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%	113.4 / NA	36	*412* (TAG→TAA)	intR	Rac prophage, integrase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (19/17);  total (19/17)

TCGCCCACGTTACGACGCAGACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGC  >  NC_000913/1411866‑1412119                                                                                                                                       |                                                                                                                        tCGCCCACGTTACGACGCAGACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTGTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACg                                                                                                                     >  1:572443/1‑139 (MQ=255)       aCGTTACGACGCAGACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAAcc                                                                                                               <  2:426167/139‑1 (MQ=255)        cGTTACGACGCAGACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACcg                                                                                                              <  1:695409/139‑1 (MQ=255)            acgacgCAGACGTTTTTGTAATTTGTTCAGGTTGTATTGTGCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCa                                                                                                          <  2:768279/139‑1 (MQ=255)                          tttGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTAt                                                                                            >  1:310953/1‑139 (MQ=255)                                        aGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCa                                                                              >  1:753096/1‑139 (MQ=255)                                             gTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtca                                                                         <  2:750287/139‑1 (MQ=255)                                             gTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtca                                                                         <  2:259376/139‑1 (MQ=255)                                               aTTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtcatc                                                                       <  2:630006/139‑1 (MQ=255)                                               aTTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtcatc                                                                       <  2:692551/139‑1 (MQ=255)                                               aTTGTTCTTTCTTTCTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGTGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGATATCTGTTCGTCGTTCCTGtcatc                                                                       <  2:489991/139‑1 (MQ=255)                                                    tctttcttTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtcatc                                                                       <  2:553033/134‑1 (MQ=255)                                                    tctttcttTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtcatc                                                                       >  1:553033/1‑134 (MQ=255)                                                    tctttcttTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATcc                                                                  >  2:379937/1‑139 (MQ=255)                                                        tctttGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACAt                                                              >  2:731638/1‑139 (MQ=255)                                                          tttGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATAc                                                            >  2:447869/1‑139 (MQ=255)                                                           ttGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATAcc                                                           <  2:558179/139‑1 (MQ=255)                                                                        aTTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATac                                              <  2:753096/139‑1 (MQ=255)                                                                                            ttCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTaa                                                       >  1:495300/1‑110 (MQ=255)                                                                                            ttCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTaa                                                       <  2:495300/110‑1 (MQ=255)                                                                                            ttCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATg                          <  1:331893/139‑1 (MQ=255)                                                                                                ctGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCTCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGcccc                      >  1:399208/1‑139 (MQ=255)                                                                                                 tGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCa                     >  1:456655/1‑139 (MQ=255)                                                                                                    tACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAAcc                                                                                                               >  1:666302/1‑46 (MQ=255)                                                                                                    tACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAAcc                                                                                                               <  2:666302/46‑1 (MQ=255)                                                                                                      cTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtgg                <  2:592123/139‑1 (MQ=255)                                                                                                       tAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtggc               <  1:569496/139‑1 (MQ=255)                                                                                                         aaTGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtggctg             >  2:736995/1‑139 (MQ=255)                                                                                                         aaTGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtggctg             >  2:354169/1‑139 (MQ=255)                                                                                                         aaTGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtggctg             >  1:44605/1‑139 (MQ=255)                                                                                                             gggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCta         >  1:218060/1‑139 (MQ=255)                                                                                                             gggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCta         >  2:125736/1‑139 (MQ=255)                                                                                                             gggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCta         >  1:602579/1‑139 (MQ=255)                                                                                                             gggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCta         >  1:278026/1‑139 (MQ=255)                                                                                                                cAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATaa      >  1:2885/1‑139 (MQ=255)                                                                                                                    ttGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGc  <  2:572443/139‑1 (MQ=255)                                                                                                                                       |                                                                                                                        TCGCCCACGTTACGACGCAGACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGC  >  NC_000913/1411866‑1412119

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑