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%	146.2 / NA	46	*412* (TAG→TAA)	intR	Rac prophage, integrase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (19/27);  total (19/27)

CGTTACGACGCAGACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTG  >  NC_000913/1411873‑1412133                                                                                                                                |                                                                                                                                      cGTTACGACGCAGACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACcg                                                                                                                            <  1:506754/139‑1 (MQ=255)           cAGACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAAc                                                                                                                  <  2:115819/139‑1 (MQ=255)                   tttGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTAt                                                                                                          >  2:224042/1‑139 (MQ=255)                        aaTTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACGTTGCAATTACGATAACCGCGCATTCAACATGGCTATCGGtg                                                                                                     <  1:555450/139‑2 (MQ=255)                              ttCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTcgtcgt                                                                                               >  2:241872/1‑139 (MQ=255)                                    ttGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGt                                                                                         <  1:241872/139‑1 (MQ=255)                                      gTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtca                                                                                       <  1:860652/139‑1 (MQ=255)                                        aTTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtcatc                                                                                     <  2:644598/139‑1 (MQ=255)                                        aTTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtcatc                                                                                     <  1:224042/139‑1 (MQ=255)                                                 tctttGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACAt                                                                            >  1:322970/1‑139 (MQ=255)                                                 tctttGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACAt                                                                            >  1:85822/1‑139 (MQ=255)                                                     tGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCg                                                                        >  1:327460/1‑139 (MQ=255)                                                      gTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGt                                                                       <  2:85822/139‑1 (MQ=255)                                                      gTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGt                                                                       <  2:322970/139‑1 (MQ=255)                                                         aTTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTaaa                                                                    <  2:327460/139‑1 (MQ=255)                                                                 aTTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATac                                                            <  1:872496/139‑1 (MQ=255)                                                                           attattTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTgcg                                                  <  1:563290/139‑1 (MQ=255)                                                                             tattTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCa                                                <  2:26975/139‑1 (MQ=255)                                                                                       ctctGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAAc                                                                                                                  <  2:872351/63‑1 (MQ=255)                                                                                       ctctGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAAc                                                                                                                  >  1:872351/1‑63 (MQ=255)                                                                                         ctGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAAcc                                                                                                                             <  1:420879/50‑1 (MQ=255)                                                                                         ctGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAAcc                                                                                                                             >  2:420879/1‑50 (MQ=255)                                                                                                  aaTGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtggctg                           >  2:607207/1‑139 (MQ=255)                                                                                                  aaTGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtggctg                           <  1:456715/139‑1 (MQ=255)                                                                                                      gggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtca                                                                                       >  1:515210/1‑75 (MQ=255)                                                                                                      gggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtca                                                                                       <  2:515210/75‑1 (MQ=255)                                                                                                       ggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTtcgtcg                                                                                                >  2:254008/1‑65 (MQ=255)                                                                                                       ggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTtcgtcg                                                                                                <  1:254008/65‑1 (MQ=255)                                                                                                       ggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATg                                        <  2:304843/121‑1 (MQ=255)                                                                                                       ggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATg                                        >  1:304843/1‑121 (MQ=255)                                                                                                       ggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATg                                        <  1:341250/121‑1 (MQ=255)                                                                                                       ggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATg                                        >  2:341250/1‑121 (MQ=255)                                                                                                       ggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtgg                              <  1:771070/131‑1 (MQ=255)                                                                                                       ggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtgg                              >  2:771070/1‑131 (MQ=255)                                                                                                         cAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtca                                                                                       <  2:425269/72‑1 (MQ=255)                                                                                                         cAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtca                                                                                       >  1:425269/1‑72 (MQ=255)                                                                                                            aTTGGGGGCAAACTTTGCAATTACGATAACCGCGCCTTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtggc                             <  1:346692/127‑1 (MQ=255)                                                                                                            aTTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtggc                             >  2:346692/1‑127 (MQ=255)                                                                                                            aTTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATg                 >  1:7639/1‑139 (MQ=255)                                                                                                              tGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGcc               <  1:607207/139‑1 (MQ=255)                                                                                                              tGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGcc               <  2:7639/139‑1 (MQ=255)                                                                                                                     aaaCTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTgcg                                                  <  2:945033/97‑1 (MQ=255)                                                                                                                     aaaCTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTgcg                                                  >  1:945033/1‑97 (MQ=255)                                                                                                                     aaaCTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtgg                              >  2:848066/1‑117 (MQ=255)                                                                                                                     aaaCTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtgg                              <  1:848066/117‑1 (MQ=255)                                                                                                                           tGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTg  >  2:987508/1‑139 (MQ=255)                                                                                                                                |                                                                                                                                      CGTTACGACGCAGACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTG  >  NC_000913/1411873‑1412133

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑