Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,787,510	T→C	intergenic (+56/‑184)	zipA_3 → / → manR_2	Cell division protein ZipA/Transcriptional regulator ManR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,787,510	0	T	C	100.0%	98.4 / NA	28	intergenic (+56/‑184)	zipA_3/manR_2	Cell division protein ZipA/Transcriptional regulator ManR
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (11/17);  total (11/17)

AATAAATCAAATAATACCAATACGCCTTCTAAACAAACACCTCAAGCACAATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGTGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGTTAAAATCATATAAAAGTTCGCTTTAATGTCATTGACGTATGTATAAGCTCTCAT  >  USA300TCH1516_ALE/2787389‑2787626                                                                                                                          |                                                                                                                     aataaATCAAATAATACCAATACGCCTTCTAAACAAACACCTCAAGCACAATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCt                                                                                            <  4:56116/148‑1 (MQ=255)  ataaATCAAATAATACCAATACGCCTTCTAAACAAACACCTCAAGCACAATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCtt                                                                                           >  3:238162/1‑148 (MQ=255)     aaTCAAATAATACCAATACGCCTTCTAAACAAACACCTCAAGCACAATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTAct                                                                                        <  3:54011/148‑1 (MQ=255)       tCAAATAATACCAATACGCCTTCTAAACAAACACCTCAAGCACAATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTActgc                                                                                      >  4:74478/1‑148 (MQ=255)            taataCCAATACGCCTTCTAAACAAACACCTCAAGCACAATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTc                                                                                 <  3:323319/148‑1 (MQ=255)            taataCCAATACGCCTTCTAAACAAACACCTCAAGCACAATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTc                                                                                 <  3:198410/148‑1 (MQ=255)             aataCCAATCCCCCTTCTAACCAACCCCCTCAAGCACAATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTActg                                                                                       <  2:25900/141‑1 (MQ=255)             aataCCAATACGCCTTCTAAACAAACACCTCAAGCACAATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGCAATATCTGActg                                                                                       <  1:48645/141‑1 (MQ=255)              ataCCAATACGCCTTCTAAACAAACACCTCAAGCACAATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTActgc                                                                                      >  2:42550/1‑141 (MQ=255)                aCCAATACGCCTTCTAAACAAACACCTCAAGCACAATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTActgctg                                                                                    >  2:3331/1‑141 (MQ=255)                aCCAATACGCCTTCTAAACAAACACCTCAAGCACAATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTa                                                                             >  3:311093/1‑148 (MQ=255)                  cAATACGCCTTCTAAACAAACACCTCAAGCACAATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTAtt                                                                           >  3:250936/1‑148 (MQ=255)                            tCTAAACAAACACCTCAAGCACAATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTc                                                                 >  4:66004/1‑148 (MQ=255)                                            aaGCACAATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGt                                                        <  1:54046/141‑1 (MQ=255)                                               cacaATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACCGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGTTAATATCata                                              <  4:354712/148‑1 (MQ=255)                                                          aaataTTCATCAATTGCCCGACACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGTTAAAATCATATAAAAGTTCGc                                   <  4:129759/148‑1 (MQ=255)                                                           aaaaTTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGTTAAAATCATATAAAAGTTCGCt                                  >  4:208620/1‑148 (MQ=255)                                                           aaaaTTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGTTAAAATCATATAAAAGTTCGCt                                  <  4:270676/148‑1 (MQ=255)                                                           aaaaTTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGTTAAAATCATATAAAAGTTCGCt                                  >  4:46067/1‑148 (MQ=255)                                                            aaaTTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGTTAAAATCATATAAAAGTTCGCtt                                 <  3:339360/148‑1 (MQ=255)                                                            aaaTTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGTTAAAATCATATAAAAGTTCGCtt                                 <  4:53186/148‑1 (MQ=255)                                                                         gCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGTTAAAATCATATAAAAGTTCGCTTTAATGTCATTGAc                    <  3:172036/148‑1 (MQ=255)                                                                            tGATACGTCCACAAGTACTATTTGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGTTAAAATCATATAAAAGTTCGCTTTAATGTCATTGACgta                 <  3:22997/148‑1 (MQ=255)                                                                            tGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGTTAAAATCATATAAAAGTTCGCTTTAATGTCATTGACgta                 <  4:196605/148‑1 (MQ=255)                                                                              aTACGTCCACAAGTACCAGATGCATAAATTCAGAACAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGTTAAAATCATATAAAAGTTCGCTTTAATGTCATTGACgtatg               <  4:175080/148‑1 (MQ=255)                                                                                  gTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGTTAAAATCATATAAAAGTTCGCTTTAATGTCATTGACGTATGtata           >  3:184676/1‑148 (MQ=255)                                                                                  gTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGTTAAAATCATATAAAAGTTCGCTTTAATGTCATTGACGTATGtata           >  3:273617/1‑148 (MQ=255)                                                                                           tACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGTTAAAATCATATAAAAGTTCGCTTTAATGTCATTGACGTATGTATAAGCTCTCAt  <  3:319508/148‑1 (MQ=255)                                                                                                                          |                                                                                                                     AATAAATCAAATAATACCAATACGCCTTCTAAACAAACACCTCAAGCACAATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGTGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGTTAAAATCATATAAAAGTTCGCTTTAATGTCATTGACGTATGTATAAGCTCTCAT  >  USA300TCH1516_ALE/2787389‑2787626

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑