Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	964,139	A→G	intergenic (+27/‑181)	ihfB → / → ycaI	integration host factor subunit beta/conserved inner membrane protein YcaI

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	964,139	0	A	G	100.0%	139.6 / NA	38	intergenic (+27/‑181)	ihfB/ycaI	integration host factor subunit beta/conserved inner membrane protein YcaI
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (19/19);  total (19/19)

CGTACCGGACGTAATCCGAAGACTGGCGATAAAGTAGAACTGGAAGGAAAATACGTTCCTCACTTTAAACCTGGTAAAGAACTGCGCGATCGCGCCAATATTTACGGTTAAGTTTTTTACTCAAACTTGAACGAGAGAAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAATCTGGAACTGGAAGCTGCCTCGCAGAGTTTTGAACAGTTTTCACCCTTTCGTTAAATTCTTCTGAATATGCCTCGGGGAACGCAAAATTCCCACCA  >  NC_000913/964002‑964270                                                                                                                                          |                                                                                                                                    cGTACCGGACGTAATCCGAAGACTGGCGATAAAGTAGAACTGGAAGGAAAATACGTTCCTCACTTTAAACCTGGTAAAGAACTGCGCGATCGCGCCAATATTTACGGTTAAGTTTTTTACTCAAACTTGAACGAGAGgaa                                                                                                                                   >  1:767602/1‑140 (MQ=255)   tACCGGACGTAATCCGAAGACTGGCGATAAAGTAGAACTGGAAGGAAAATACGTTCCTCACTTTAAACCTGGTAAAGAACTGCGCGATCGCGCCAATATTTACGGTTAAGTTTTTTACTCAAACTTGAACGAGAGGAAAg                                                                                                                                 <  1:48594/140‑1 (MQ=255)        gACGTAATCCGAAGACTGGCGATAAAGTAGAACTGGAAGGAAAATACGTTCCTCACTTTAAACCTGGTAAAGAACTGCGCGATCGCGCCAATATTTACGGTTAAGTTTTTTACTCAAACTTGAACGAGAGGAAAGCACCt                                                                                                                            <  2:919116/140‑1 (MQ=255)         aCGTAATCCGAAGACTGGCGATAAAGTAGAACTGGAAGGAAAATACGTTCCTCACTTTAAACCTGGTAAAGAACTGCGCGATCGCGCCAATATTTACGGTTAAGTTTTTTACTCAAACTTGAACGAGAGGAAAGCACCTg                                                                                                                           >  1:703368/1‑140 (MQ=255)             aaTCCGAAGACTGGCGATAAAGTAGAACTGGAAGGAAAATACGTTCCTCACTTTAAACCTGGTAAAGAACTGCGCGATCGCGCCAATATTTACGGTTAAGTTTTTTACTCAAACTTGAACGAGAGGAAAGCAcc                                                                                                                             <  2:469230/134‑1 (MQ=255)             aaTCCGAAGACTGGCGATAAAGTAGAACTGGAAGGAAAATACGTTCCTCACTTTAAACCTGGTAAAGAACTGCGCGATCGCGCCAATATTTACGGTTAAGTTTTTTACTCAAACTTGAACGAGAGGAAAGCAcc                                                                                                                             >  1:469230/1‑134 (MQ=255)               tCCGAAGACTGGCGATAAAGTAGAACTGGAAGGAAAATACGTTCCTCACTTTAAACCTGGTAAAGAACTGCGCGATCGCGCCAATATTTACGGTTAAGTTTTTTACTCAAACTTGAACGAGAGGAAAGCACCTGTCGGGt                                                                                                                     >  2:97189/1‑140 (MQ=255)                   aaGACTGGCGATAAAGTAGAACTGGAAGGAAAATACGTTCCTCACTTTAAACCTGGTAAAGAACTGCGCGATCGCGCCAATATTTACGGTTAAGTTTTTTACTCAAACTTGAACGAGAGGAAAGCACCTGTCGGGTGCtt                                                                                                                 >  2:10934/1‑140 (MQ=255)                        tGGCGATAAAGTAGAACTGGAAGGAAAATACGTTCCTCACTTTAAACCTGGTAAAGAACTGCGCGATCGCGCCAATATTTACGGTTAAGTTTTTTACTCAAACTTGAACGAGAGGAAAGCACCTGTCGGGTGCTTTTTTc                                                                                                            >  1:93042/1‑140 (MQ=255)                               aaaGTAGAACTGGAAGGAAAATACGTTCCTCACTTTAAACCTGGTAAAGAACTGCGCGATCGCGCCAATATTTACGGTTAAGTTTTTTACTCAAACTTGAACGAGAGGAAAGCACCTGTCGGGTGCTTTTTTCATTtctc                                                                                                     <  1:462573/140‑1 (MQ=255)                                        cTGGAAGGAAAATACGTTCCTCACTTTAAACCTGGTAAAGAACTGCGCGATCGCGCCAATATTTACGGTTAAGTTTTTTACTCAAACTTGAACGAGAGGAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAATctgga                                                                                            >  1:728473/1‑140 (MQ=255)                                              ggaaAATACGTTCCTCACTTTAAACCTGGTAAAGAACTGCGCGATCGCGCCAATATTTACGGTTAAGTTTTTTACTCAAACTTGAACGAGAGGAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAATctggaactgga                                                                                      <  1:97189/140‑1 (MQ=255)                                                   aTACGTTCCTCACTTTAAACCTGGTAAAGAACTGCGCGATCGCGCCAATATTTACGGTTAAGTTTTTTACTCAAACTTGAACGAGAGGAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAATCTGGAACTGGAAGCTg                                                                                 >  2:415648/1‑140 (MQ=255)                                                       gTTCCTCACTTTAAACCTGGTAAAGAACTGCGCGATCGCGCCAATATTTACGGTTAAGTTTTTTACTCAAACTTGAACGAGAGGAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAATCTGGAACTGGAAGCTGCCTc                                                                             <  1:108738/140‑1 (MQ=255)                                                          ccTCACTTTAAACCTGGTAAAGAACTGCGCGATCGCGCCAATATTTACGGTTAAGTTTTTTACTCAAACTTGAACGAGAGGAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAATCTGGAACTGGAAGCTGCCTCGCa                                                                          <  1:905644/140‑1 (MQ=255)                                                          ccTCACTTTAAACCTGGTAAAGAACTGCGCGATCGCGCCAATATTTACGGTTAAGTTTTTTACTCAAACTTGAACGAGAGGAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAATCTGGAACTGGAAGCTGCCTCGCa                                                                          <  2:896228/140‑1 (MQ=255)                                                            tCACTTTAAACCTGGTAAAGAACTGCGCGATCGCGCCAATATTTACGGTTAAGTTTTTTACTCAAACTTGAACGAGAGGAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAATCTGGAACTGGAAGCTGCCTCGCaga                                                                        <  2:692821/140‑1 (MQ=255)                                                                    aaCCTGGTAAAGAACTGCGCGATCGCGCCAATATTTACGGTTAAGTTTTTTACTCAAACTTGAACGAGAGGAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAATCTGGAACTGGAAGCTGCCTCGCAGAGTTTTGaa                                                                <  1:561807/140‑1 (MQ=255)                                                                    aaCCTGGTAAAGAACTGCGCGATCGCGCCAATATTTACGGTTAAGTTTTTTACTCAAACTTGAACGAGAGGAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAATCTGGAACTGGAAGCTGCCTCGCAGAGTTTTGaa                                                                <  2:349681/140‑1 (MQ=255)                                                                     aCCTGGTAAAGAACTGCGCGATCGCGCCAATATTTACGGTTAAGTTTTTTACTCAAACTTGAACGAGAGGAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAATCTGGAACTGGAAGCTGCCTCGCAGAGTTTTGAAc                                                               >  2:81842/1‑140 (MQ=255)                                                                       cTGGTAAAGAACTGCGCGATCGCGCCAATATTTACGGTTAAGTTTTTTACTCAAACTTGAACGAGAGGAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAATCTGGAACTGGAAGCTGCCTCGCAGAGTTTTGAACAg                                                             >  1:456577/1‑140 (MQ=255)                                                                          gTAAAGAACTGCGCGATCGCGCCAATATTTACGGTTAAGTTTTTTACTCAAACTTGAACGAGAGGAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAATCTGGAACTGGAAGCTGCCTCGCAGAGTTTTGAACAGttt                                                          >  2:154566/1‑140 (MQ=255)                                                                           tAAAGAACTGCGCGATCGCGCCAATATTTACGGTTAAGTTTTTTACTCAAACTTGAACGAGAGGAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAATCTGGAACTGGAAGCTGCCTCGCAGAGTTTTGAACAGtttt                                                         <  1:738636/140‑1 (MQ=255)                                                                                aaCTGCGCGATCGCGCCAATATTTACGGTTAAGTTTTTTACTCAAACTTGAACGAGAGGAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAATCTGGAACTGGAAGCTGCCTCGCAGAGTTTTGAACAGTTTTCAccc                                                    >  2:117189/1‑140 (MQ=255)                                                                                 aCTGCGCGATCGCGCCAATATTTACGGTTAAGTTTTTTACTCAAACTTGAACGAGAGGAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAATCTGGAACTGGAAGCTGCCTCGCAGAGTTTTGAACAGTTTTCACCCt                                                   <  1:154566/140‑1 (MQ=255)                                                                                  cTGCGCGATCGCGCCAATATTTACGGTTAAGTTTTTTACTCAAACTTGAACGAGAGGAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAATCTGGAACTGGAAGCTGCCTCGCAGAGTTTTGAACAGTTTTCACCCtt                                                  <  2:93042/140‑1 (MQ=255)                                                                                    gcgcGATCGCGCCAATATTTACGGTTAAGTTTTTTACTCAAACTTGAACGAGAGGAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAATCTGGAACTGGAAGCTGCCTCGCAGAGTTTTGAACAGTTTTCACCCTTTc                                                >  2:599322/1‑140 (MQ=255)                                                                                    gcgcGATCGCGCCAATATTTACGGTTAAGTTTTTTACTCAAACTTGAACGAGAGGAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAATCTGGAACTGGAAGCTGCCTCGCAGAGTTTTGAACAGTTTTCACCCTTTc                                                >  1:32917/1‑140 (MQ=255)                                                                                                        aCGGTTAAGTTTTTTACTCAAACTTGAACGAGAGGAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAATCTGGAACTGGAAGCTGCCTCGCAGAGTTTTGAACAGTTTTCACCCTTTCGTTAAATTCTTCTGAATATg                            >  2:40245/1‑140 (MQ=255)                                                                                                        aCGGTTAAGTTTTTTACTCAAACTTGAACGAGAGGAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAATCTGGAACTGGAAGCTGCCTCGCAGAGTTTTGAACAGTTTTCACCCTTTCGTTAAATTCTTCTGAATATg                            >  1:848258/1‑140 (MQ=255)                                                                                                               aGTTTTTTACTCAAACTTGAACGAGAGGAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAATCTGGAACTGGAAGCTGCCTCGCAGAGTTTTGAACAGTTTTCACCCTTTCGTTAAATTCTTCTGAATATGCCTCggg                     >  2:205196/1‑140 (MQ=255)                                                                                                               aGTTTTTTACTCAAACTTGAACGAGAGGAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAATCTGGAACTGGAAGCTGCCTCGCAGAGTTTTGAACAGTTTTCACCCTTTCGTTAAATTCTTCTGAATATGCCTCggg                     >  2:730815/1‑140 (MQ=255)                                                                                                               aGTTTTTTACTCAAACTTGAACGAGAGGAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAATCTGGAACTGGAAGCTGCCTCGCAGAGTTTTGAACAGTTTTCACCCTTTCGTTAAATTCTTCTGAATATGCCTCggg                     >  1:439638/1‑140 (MQ=255)                                                                                                                gTTTTTTACTCAAACTTGAACGAGAGGAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAATCTGGAACTGGAAGCTGCCTCGCAGAGTTTTGAACAGTTTTCACCCTTTCGTTAAATTCTTCTGAATATGCCTCgggg                    <  2:32917/140‑1 (MQ=255)                                                                                                                      tACTCAAACTTGAACGAGAGGAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAATCTGGAACTGGAAGCTGCCTCGCAGAGTTTTGAACAGTTTTCACCCTTTCGTTAAATTCTTCTGAATATGCCTCGGGGAACGCa              >  1:470717/1‑140 (MQ=255)                                                                                                                             aCTTTAACGAGAGGAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAATCTGGAACTGGAAGCTGCCTCGCAGAGTTTTGAACAGTTTTCACCCTTTCGTTAAATTCTTCTGAATATGCCTCGGGGAACGCAAAATTcc       <  2:848258/140‑1 (MQ=255)                                                                                                                             aCTTGAACGAGAGGAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAATCTGGAACTGGAAGCTGCCTCGCAGAGTTTTGAACAGTTTTCACCCTTTCGTTAAATTCTTCTGAATATGCCTCGGGGAACGCAAAATTcc       <  2:447345/140‑1 (MQ=255)                                                                                                                             aCTTGAACGAGAGGAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAATCTGGAACTGGAAGCTGCCTCGCAGAGTTTTGAACAGTTTTCACCCTTTCGTTAAATTCTTCTGAATATGCCTCGGGGAACGCAAAATTcc       <  2:728473/140‑1 (MQ=255)                                                                                                                                  aaCGAGAGGAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAATCTGGAACTGGAAGCTGCCTCGCAGAGTTTTGAACAGTTTTCACCCTTTCGTTAAATTCTTCTGAATATGCCTCGGGGAACGCAAAATTCccacca  <  1:415648/140‑1 (MQ=255)                                                                                                                                          |                                                                                                                                    CGTACCGGACGTAATCCGAAGACTGGCGATAAAGTAGAACTGGAAGGAAAATACGTTCCTCACTTTAAACCTGGTAAAGAACTGCGCGATCGCGCCAATATTTACGGTTAAGTTTTTTACTCAAACTTGAACGAGAGAAAAGCACCTGTCGGGTGCTTTTTTCATTTCTCTAATCTGGAACTGGAAGCTGCCTCGCAGAGTTTTGAACAGTTTTCACCCTTTCGTTAAATTCTTCTGAATATGCCTCGGGGAACGCAAAATTCCCACCA  >  NC_000913/964002‑964270

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑