Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,357,202	C→T	intergenic (‑92/+221)	sapA ← / ← ymjA	putative periplasmic binding protein SapA/DUF2543 domain‑containing protein YmjA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,357,202	0	C	T	100.0%	115.7 / NA	35	intergenic (‑92/+221)	sapA/ymjA	putative periplasmic binding protein SapA/DUF2543 domain‑containing protein YmjA
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (20/15);  total (20/15)

GCTTTGGATGGGTTAAAGGTGTTGACTTGCCCGCTGACGCAATAGACAAAACCGCTGTCGCGGATATCAGCATGCGGGGGAGATTCAGGCGCGGCGATTGCCTGACCACTCACAAGTCCAGCAATCACCAAAAGAGACGATAATACCTGGCGCATAATATTAAGGGATTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCCGTGTGGTTGGTCGTTGAACAGGTG‑ACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGCACGCTGCAGTGCGTGTCATTGTTAGCCAGATGCGGCGTGAACGCTTTATCCGGACAACGATACTGACCGATCGTCTGCAATTAAATCAT  >  NC_000913/1356956‑1357423                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                               gCTTTGGATGGGTTAAAGGTGTTGACTTGCCCGCTGACGCAATAGACAAAACCGCTGTCGCGGATATCAGCATGCGGGGGAGATTCAGGCGCGGCGATTGCCTGACCACTCACAAGTCCAGCAATCACCAAAAGAGACGATAATACCTGGCGCATAATATTAAGGGATTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTgtgt                                                                                                                                                                                                                            >  1:438285/1‑251 (MQ=255)           ggTTAAAGGTGTTGACTTGCCCGCTGACGCAATAGACAAAACCGCTGTCGCGGATATCAGCATGCGGGGGAGATTCAGGCGCGGCGATTGCCTGACCACTCACAAGTCCAGCAATCACCAAAAGAGACGATAATACCTGGCGCATAATATTAAGGGATTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGt                                                                                                                                                                                                                  <  1:195817/251‑1 (MQ=255)                       ggACTTGCCCGCTGACGCAATAGACAAAACCGATGTCGCGGATATCAGCATGGTGGGGAGATTCAGGCGCGGCGATTGCCTGACCACTCACAAGTCCAGCAATCACCAAAAGAGACGATAATACCTGGCGCATAATATTAAGGGATTTTATGTAAAGAGGCTATCTGACTAATATTTAATGACATGTGCCATTACCGCTTGTGTTCAGGGGTCGTAATGAGAGCTGTGTTGTTGGTCGtggatctggtgtc                                                                                                                                                                                                      <  2:255086/250‑13 (MQ=255)                               ccGCTGACGCAATAGACAAAACCGCTGTCGCGGCTATCAGCCTGCGGGGGAGATTCAGGCGCGGCGATTGCCTGACCACTCACAAGACCCGCAATCACCAAAAGAGACGCTACTACCTGGCGCATAATATTAAGGGCTTTTATGTAAAGCGGCTATCTTACTAATATTTAATCAAATTTGCCCTTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTG‑ACGTCGCCAt                                                                                                                                                                                             >  2:420677/1‑251 (MQ=255)                                                aaaaCCGCTGTCGCGGATATCAGCATGCGGGGGAGATTCAGGCGCGGCGATTGCCTGACCACTCACAAGTCCAGCAATCACCAACAGAGACGATAATACCTGGCGCATAATATTAAGGGATTTTATGTAAAGCGGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTATGTTCAGGGGTCGTATTGAGGGCTGTGTGGTTGGTCGTTGAACAGGTG‑ACGTCGCCATCTGTTCAACATTCGTAc                                                                                                                                                                            >  2:87660/1‑251 (MQ=255)                                                       cTGTCGCGGATATCAGCATGCGGGGGAGATTCAGGCGCGGCGATTGCCTGACCACTCACAAGTCCAGCAATCACCAAAAGAGACGATAATACCTGGCGCATAATATTAAGGGATTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTG‑ACGTCGCCATCTGTTCAACATTCGTACCCGTGAt                                                                                                                                                                     >  2:290073/1‑251 (MQ=255)                                                                  atCAGCATGCGGGGGAGATTCAGGCGCGGCGATTGCCTGACCACTCACAAGTCCAGCAATCACCAAAAGAGACGATAATACCTGGCGCATAATATTAAGGGATTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATGTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTG‑ACGTCTCCATCTGTTCAACATTCGTACCCGTGATTTCTctataac                                                                                                                                                          <  2:431395/251‑1 (MQ=255)                                                                        atgagtggaggatacAGGCGCGACCATTGCCTGACCCCTCACAAGTCCAGCAAACACCAAAAGAGACAATAATACCTGGCGCATAATATTAAGGGATTTTATAACACAACGCTATCTTACTAATATTTAATGTCATTTGCCATTACCGTTTGGGATCAGGAGTCGTACTGAGGGATGTGTGGTTGGTCGAAGAACAGGAG‑ACGTCGCCATCTGTTCAACATACGTACCCGTGATTTCTctataactatca                                                                                                                                                     >  2:296080/15‑248 (MQ=255)                                                                                  gaTTCAGGCGCGGCGATTGCCTGACCACTCACAAGTCCAGCAATCACCAAAAGAGACGATAATACCTGGCGCATAATCTTAAGGGATTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTG‑ACGTCGCCATCTGTTCAACATTCGTCCCCGTGATTTCTCTATAACTATAACTCACAgcac                                                                                                                                           >  1:249438/1‑247 (MQ=255)                                                                                  gaTTCAGGCGCGGCGATTGCCTGACCACTCACAAGTCCAGCAATCACCAAAAGAGACGATAATACCTGGCGCATAAGATTAAGGGATTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGTGCTGTTTGGTTGGGCGTTGAACAGGTG‑ACGTCGCCATCTGTGCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGaaca                                                                                                                                          <  1:420677/251‑1 (MQ=255)                                                                                             ggcgATTGCCTGACCACTCACAAGTCCAGCAATCACCAAAAGAGACGATAATACCTGGCGCATAATATTAAGGGATTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTG‑ACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCgagg                                                                                                                               >  1:94863/1‑251 (MQ=255)                                                                                                    gCCTGACCACTCACAAGTCCAGCAATCACCAAAAGAGACGATAATACCTGGCGCATAATATTAAGGGATTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTG‑ACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCaga                                                                                                                         <  1:72975/250‑1 (MQ=255)                                                                                                           cACTCACAAGTCCAGCAATCACCAAAAGAGACGATAATACCTGGCGCATAATATTAAGGGATTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTG‑ACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACg                                                                                                                 >  1:379221/1‑251 (MQ=255)                                                                                                                  aaGTCCAGCAATCAACAAAAGAGACGATAATACCTGGCGCATAATATTAAGGGATTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTG‑ACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACGAGCGTga                                                                                                          <  2:213818/251‑1 (MQ=255)                                                                                                                                               ataCCTGGCGCATAATATTAAGGGATTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATTTGCCATTCCCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTG‑ACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGCACGCTGCAGTGCgt                                                                             >  1:56583/1‑251 (MQ=255)                                                                                                                                                taCCTGGCGCATAATATTAAGGGATTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTG‑ACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGCACGCTGCAGTGCgtg                                                                            >  1:221221/1‑251 (MQ=255)                                                                                                                                                           taataTTAAGGGATTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTGCAC‑TCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGCACGCTGCAGTGCGTGTCATTGTTAGc                                                                 >  1:395367/1‑251 (MQ=255)                                                                                                                                                            aataTTAAGGGATTGTATGTAAAGAGGCTATCTTACTAATATTTAATGACAGTTGCCATTACCTTTTGTGTTCAGGGGGCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTG‑ACGTCGCCATCTGTTCAACATTCGTACCCGTGATGTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGTTACGAGCGTGAGAAACCCATTAAATCACGCTGCAGTGCGTGTCATTGTTAGcc                                                                <  2:251518/251‑1 (MQ=255)                                                                                                                                                                     ggATTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTG‑ACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGCACGCTGCAGTGCGTGTCATTGTTAGCCAGATgcggc                                                       >  2:209002/1‑251 (MQ=255)                                                                                                                                                                       aTTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATTTTCCATTACCGTTTGTGTTCAGGGGTCGTAATCAGGGCTGTGTGGTTGGTCGTTGCACAGGTG‑ACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGCACGCTGCAGTGCGTGTCATTGTTAGCCAGATgcggcgg                                                     >  1:420819/1‑250 (MQ=255)                                                                                                                                                                                    agGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTG‑ACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGCACGCTGCAGTGCGTGTCATTGTTAGCCAGATGCGGCGTGAACGCTTTATcc                                        >  1:288130/1‑251 (MQ=255)                                                                                                                                                                                        tATCTTACCAATCTTTAATGCCATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTG‑ACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGCACGCTGCAGTGCGTGTCATTGTTAGCCAGATGCGGCGCGAACGCTTTATCCGGAc                                    >  2:154330/1‑251 (MQ=255)                                                                                                                                                                                             ttcTAAGATTTAATGTCAGTTGCCATGCCCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTTTGGTTGGTCGTTGAACAGGTG‑ACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGCACGCTGCAGTGCGTGTCATTGTTAGCCAGATGCGGCGTGAACGCTTTAGCCGGACAAc                                 <  2:15342/247‑1 (MQ=255)                                                                                                                                                                                              aCTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTG‑ACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCgag                                                                                                                                >  2:227889/1‑153 (MQ=255)                                                                                                                                                                                              aCTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTG‑ACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCgag                                                                                                                                <  1:227889/153‑1 (MQ=255)                                                                                                                                                                                              aCTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTG‑ACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGCACGCTGCAGTGCGTGTCATTGTTAGCCAGATGCGGCGTGAACGCTTTATCCGGACAACGAt                              <  2:56583/251‑1 (MQ=255)                                                                                                                                                                                               cTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTG‑CCGTCGCCCTCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGCACGCTGCAGTGCGTGTCATTGTTAGCCAGATGCGGCGTGAACGCTTTATCCGGACAACGAt                              >  1:432412/1‑250 (MQ=255)                                                                                                                                                                                                  atatTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTG‑ACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGCACGCTGCAGTGCGTGTCATTGTTAGCCAGATGCGGCGTGAACGCTTTATCCGGACAACGATACTg                          <  2:94863/251‑1 (MQ=255)                                                                                                                                                                                                      ttAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTG‑ACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGCACGCTGCAGTGCGTGTCATTGTTAGCCAGATGCGGCGTGAACGCTTTATCCGGACAACGAGACTGAcc                       <  2:432412/250‑1 (MQ=255)                                                                                                                                                                                                                 tGCCATTACCGCTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGCACAGGTG‑ACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGCACAACTTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGCACGCTGCAGTGCGTGTCATTGTTAGCCAGATGCGGCGTGAACGCTTTATCCGGACAACGATACTGACCGATCGTCTGCa            >  2:429395/1‑250 (MQ=255)                                                                                                                                                                                                                     aTTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTG‑ACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGCACGCTGCAGTGCGTGTCATTGTTAGCCAGATGCGGCGTGAACGCTTTATCCGGACAACGATACTGACCGATCGTCTGCAATTa        >  2:293777/1‑250 (MQ=255)                                                                                                                                                                                                                       tACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTG‑ACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGCACGCTGCAGTGCTTGTCATTGTTAGCCAGATGCGGCGTGAACGCTTTATCCGGACAACGATACTGGCCGATCGTCTGCAATTaaa      <  2:438285/250‑1 (MQ=255)                                                                                                                                                                                                                          cGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTG‑ACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGCACGCTGCAGTGCGTGTCATTGTTAGCCAGATGCGGCGTGAACGCTTTATCCGGACAACGATACTGACCGATCGTCTGCAATTAAAtcat  <  1:171735/251‑1 (MQ=255)                                                                                                                                                                                                                              tgtgTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTG‑ACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGaac                                                                                                                                           <  2:325216/110‑1 (MQ=255)                                                                                                                                                                                                                              tgtgTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTG‑ACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGaac                                                                                                                                           >  1:325216/1‑110 (MQ=255)                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                               GCTTTGGATGGGTTAAAGGTGTTGACTTGCCCGCTGACGCAATAGACAAAACCGCTGTCGCGGATATCAGCATGCGGGGGAGATTCAGGCGCGGCGATTGCCTGACCACTCACAAGTCCAGCAATCACCAAAAGAGACGATAATACCTGGCGCATAATATTAAGGGATTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCCGTGTGGTTGGTCGTTGAACAGGTG‑ACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGCACGCTGCAGTGCGTGTCATTGTTAGCCAGATGCGGCGTGAACGCTTTATCCGGACAACGATACTGACCGATCGTCTGCAATTAAATCAT  >  NC_000913/1356956‑1357423

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑