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%	212.4 / NA	66	*412* (TAG→TAA)	intR	Rac prophage, integrase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (33/33);  total (33/33)

CTTCGCCCACGTTACGACGCAGACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCAT  >  NC_000913/1411864‑1412101                                                                                                                                         |                                                                                                      cTTCGCCCACGTTACGACGCAGACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTa                                                                                                     >  2:1084096/1‑139 (MQ=255)              acgacgCAGACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCa                                                                                        <  1:1084096/139‑1 (MQ=255)                     aGACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACa                                                                                 >  2:1165515/1‑139 (MQ=255)                                   tttGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTtcg                                                                   <  2:738237/139‑1 (MQ=255)                                      gTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTtcgtcg                                                                <  1:1165515/139‑1 (MQ=255)                                       ttCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTcgtcgt                                                               >  2:1362224/1‑139 (MQ=255)                                            gTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATg                                                          >  1:1432558/1‑139 (MQ=255)                                             ttGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGt                                                         >  1:1562819/1‑139 (MQ=255)                                                  ttGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtcatca                                                    <  2:1018863/139‑1 (MQ=255)                                                      tctttcttTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCaa                                                   <  2:417225/136‑1 (MQ=255)                                                      tctttcttTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCaa                                                   >  1:417225/1‑136 (MQ=255)                                                       ctttctttGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATgg                                                                              >  1:746591/1‑108 (MQ=255)                                                       ctttctttGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATgg                                                                              <  2:746591/108‑1 (MQ=255)                                                       ctttctttGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCAt                                                           >  2:993499/1‑127 (MQ=255)                                                       ctttctttGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCAt                                                           <  1:993499/127‑1 (MQ=255)                                                       ctttctttGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtca                                                       <  2:961812/131‑1 (MQ=255)                                                       ctttctttGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtca                                                       >  1:961812/1‑131 (MQ=255)                                                         ttctttGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCcaca                                             <  1:1362224/139‑1 (MQ=255)                                                          tctttGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtca                                                       >  1:280883/1‑128 (MQ=255)                                                          tctttGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtca                                                       <  2:280883/128‑1 (MQ=255)                                                               gTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTtc                                                                    <  1:532445/110‑1 (MQ=255)                                                               gTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTtc                                                                    >  2:532445/1‑110 (MQ=255)                                                               gTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtca                                                       <  1:1135795/123‑1 (MQ=255)                                                               gTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtca                                                       >  2:1135795/1‑123 (MQ=255)                                                               gTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGt                                       <  2:1432558/139‑1 (MQ=255)                                                                    ttgttgATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtcatc                                                     >  2:896221/1‑120 (MQ=255)                                                                    ttgttgATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTATTCGTCGTTCATGtcatc                                                     <  1:896221/120‑1 (MQ=255)                                                                          aTTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTAGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGACTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATac                            >  1:519494/1‑139 (MQ=255)                                                                                    attattTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAAc                                                                                  >  2:484897/1‑75 (MQ=255)                                                                                    attattTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAAc                                                                                  <  1:484897/75‑1 (MQ=255)                                                                                                           aaTGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACcg                                                                                            <  2:162151/42‑1 (MQ=255)                                                                                                           aaTGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACcg                                                                                            >  1:162151/1‑42 (MQ=255)                                                                                                           aaTGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAAc                                                                                  >  2:1043459/1‑52 (MQ=255)                                                                                                           aaTGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAAc                                                                                  <  1:1043459/52‑1 (MQ=255)                                                                                                           aaTGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTc                                                             >  1:1547603/1‑73 (MQ=255)                                                                                                           aaTGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTc                                                             <  2:1547603/73‑1 (MQ=255)                                                                                                           aaTGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtcat                                                      >  2:953046/1‑80 (MQ=255)                                                                                                           aaTGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtcat                                                      <  1:953046/80‑1 (MQ=255)                                                                                                             tGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtcatc                                                     >  2:250688/1‑79 (MQ=255)                                                                                                             tGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtcatc                                                     <  1:250688/79‑1 (MQ=255)                                                                                                               gggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTaa                                     <  1:754850/93‑1 (MQ=255)                                                                                                               gggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTaa                                     >  2:754850/1‑93 (MQ=255)                                                                                                                ggCAAATTGGGGGCAAACTTTGCAATTACGATAACcgc                                                                                           >  2:994807/1‑38 (MQ=255)                                                                                                                ggCAAATTGGGGGCAAACTTTGCAATTACGATAACcgc                                                                                           <  1:994807/38‑1 (MQ=255)                                                                                                                ggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAAc                                                                                  >  2:117805/1‑47 (MQ=255)                                                                                                                ggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAAc                                                                                  <  1:117805/47‑1 (MQ=255)                                                                                                                ggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtcatc                                                     >  2:1055919/1‑76 (MQ=255)                                                                                                                ggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTaa                                     <  1:346305/92‑1 (MQ=255)                                                                                                                ggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTaa                                     >  2:346305/1‑92 (MQ=255)                                                                                                                ggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCAt  >  2:674277/1‑127 (MQ=255)                                                                                                                ggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCAt  <  1:674277/127‑1 (MQ=255)                                                                                                                ggCAAATTGGGGGAAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCTTGtcatc                                                     <  1:1055919/76‑1 (MQ=255)                                                                                                                     aTTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAAc                                                                                  >  2:456435/1‑42 (MQ=255)                                                                                                                     aTTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAAc                                                                                  <  1:456435/42‑1 (MQ=255)                                                                                                                     aTTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTaa                                     <  2:639756/87‑1 (MQ=255)                                                                                                                     aTTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTaa                                     >  1:639756/1‑87 (MQ=255)                                                                                                                     aTTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTgcg                  >  1:906178/1‑106 (MQ=255)                                                                                                                     aTTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTgcg                  <  2:906178/106‑1 (MQ=255)                                                                                                                          gggCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCAt                                                           <  1:200816/60‑1 (MQ=255)                                                                                                                          gggCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCAt                                                           >  2:200816/1‑60 (MQ=255)                                                                                                                              aaaCTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGtt             >  1:870193/1‑102 (MQ=255)                                                                                                                              aaaCTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGtt             <  2:870193/102‑1 (MQ=255)                                                                                                                               aaCTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATg        <  1:1323729/106‑1 (MQ=255)                                                                                                                               aaCTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATg        >  2:1323729/1‑106 (MQ=255)                                                                                                                                   ttGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATac                            <  2:264564/82‑1 (MQ=255)                                                                                                                                   ttGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATac                            >  1:264564/1‑82 (MQ=255)                                                                                                                                         |                                                                                                      CTTCGCCCACGTTACGACGCAGACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCAT  >  NC_000913/1411864‑1412101

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑