Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	89,089	C→A	intergenic (+57/‑545)	cra → / → mraZ	DNA‑binding transcriptional dual regulator Cra/DNA‑binding transcriptional repressor MraZ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	89,089	0	C	A	94.1%	98.1 / ‑3.1	34	intergenic (+57/‑545)	cra/mraZ	DNA‑binding transcriptional dual regulator Cra/DNA‑binding transcriptional repressor MraZ
Reads supporting (aligned to +/- strand):  ref base C (1/1);  new base A (9/23);  total (10/24)
Fisher's exact test for biased strand distribution p-value = 5.08e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.12e-01

GGCGATAACGAACTGCTCGACTTCTTACAGTGTCCGGTGCTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGGCAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATGCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGTTTTTGCATTATTTTGTTACATGCGGCGATGAATTGCCGATTTAACAAACACTTTTCTTTGCTTTTGCGCAAACCCGCTGGCATCAAGCGCCACACAGACGTAACAAGGACTGTTAA  >  NC_000913/88847‑89331                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                   ggCGATAACGAACTGCTCGACTTCTTACAGTGTCCGGTGCTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGGCAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGAATGGACATc                                                                                                                                                                                                                                            <  1:85006/251‑1 (MQ=255)     aTAACGAACTGCTCGACTTCTTACAGTGTCCGGTGCTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGGCAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGAATGGACATCAata                                                                                                                                                                                                                                        <  1:355827/251‑1 (MQ=255)           aacgtctcgactatgtACAGTTTCCGGTGCTGTCAGTGGCTCAACGGCACCGCGATGTTGCAGAGCGTGTGCTGGAGATGGTCCTGGCAAGCCTGGACGAGCCGCGTATGCCAAACCCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAATCCGCGAACAAAAATACGCGCCACGTGAATCTTCCTCTGGCGCGTAGTGTACGGGAATGGACATCAATATCCTTa                                                                                                                                                                                                                                  <  2:631575/236‑1 (MQ=255)               gCTCTACTGCTTACAGTGTCCGGTGCTGGCAGTGGCTCAACGGCCCCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGGCAAGCCTTGACGAACCGCGTAAGCCAAAACCTGGTGTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGAATGGACATCAATATCCTTaaa                                                                                                                                                                                                                                <  2:148594/249‑1 (MQ=255)                   gACTTCTTACAGTGTCCGGTGCTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGGCAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGAATGGACATCAATATCCTTAAAGTAAAt                                                                                                                                                                                                                          <  1:157/251‑1 (MQ=255)                                                ggCTAAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGGCAAGACTGGACGAACCGCGGAAGCCAAATCCTGGTTTAACGCGCATTAAACGTAAGCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGAATGGACATCAATATCCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATaagt                                                                                                                                                                                             <  2:509823/251‑3 (MQ=255)                                                     aaCGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGGCAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGAATGGACATCAATATCCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATaagttcttt                                                                                                                                                                                        >  1:462260/1‑244 (MQ=255)                                                                       cAGAGCGTGTGCTGGAGATTGTCCTGGCAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGAATGGACATCAATATCCTTAAAGTAAAGAAGACGATTCCTGACTATTATTGATAAGTTCTTTTAAACCCGCCCGttaatt                                                                                                                                                                      <  1:261095/251‑1 (MQ=255)                                                                        agagCGTGAGCTGGAGTTTGTCCTGGCAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGCAGAGTACGGGAATGGACATCAATATCCTTCAAATAAATAAGACTATTCCTGACTATTATTGATAAGTTCTTTTAAACCCGCCCGttattt                                                                                                                                                                      >  2:665496/1‑247 (MQ=255)                                                                                    ggAGATTGTCCTGGCAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGAATGGACATCAATATCCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAGTTCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTg                                                                                                                                                         <  1:207530/251‑1 (MQ=255)                                                                                        atggTCCTGGCAAGCCGTGACGAACCGCGTAAGCCAAAGCATGGTTTAACGCGCATTAAACTTAACCTCTAGCGCCGCGGCGTGCGAAGCCGTAGCTAAGCCGCTAACAAAAATACGAGCCAGGTGAATTTCCCTCTGGCGTGTAGAGTACGTGAATGGACATCAATATCCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAGTACTTTGAAACCCGCCCGTTAAATACCTCACCAGCTGaaag                                                                                                                                                     <  2:277889/248‑2 (MQ=255)                                                                                             ccTGGCAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGAATGGACATCAATATCCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAGTTCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTcac                                                                                                                                                 <  1:89450/250‑1 (MQ=255)                                                                                                ggaaaGCCTGGACGAACCGCGTAATCCAAAACCGGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGGGCGCAGCCGTAGCTAAGCCGCGAACAAAAATACGCTCCAGGTGAATTTCCATCTGGCGCGTAGAGTACGGGAATGGACATCAATATCCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAGTTCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGATATTCACaat                                                                                                                                              <  2:455028/247‑1 (MQ=255)                                                                                                                   cgTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGAATGGACATCAATATCCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAGTTCTTTTAAACCCGCCCGTTAATTAACTCACCAGCAGAAATTCACAATAATTAAGTGATATCGAAAgc                                                                                                                          >  2:682166/1‑251 (MQ=255)                                                                                                                          cAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATGCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGtttt                                                                                                                   >  1:422246/1‑251 (MQ=255)                                                                                                                              atcgggTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGAATGGACATCAATATCCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAGTTCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGTTTTTGCa                                                                                                               <  2:114628/247‑1 (MQ=255)                                                                                                                                  ggTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTATCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGAATGGACATCAATATCCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAGTTCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGTTTTTGCatta                                                                                                            <  2:600578/250‑1 (MQ=255)                                                                                                                                  ggTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGAATGGACATCAATATCCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAGTTCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGTTTTTGCa                                                                                                               >  1:114628/1‑247 (MQ=255)                                                                                                                                   gTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGAATGGACATCAATATCCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAGTTCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGTTTTTGCattatt                                                                                                          <  2:475125/251‑1 (MQ=255)                                                                                                                                     ttAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGAATGGACATCAATATCCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAGTTCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGTTTTTGCATTAttt                                                                                                         <  2:522704/250‑1 (MQ=255)                                                                                                                                                 aaaCGTAATCTCTATCGCCGCGGCGTGCCCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGAATGGACATCAATATCCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAGTTCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGTTTTTGCATTATTTTGTTACATgcaga                                                                                            <  2:129328/251‑4 (MQ=255)                                                                                                                                                                  ccgtggcgTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGAATGGACATCAATATCCTTAAAGTAAATAAGACTATTCCTTACTATTATTGATAAGTTCTTTTAAACCCTCCCGTTAATTAACTCACCAGCTTAAATTCACAATAATTAAGTGATATCGACAGCGCGTTTTTGCATTATTTTGTTACATGCAGAGATGAATTGCCGATTTa                                                                           <  1:388329/247‑1 (MQ=255)                                                                                                                                                                       gcgTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGAATGGACATCAATATCCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAGTTCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGTTTTTGCATTATTTTGTTACATGCAGAGATGAATTGCCGATTTaacaag                                                                      <  1:577591/251‑2 (MQ=255)                                                                                                                                                                             ccAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGTGCGTAGAGTACGGTAATGGACATCAATATCCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAGTTCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGTTTTTGCATTATTTTGTTACATGCAGAGATGAATTGCCGATTTAACAAGCACttt                                                                <  2:107407/250‑1 (MQ=255)                                                                                                                                                                               aGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGAATGGACATCAATATCCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAGTTCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGTTTTTGCATTATTTTGTTACATGCAGAGATGAATTGCCGATTTAACAAGCACTTTTc                                                              >  1:418095/1‑251 (MQ=255)                                                                                                                                                                                   gTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGTATTTCCCGCTGGCGCGTAGAGTACGGGAATGGACATCAATATCCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAGTTCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGTTTTTGCATTATTTTGTTACATGCAGAGATGAATTGCCGATTTAACAAGCACTTTTCTTTg                                                          <  2:376287/251‑1 (MQ=255)                                                                                                                                                                                      gCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGAATGGACATCAATATCCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAGTTCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGTTTTTGCATTATTTTGTTACATGCAGAGATGAATTGCCGATTTAACAAGCACTTTTCTTTGCtt                                                       >  1:299418/1‑251 (MQ=255)                                                                                                                                                                                                       aaTACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGAATGGACATCAATATCCTTAAAGTAAATAAGTCTATTCCTGACTATTATTGATAAGTTCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGTTTTTGCATTATTTTGTTACATGCAGAGATGAATTGCCGATTTAACAAGCACTTTTCTTTGCTTTTGCGCAAACCCGCTgg                                      <  1:373756/251‑1 (MQ=255)                                                                                                                                                                                                          aCGCGCCAGGTGAATTCCCCTCTTGCTCGTAGAGTACGGGAAGTGACATCAATATCCTTAAAGTAAAAAAATCTATTCCTTACTATTATTGATAAGTTCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGTTTTTGCATTATTTTGTTACATGCAGAGATGAATTGCCGATTTAACAAGCACTTTTCTTTGCTTTTGCGCAAACCCGCTGGCAt                                   <  2:138848/251‑1 (MQ=255)                                                                                                                                                                                                                     gAATTTCCCTCTGGCGGGTAGAGTGCGGGAATGGACATCAATATCCTTAAAGTAAATAAGACTATTCCTGACTATTAGTGATAAGTTCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGTTTTTGCATTATTTTGTTACATGCAGAGATGAATTGCCGATTTAACAAGCACTGTTCTTTGCTTTTGCGCAAACCCGCTGGCATCAAGCGCcaca                        <  2:139863/251‑1 (MQ=255)                                                                                                                                                                                                                             ctctGGCGCGTAGAGTACGGGAATGGACCTCCATATCCTTAAAGTAAATAAGACTATTCCTGACTCTTATTAATAAGTTCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGTTTTTGCATTATTTTGTTACATGCAGAGATGAATTGCCGATTTAACAAGCACTTTTCTTTGCTTTTGCGCAAACCCGCTGGCATCACGCGCCACACAGACgc                 >  2:332361/1‑249 (MQ=255)                                                                                                                                                                                                                                      gTAGAGTACGGGAATGGACATCAATATCCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAGTTCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGTTTTTGCATTATTTTGTTACATGCAGAGATGAATTGCCGATTTAACAAGCACTTTTCTTTGCTTTTGCGCAAACCCGCTGGCATCAAGCGCCACACAGACGCAACAGGGACt       >  1:464507/1‑251 (MQ=255)                                                                                                                                                                                                                                          agTACGGGAATGGACATCAATATCCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAGTTCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGTTTTTGCATTATTTTGTTACATGCAGAGATGAATTGCCGATTTAACAAGCACTTTTCTTTGCTTTTGCGCAAACCCGCTGGCATCAAGCGCCACACAGACGCAACAGGGACTGtt    >  1:363228/1‑250 (MQ=255)                                                                                                                                                                                                                                           gTACGGGACGTGACAACAATATGCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATGAAGTGATATCGACAGCGCGTTTTTGCATTATTTTGTTACATGCGGCGATGAATTGCCGATTTAACAAACACTTTTCTTTGCTTTTGCGCAAACCCGCTGGCATCAAGCGCCACACAGACGTAACAAGGACTGTTaa  <  2:422246/251‑1 (MQ=255)                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                   GGCGATAACGAACTGCTCGACTTCTTACAGTGTCCGGTGCTGGCAGTGGCTCAACGTCACCGCGATGTCGCAGAGCGTGTGCTGGAGATTGTCCTGGCAAGCCTGGACGAACCGCGTAAGCCAAAACCTGGTTTAACGCGCATTAAACGTAATCTCTATCGCCGCGGCGTGCTCAGCCGTAGCTAAGCCGCGAACAAAAATACGCGCCAGGTGAATTTCCCTCTGGCGCGTAGAGTACGGGACTGGACATCAATATGCTTAAAGTAAATAAGACTATTCCTGACTATTATTGATAAATGCTTTTAAACCCGCCCGTTAATTAACTCACCAGCTGAAATTCACAATAATTAAGTGATATCGACAGCGCGTTTTTGCATTATTTTGTTACATGCGGCGATGAATTGCCGATTTAACAAACACTTTTCTTTGCTTTTGCGCAAACCCGCTGGCATCAAGCGCCACACAGACGTAACAAGGACTGTTAA  >  NC_000913/88847‑89331

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑