Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,518,356	A→G	intergenic (‑121/‑16)	fecI ← / → ykiE	RNA polymerase sigma factor FecI/protein YkiE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,518,356	0	A	G	100.0%	138.8 / NA	36	intergenic (‑121/‑16)	fecI/ykiE	RNA polymerase sigma factor FecI/protein YkiE
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (22/14);  total (22/14)

GCATCAAAAGCAGACTGGAGTTTGCGCGTCAGCCAGCTTTTCAACCAGCCGTGATGTGTGCCATAAAGCGACTCGAACGTTAAGGAAGCTGTGGTAGTGGCGCGGTCAGACATGCGGAGTGCATCAAAAGTTAATTATCACGTAGTCATATTAATATGAGAATGGTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCATGATGTGGTCTGCTATTATTGACATCCTCACTGCCCTAAAGGATGGGGATTTCGGTAATGCTGCCAACTTACTGATTTAGTGTATGATGGTGATTTTAAGGTGCTTGCGTGGCTTCCATTTCCATCAGATGTCCTTCCTGCTCCGCTACTGAAGGCGTGGTGCGTAACGGCAAAAGCACTG  >  NC_000913/4518123‑4518599                                                                                                                                                                                                                                          |                                                                                                                                                                                                                                                    gCATCAAAAGCAGACTGGAGTTTGCGCGTCAGCCAGCTTTTCAACCAGCCGTGATGTGTGCCATAAAGCGACTCGAACGTTAAGGAAGCTGTGGTAGTGGCGCGGTCAGACATGCGGAGTGCATCAAAAGTTAATTATCACGTAGTCATATTAATATGAGAATGGTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGtata                                                                                                                                                                                                                                        <  1:264222/247‑1 (MQ=255) gCATCAAAAGCAGACTGGAGTTTGCGCGTCAGCCAGCTTTTCAACCAGCCGTGATGTGTGCCATAAAGCGACTCGAACGTTAAGGAAGCTGTGGTAGTGGCGCGGTCAGACATGCGGAGTGCATCAAAAGTTAATTATCACGTAGTCATATTAATATGAGAATGGTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAAt                                                                                                                                                                                                                                    <  1:284030/251‑1 (MQ=255)   aTCAAAAGCAGAATGGAGTTTGCGCGTCAGCCAGCTTTTCAACAAGCAGTGATGTGTGCCATAAAGCGACTCGAACGTTAAGGAAGCTGTGGTAGTGGCGCGGTCAGACATGCGGAGTGCATCAAAAGTTAATTATCACGTAGTCATATTAATATGAGAATGGTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATgg                                                                                                                                                                                                                                  >  2:130706/1‑251 (MQ=255)      aaaaGCAGACTGGAGTTTGCGCGTCAGCCAGCTTTTCAACCAGCCGTGATGTGTGCCATAAAGCGACTCGAACGTTAAGGAAGCTGTGGTAGTGGCGCGGTCAGACATGCGGAGTGCATCAAAAGTTAATTATCACGTAGTCATATTAATATGAGAATGGTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGAt                                                                                                                                                                                                                               >  2:185278/1‑251 (MQ=255)           cAGACTGGAGTTTGCGCGCCAGCCAGCTTTTCAACCAGCCGTGATGTGTGCCATAAAGCGACTCGAACGTTAAGGAAGCTGTGGTAGTGGCGCGGTCATACATGCGGAGTGCATCAAAAGTTAATTATCACGTAGTCATATTAATATGAGAATGGTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGc                                                                                                                                                                                                                          <  2:3847/251‑1 (MQ=255)                   aGTTTGCGCGTCAGCCAGCTTTTCAACCAGCCGTGATGTGTGCCATAAAGCGACTCGAACGTTAAGGAAGCTGTGGTAGTGGCGCGGTCAGACATGCGGAGTGCATCAAAAGTTAATTATCACGTAGTCATATTAATATGAGAATGGTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCtt                                                                                                                                                                                                                  <  2:239192/251‑1 (MQ=255)                             tCAGCCAGCTTTTCAACCAGCCGTGATGTGTGCCATAAAGCGACTCGGACGTTAAGGAAGCTGTGGTAGTGGCGCGGTCAGACATGCGGAGTGCATCAAAAGTTAATTATCACGTAGTCATATTAATATGAGAATGGTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCAtgtg                                                                                                                                                                                                        >  1:254665/1‑251 (MQ=255)                                          cAACCAGCCGTGATGTGTGCCATAAAGCGACTCGAACGTTAAGGAAGCTGTGGTAGTGGCGCGGTCAGACATGCGGAGTGCATCAAAAGTTAATTATCACGTAGTCATATTAATATGAGAATGGTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATg                                                                                                                                                                                            <  1:302134/250‑1 (MQ=255)                                            aCCAGCCGTGATGTGTGCCATAAAGCGACTCGAACGTTAAGGAAGCTGTGGTAGTGGCGCGGTCAGACATGCGGAGTGCATCAAAAGTTAATTATCACGTAGTCATATTAATATGAGAATGGTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACt                                                                                                                                                                                         >  2:233983/1‑251 (MQ=255)                                            aCCAGCCGTGATGTGTGCCATAAAGCGACTCGAAAGTTAAGGAAGCTGTGGTAGTGGCGCGGTCAGACATGCGGAGTGCATCAAAAGTTAATTATCACGTAGTCATATTAATATGAGAATGGTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACCTGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACt                                                                                                                                                                                         <  1:354168/251‑1 (MQ=255)                                                     gATGTGTGCCATAAAGCGACTCGAACGTTAAGGAAGCTGTGGTAGTGGCGCGGTCAGACATGCGGAGTGCATCAAAAGTTAATTATCACGTAGTCATATTAATATGAGAATGGTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCATGAtgtg                                                                                                                                                                                <  1:365964/251‑1 (MQ=255)                                                                  aaGCGACTCGAACGATAAGGAAGCTGTGGTAGTGGCGCGGTCAGACATGCGGAGTGCATCAAAAGTTAATTATCACGTAGTCATATTATTATGAGAATGGCTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGCAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCATGATGTGGTCTGCTActca                                                                                                                                                                    >  2:107579‑M1/1‑246 (MQ=255)                                                                                 tAAGGAAGCTGTGGTAGTGGCGCGGTCAGACATGCGGAGTGCATCAAAAGTTAATTATCACGTAGTCATATTAATATGAGAATGGTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCATGATGTGGTCTGCTActcaaggtggaattgtgtc                                                                                                                                                     <  2:119859‑M1/250‑20 (MQ=255)                                                                                 tAAGGAAGCTGTGGTAGTGGCGCGGTCAGACATGCGGAGTGCATCAAAAGTTAATTATCACGTAGTCATATTAATATGAGAATGGTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCGCTGCTTCTGGCATGTGTCGGTCAGAATGACTCATGATGTGGTCTGCTActcaaggtggaattgtgtc                                                                                                                                                     <  2:264077‑M1/250‑20 (MQ=255)                                                                                    ggAAGCTGTGGTAGTGGCGCGGTCAGACATGCGGAGTGCATCAAAAGTTAATTATCACGTAGTCATATTAATATGAGAATGGTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCATGATGTGGTCTGCTActcaaggtggaattgtgtcgcag                                                                                                                                                 <  1:334533‑M1/251‑24 (MQ=255)                                                                                     gAAGCTGTGGTAGTGGCGCGGTCAGACATGCGGAGTGCATCAAAAGTTAATTATCACGTAGTCATATTAATATGAGAATGGTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCATGATGTGGTCTGCTActcaaggtggaattgggtcgcagt                                                                                                                                                >  2:43340‑M1/1‑227 (MQ=255)                                                                                         cTGTGGTAGTGGCGCGGTCAGACATGCGGAGTGCATCAAAAGTTAATTATCACGTAGTCATATTAATATGAGAATGGTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCATGATGTGGTCTGCTActcaaggtggaattgtgtcgcagtatac                                                                                                                                            >  1:379318‑M1/1‑223 (MQ=255)                                                                                           gtgGTAGTGGCGCGGTCAGACATGCGGAGTGCATCAAAAGTTAATTATCACGTAGTCATATTAATATGAGAATGGTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCATGATGTGGTCTGCTActcaaggtggaattgtgtcgcagtatacc                                                                                                                                           <  1:172005‑M1/250‑30 (MQ=255)                                                                                                      gcgGTCAGACATGCGGAGTGCATCAAAAGTTAATTATCACGTAGTCATATTAATATGAGAATGGTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCATGATGTGGTCTGCTActcaaggtggaattgtgtcgcagtataccgccagaaacggg                                                                                                                               <  1:233983‑M1/251‑42 (MQ=255)                                                                                                         gTCAGACATGCGGAGTGCATCAAAAGTTAATTATCACGTAGTCATATTAATATGAGAATGGTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCATGATGTGGTCTGCTActcaaggtggaattgtgtcgcagtataccgccagaaacggggat                                                                                                                            >  1:345094‑M1/1‑207 (MQ=255)                                                                                                                           aTCAAAAGTTAATTATCACGTAGTCATATTAATATGAGAATGGTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCATGATGTGGTCTGCTActcaaggtggaattgtgtcgcagtataccgccagaaacggggattaatactctttacctgtt                                                                                                          <  1:231879‑M1/251‑63 (MQ=255)                                                                                                                                           cACGTAGTCATATTAATATGAGAATGGTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCATGATGTGGTCTGCTActcaaggtggaattgtgtcgcagtataccgccagaaacggggattaatactctttacctgttacccggctacggtagc                                                                                          >  1:146043‑M1/1‑173 (MQ=255)                                                                                                                                           cACGTAGTCATATTAATATGAGAATGGTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCATGATGTGGTCTGCTActcaaggtggaattgtgtcgcagtataccgccagaaacggggattaatactctttacctgttacccggctacggtagc                                                                                          >  1:195179‑M1/1‑173 (MQ=255)                                                                                                                                                   cATATTAATATGAGAATGGTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCATGATGTGGTCTGCTActcaaggtggaattgtgtcgcagtataccgccagaaacggggattaatactctttacctgttacccggctacggtagctatccc                                                                                    >  1:37832‑M1/1‑165 (MQ=255)                                                                                                                                                    atatTAATATGAGAATGGTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCATGATGTGGTCTGCTActcaaggtggaattgtgtcgcagtataccgccagaaacggggattaatactctttacctgttacccggctacggtagctatcccagt                                                                                 <  2:155834‑M1/251‑88 (MQ=255)                                                                                                                                                           tatGAGAATGGTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCATGATGTGGTCTGCTActcaaggtggaattgtgtcgcagtataccgccagaaacggggattaatactctttacctgttacccggctacggtagctatcccagttga                                                                              >  1:150939‑M1/1‑157 (MQ=255)                                                                                                                                                                                aaTTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCATGATGTGGTCTGCTActcaaggtggaattgtgtcgcagtataccgccagaaacggggattaatactctttacctgttacccggctacggtagctatcccagttgaagatcacccacaaactgttaccc                                                       >  1:190992‑M1/1‑136 (MQ=255)                                                                                                                                                                                            aaTTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCATGATGTGGTCTGCTActcaaggtggaattgtgtcgcagtataccgccagaaacggggattaatactctttacctgttacccggctacggtagctatcccagttgaagatcacccacaaactgttacccaggcgcatacggtc                                         >  1:149367‑M1/1‑124 (MQ=255)                                                                                                                                                                                                 tttCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCATGATGTGGTCTGCTActcaaggtggaattgtgtcgcagtataccgccagaaacggggattaatactctttacctgttacccggctacggtagctatcccagttgaagatcacccacaaactgttacccaggcgcatacggtccatc                                     >  2:46214‑M1/1‑119 (MQ=255)                                                                                                                                                                                                     cAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCATGATGTGGTCTGCTActcaaggtggaattgtgtcgcagtataccgccagaaacggggattaatactctttacctgttacccggctacggtagctatcccagttgaagatcacccacaaactgttacccaggcgcatacggtccatcacgcg                                >  2:177331‑M1/1‑115 (MQ=255)                                                                                                                                                                                                          gACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCATGATGTGGTCTGCTActcaaggtggaattgtgtcgcagtataccgccagaaacggggattaatactctttacctgttacccggctacggtagctatcccagttgaagatcacccacaaactgttacccaggcgcatacggtccatcacgcgttcgc                           >  1:88952‑M1/1‑110 (MQ=255)                                                                                                                                                                                                           aCATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCATGATGTGGTCTGCTActcaaggtggaattgtgtcgcagtataccgccagaaacggggattaatactctttacctgttacccggctacggtagctatcccagttgaagatcacccacaaactgttacccaggcgcatacggtccatcacgcgttcgcc                          >  1:194816‑M1/1‑109 (MQ=255)                                                                                                                                                                                                                 ttAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCATGATGTGGTCTGCTActcaaggtggaattgtgtcgcagtataccgccagaaacggggcttaatactctttacctgttacccggctacggtagctatcccagttgaagatcacccacaaactgttacccaggcgcatacggtccatcacgcgttcgcccagca                     >  2:262001‑M1/1‑103 (MQ=255)                                                                                                                                                                                                                             ttttCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGACTGACTCATGATGTGGTCTGCTActcaaggtggaattgtgtcgcagtataccgccagaaacggggattaatactctttacctgttacccggctacggtagctatcccagttgaagatcacccacaaactgttacccaggcgcatacggtccatcacgcgttcgcccagcaacttggtcatctc        >  1:337647‑M1/1‑91 (MQ=255)                                                                                                                                                                                                                                 cTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCATGATGTGGTCTGCTActcaaggtggaattgtgtcgcagtataccgccagaaacggggattaatactctttacctgttacccggctacgggagctatcccagttgaagatcacccacaaactgttacccaggcgcatacggtccatcacgcgttcgcccagcaacttggtcatctcttcc    >  1:61604‑M1/1‑87 (MQ=255)                                                                                                                                                                                                                                   aaGTGTTGTAAGGGAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCATGATGTGGTCTGCTActcaaggtggaattgtgtcgcagtataccgccagaaacggggattaatactctttacctgttaccctgctacggtcgctatccaagttgcagatcacccacaaactgttacccaggcgcttacgttccatcacgcgttctcccagcaacttgttattctcttccat  >  2:140263‑M1/1‑85 (MQ=255)                                                                                                                                                                                                                                          |                                                                                                                                                                                                                                                    GCATCAAAAGCAGACTGGAGTTTGCGCGTCAGCCAGCTTTTCAACCAGCCGTGATGTGTGCCATAAAGCGACTCGAACGTTAAGGAAGCTGTGGTAGTGGCGCGGTCAGACATGCGGAGTGCATCAAAAGTTAATTATCACGTAGTCATATTAATATGAGAATGGTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCATGATGTGGTCTGCTATTATTGACATCCTCACTGCCCTAAAGGATGGGGATTTCGGTAATGCTGCCAACTTACTGATTTAGTGTATGATGGTGATTTTAAGGTGCTTGCGTGGCTTCCATTTCCATCAGATGTCCTTCCTGCTCCGCTACTGAAGGCGTGGTGCGTAACGGCAAAAGCACTG  >  NC_000913/4518123‑4518599

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑