Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	419,364	T→C	intergenic (+180/‑227)	phoR → / → brnQ	sensory histidine kinase in two‑component regulatory system with PhoB/branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	419,364	0	T	C	100.0%	148.9 / NA	40	intergenic (+180/‑227)	phoR/brnQ	sensory histidine kinase in two‑component regulatory system with PhoB/branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (19/21);  total (19/21)

ATGCTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTAACGCGGTAAATCGAAAAACTATTCTTCGCCGCGCCTGGTTGGGAGTATTTCCCGCTAAA  >  NC_000913/419222‑419504                                                                                                                                               |                                                                                                                                             aTGCTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCCCTGGtttt                                                                                                                                      >  2:62284/1‑151 (MQ=255)     tGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCCCTGGttttt                                                                                                                                     >  2:263773/1‑148 (MQ=255)           aTTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCCCTGGTTTTTAGATCcct                                                                                                                             <  2:500203/150‑1 (MQ=255)                cTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGc                                                                                                                       >  1:355216/1‑151 (MQ=255)                  ttGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGc                                                                                                                       <  2:626129/149‑1 (MQ=255)                   tGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCtt                                                                                                                     <  1:187915/150‑1 (MQ=255)                    gCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCttt                                                                                                                    <  2:626748/150‑1 (MQ=255)                      aGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTaaa                                                                                                                 <  2:352994/151‑1 (MQ=255)                         cAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTAAAACg                                                                                                              <  2:660025/151‑1 (MQ=255)                         cAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTAAAACg                                                                                                              >  1:209575/1‑151 (MQ=255)                                       tAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTa                                                                                                 >  2:552472/1‑150 (MQ=255)                                         gATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAAt                                                                                              <  1:558514/151‑1 (MQ=255)                                             ttACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTgc                                                                                           <  2:46779/150‑1 (MQ=255)                                             ttACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTgc                                                                                           <  2:442360/150‑1 (MQ=255)                                                   cGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTc                                                                                      >  2:614787/1‑149 (MQ=255)                                                     aTTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGt                                                                                  <  2:123945/151‑1 (MQ=255)                                                             ttttttGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCAt                                                                          >  2:79137/1‑151 (MQ=255)                                                                  tGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATactg                                                                      <  2:411006/150‑1 (MQ=255)                                                                        cATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCAt                                                               >  2:429952/1‑151 (MQ=255)                                                                         aTGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCAtt                                                              >  2:155707/1‑151 (MQ=255)                                                                            aTTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTaa                                                            >  1:61389/1‑150 (MQ=255)                                                                             ttAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTAAcg                                                          >  2:161748/1‑151 (MQ=255)                                                                              tAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTAAcgc                                                         >  1:207512/1‑151 (MQ=255)                                                                                              aCGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTAACGCGGTAAATCGAAAAACt                                         >  2:303210/1‑151 (MQ=255)                                                                                                ggAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTAACGCGGTAAATCGAAAAACTAt                                       <  1:62285/151‑1 (MQ=255)                                                                                                  aaaTAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTAACGCGGTAAATCGAAAAACTAttc                                     >  2:591561/1‑151 (MQ=255)                                                                                                    aTAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTAACGCGGTAAATCGAAAAACTAttctt                                   <  1:255341/151‑1 (MQ=255)                                                                                                      aGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTAACGCGGTAAATCGAAAAACTAttcttc                                  <  2:188211/150‑1 (MQ=255)                                                                                                                aCTGGTTGGTGATTTCTTATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTAACGCGGTAAATCGAAAAACTATTCTTCGCCGCGCCTgg                       <  1:310959/151‑1 (MQ=255)                                                                                                                  tggttggtGATTTCTTATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTAACGCGGTAAATCGAAAAACTATTCTTCGCCGCGCCTGGtt                     >  2:195813/1‑151 (MQ=255)                                                                                                                   ggttggtGATTTCTTATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTAACGCGGTAAATCGAAAAACTATTCTTCGCCGCGCCTGGtt                     <  1:513409/150‑1 (MQ=255)                                                                                                                     ttggtGATTTCTTATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTAACGCGGTAAATCGAAAAACTATTCTTCGCCGCGCCTGGTTggg                  >  1:242367/1‑151 (MQ=255)                                                                                                                        gtGATTTCTTATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTAACGCGGTAAATCGAAAAACTATTCTTCGCCGCGCCTGGTTGGGAGt               <  2:495256/151‑1 (MQ=255)                                                                                                                          gATTTCTTATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTAACGCGGTAAATCGAAAAACTATTCTTCGCCGCGCCTGGTTGGGAGTa              <  2:20489/150‑1 (MQ=255)                                                                                                                          gATTTCTTATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTAACGCGGTAAATCGAAAAACTATTCTTCGCCGCGCCTGGTTGGGAGTAt             <  2:378957/151‑1 (MQ=255)                                                                                                                                ttATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTAACGCGGTAAATCGAAAAACTAttctt                                   >  2:352809/1‑123 (MQ=255)                                                                                                                                ttATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTAACGCGGTAAATCGAAAAACTAttctt                                   <  1:352806/123‑1 (MQ=255)                                                                                                                                ttATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTAACGCGGTAAATCGAAAAACTATTCTTCGCCGCGCCTGGTTGGGAGTATTTCCCg       >  2:246647/1‑151 (MQ=255)                                                                                                                                 tATCGCTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTAACGCGGTAAATCGAAAAACTATTCTTCGCCGCGCCTGGTTGGGAGTATTTCCCg       <  2:538096/150‑1 (MQ=255)                                                                                                                                      cTATATACCCCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTAACGCGGTAAATCGAAAAACTATTCTTCGCCGCGCCTGGTTGGGAGTATTTCCCGCTaaa  >  1:186511/1‑150 (MQ=255)                                                                                                                                               |                                                                                                                                             ATGCTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTAACGCGGTAAATCGAAAAACTATTCTTCGCCGCGCCTGGTTGGGAGTATTTCCCGCTAAA  >  NC_000913/419222‑419504

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑