               ccGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAgg                                 <  2:226608/139‑1 (MQ=255)                                                                                                cgcgCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGc                                <  1:331869/139‑1 (MQ=255)                                                                                                  cgcAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTaga                                                                           <  2:404434/94‑1 (MQ=255)                                                                                                  cgcAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTaga                                                                           >  1:404434/1‑94 (MQ=255)                                                                                                  cgcAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCgg                              >  1:351687/1‑139 (MQ=255)                                                                                                  cgcAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCgg                              >  2:157367/1‑139 (MQ=255)                                                                                                     aaCAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCGGTAc                           <  2:351687/139‑1 (MQ=255)                                                                                                          gACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACg                                                                 >  2:349662/1‑96 (MQ=255)                                                                                                          gACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACg                                                                 <  1:349662/96‑1 (MQ=255)                                                                                                               cGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATAc                                                                  <  2:396344/90‑1 (MQ=255)                                                                                                               cGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATAc                                                                  >  1:396344/1‑90 (MQ=255)                                                                                                                    aaaCCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCg                                                                                         <  1:13842/62‑1 (MQ=255)                                                                                                                    aaaCCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCg                                                                                         >  2:13842/1‑62 (MQ=255)                                                                                                                         gAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCGGTACTGGTACACATCTATTTTACg       <  2:378107/139‑1 (MQ=255)                                                                                                                         gAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCGGTACTGGTACACATCTATTTTACg       <  1:524601/139‑1 (MQ=255)                                                                                                                              aGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATc                                                                                   >  2:392252/1‑58 (MQ=255)                                                                                                                              aGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATc                                                                                   <  1:392252/58‑1 (MQ=255)                                                                                                                              aGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCGGTACTGGTACACATCTATTTTACGCAAGa  >  2:350907/1‑139 (MQ=255)                                                                                                                                           |                                                                                                                              GTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTG‑TTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCGGTACTGGTACACATCTATTTTACGCAAGA  >  NC_000913/4400471‑4400733

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑