Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,412,000	C→T	*412* (TAG→TAA)	intR ←	Rac prophage, integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,412,000	0	C	T	100.0%	133.3 / NA	42	*412* (TAG→TAA)	intR	Rac prophage, integrase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (20/22);  total (20/22)

CGTTACGACGCAGACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTC  >  NC_000913/1411873‑1412130                                                                                                                                |                                                                                                                                   cGTTACGACGCAGACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACcg                                                                                                                         >  1:356071/1‑139 (MQ=255)   ttACTACGCAGACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTCGCAATTACGATAACcgcg                                                                                                                       <  1:885435/139‑1 (MQ=255)   ttACGACGCAGACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACcgcg                                                                                                                       >  1:158635/1‑139 (MQ=255)                  ttttGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTa                                                                                                        <  1:1064034/139‑1 (MQ=255)                   tttGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTAt                                                                                                       <  2:158635/139‑1 (MQ=255)                              ttCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATg                                                                                                            >  2:16554/1‑123 (MQ=255)                              ttCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATg                                                                                                            <  1:16554/123‑1 (MQ=255)                                  ggTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCAt                                                                                        <  1:544647/139‑1 (MQ=255)                                   gTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCa                                                                                                                     >  2:760492/1‑109 (MQ=255)                                   gTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCa                                                                                                                     <  1:760492/109‑1 (MQ=255)                                        aTTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtcatc                                                                                  <  2:356071/139‑1 (MQ=255)                                        aTTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtcatc                                                                                  >  2:1237189/1‑139 (MQ=255)                                             tctttcttTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtcatc                                                                                  >  2:1253515/1‑134 (MQ=255)                                             tctttcttTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtcatc                                                                                  <  1:1253515/134‑1 (MQ=255)                                                                      cTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCAt                                                    <  1:66962/139‑1 (MQ=255)                                                                                    gTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCcac                                                                           <  2:90197/102‑1 (MQ=255)                                                                                    gTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCcac                                                                           >  1:90197/1‑102 (MQ=255)                                                                                     ttCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCaa                                                                                <  1:1175322/96‑1 (MQ=255)                                                                                     ttCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCaa                                                                                >  2:1175322/1‑96 (MQ=255)                                                                                       ctctGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTtcg                                                                                                <  2:905911/78‑1 (MQ=255)                                                                                       ctctGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTtcg                                                                                                >  1:905911/1‑78 (MQ=255)                                                                                                  aaTGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTAt                                                                                                       >  1:193706/1‑60 (MQ=255)                                                                                                  aaTGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTAt                                                                                                       <  2:193706/60‑1 (MQ=255)                                                                                                  aaTGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCAt                                                    <  1:171033/111‑1 (MQ=255)                                                                                                  aaTGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCAt                                                    >  2:171033/1‑111 (MQ=255)                                                                                                      ggtcAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGtt                                                                                           <  2:918558/65‑1 (MQ=255)                                                                                                      gggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGc                                                                                                          >  2:329533/1‑53 (MQ=255)                                                                                                      gggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGc                                                                                                          <  1:329533/53‑1 (MQ=255)                                                                                                      gggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGtt                                                                                           >  1:918558/1‑68 (MQ=255)                                                                                                       ggtaaaTTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAAttt                                                              <  2:179403/93‑1 (MQ=255)                                                                                                       ggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCAtt                                                                                                                   <  2:471560/43‑1 (MQ=255)                                                                                                       ggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCAtt                                                                                                                   >  1:471560/1‑43 (MQ=255)                                                                                                       ggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCaa                                                                                                                <  1:784908/46‑1 (MQ=255)                                                                                                       ggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCaa                                                                                                                >  2:784908/1‑46 (MQ=255)                                                                                                       ggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTaa                                                                  >  2:381716/1‑92 (MQ=255)                                                                                                       ggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTaa                                                                  <  1:381716/92‑1 (MQ=255)                                                                                                       ggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAAttt                                                              >  1:179403/1‑96 (MQ=255)                                                                                                            aTTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATg              >  2:476762/1‑139 (MQ=255)                                                                                                            aTTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATg              >  2:499379/1‑139 (MQ=255)                                                                                                                      aaCTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtca                                                                                    <  1:568582/59‑1 (MQ=255)                                                                                                                      aaCTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtca                                                                                    >  2:568582/1‑59 (MQ=255)                                                                                                                        cTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTc  <  1:499379/139‑1 (MQ=255)                                                                                                                                |                                                                                                                                   CGTTACGACGCAGACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTC  >  NC_000913/1411873‑1412130

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑