Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,771,061	2 bp→CG	coding (381‑382/444 nt)	yfjS →	CP4‑57 prophage; inner membrane lipoprotein YfjS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,771,061	0	T	C	100.0%	30.8 / NA	16	Y127Y (TAT→TAC)	yfjS	CP4‑57 prophage; inner membrane lipoprotein YfjS
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (9/7);  total (9/7)
*	NC_000913	2,771,062	0	T	G	100.0%	31.0 / NA	16	S128A (TCC→GCC)	yfjS	CP4‑57 prophage; inner membrane lipoprotein YfjS
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (9/7);  total (9/7)

GACAATATCAAACTGGAATACCACGAAGTTACGGACCCGTATACGAAAGAAAAATACTTCGAATATTCCCATGACGGCAAACTGATGGGACGGCTGCTGATACCGTCAAACCCTGATAACCGGGAATAAAAACAACGAGAAAGGAGACATAAATGAAAATACGTTCACTAAGCCGGTTTGTACTGGCAA  >  NC_000913/2770996‑2771184                                                                  ||                                                                                                                           gataacatCAAACTGGAATACCTGGAGGTTACGGACCTGTATACCAAAGAAAAATACTTTGAGTACGCCCATGACGGCAAACTGATGGGACGGCTGCTGATACCGTCAAACCCTGATAACCGGGAATAAAAACAACgaga                                                   <  1:255433/134‑1 (MQ=14)  ataacatCAAACTGGAATACCAGGAGGTGACGGACCCGTATACCAAAGAAAAATACTTTGAGTACGCCCATGACGGCAAACTGATGGGACGGCTGCTGATACCGCCAAACCCTGATACCCGGAAATAAAAACAACGAGaa                                                  >  2:297386/6‑140 (MQ=11)           aaCTGGAATACCAGGAGGTGACGGACCCGTATACCAAAGAAAAATACTTTGAGTACGCCCATGACGGCAAACTGATGGGACGGCTGCTGATACCGTCAAACCCTGATAACCGGGAATAAAAACAACGAGAAAGGAGACAt                                         <  2:535072/140‑1 (MQ=14)              tGGAATACCAGGAGGTGACGGACCCGTATACCAAAGAAAAATACTTTGAGTACGCCCATGACGGCAAACTGATGGGACGGCTGCTGATACCGTCAAACCCTGATAACCGGGAATAAAAACAACGAGAAAGGAGACATaaa                                      >  1:472993/1‑140 (MQ=11)                    aCCAGGAGGTGACGGACCCGTATACCAAAGAAAAATACTTTGAGTACGCCCATGACGGCAAACTGATGGGACGGCTGCTGATACCGTCAAACCCTGATAACCGGGAATAAAAACAACGAGAAAGGAGACATAAATGaaaa                                <  2:154615/140‑1 (MQ=17)                          aggtgaCGGACCCGTATACCAAAGAAAAATACTTTGAGTACGCCCATGACGGCAAACTGATGGGACGGCTGCTGATACCGTCAAACCCTGATAACCGGGAATAAAAACAACGAGAAAGGAGACATAAATGAAAATACGtt                          >  2:701235/6‑140 (MQ=14)                               aCGGACCCGTATACCAAAGAAAAATACTTTGAGTACGCCCATGACGGCAAACTGATGGGACGGCTGCTGATACCGTCAAACCCTGATAACCGGGAATAAAAACAACGAGAAAGGAGACATaaa                                      <  1:722247/123‑1 (MQ=18)                               aCGGACCCGTATACCAAAGAAAAATACTTTGAGTACGCCCATGACGGCAAACTGATGGGACGGCTGCTGATACCGTCAAACCCTGATAACCGGGAATAAAAACAACGAGAAAGGAGACATaaa                                      >  2:722247/1‑123 (MQ=14)                                    cccGTATACCAAAGAAAAATACTTTGAGTACGCCCATGACGGCAAACTGATGGGACGGCTGCTGATACCGTCAAACCCTGATAACCGGGAATAAAAACAACGAGAAAGGAGACATAAATGAAAATACGTTCACTAAGCCg                >  2:25691/1‑140 (MQ=17)                                      cGTATACCAAAGAAAAATACTTTGAGTACGCCCATGACGGCAAACTGATGGGACGGCTGCTGATACCGTCAAACCCTGATAACCGGGAATAAAAACAACGAGAAAGGAGACATAAATGAAAATACGTTCACTAAGCCGGt              <  1:576283/140‑1 (MQ=18)                                        tataCCAAAGAAAAATACTTTGAGTACGCCCATGACGGCAAACTGATGGGACGGCTGCTGATACCGTCAAACCCTGATAACCGGGAATAAAAACAACGAGAAAGGAGACAGAAAAGAAAATACGCTCACTAAGCCGGttt            >  1:283700/1‑140 (MQ=17)                                             caaagaaaAATACTTTGAGTACGCCCATGACGGCAAACTGATGGGACGGCTGCTGATACCGTCAAACCCTGATAACCGGGAATAAAAACAACGAGAAAGGAGACATAAATGAAAATACGTTCACTAAGCCGGTTTGTACt       >  1:47213/2‑140 (MQ=18)                                                agaaaAATACTTTGAGTCCGCCTATGACGGCAAACAGATGGGACGGCTGCTGATACCGTCAAACCCTGATAACCGGGAATAAAAACAACGAGAAAGGAGACATAAATGAAAATACGTTCACTAAGCCGGTTTGTACTGGc    <  2:283700/140‑1 (MQ=255)                                                agaaaAATACTTTGAGTACGCCCATGACGGCAAACGGATGGGACGGCTGCTGATACCGTCAAACCCTGATAACCGGGAATAAAAACAACGAGAAAGGAGACATAAATGAAAATACGTTCACTAAGCCGGTTTGTACTGGc    <  1:631872/140‑1 (MQ=21)                                                  aaaaaTACTTTGAGTACGCCCATGACGGCAAACTGATGGGACGGCTGCTGATACCGTCAAACCCTGATAACCGGGAATAAAAACAACGAGAAAGGAGACATAAATGAAAATACGTTCACTAAGCCGGTTTGTACTGGCaa  >  2:594438/1‑140 (MQ=18)                                                  aaaaaTACTTTGAGTACGCCCATGACGGCAAACTGATGGGACGGCTGCTGATACCGTCAAACCCTGATAACCGGGAATAAAAACAACGAGAAAGGAGACATAAATGAAAACACGCTCACTAAGCAGGTTTGTACTGGCaa  >  1:358723/1‑140 (MQ=21)                                                                  ||                                                                                                                           GACAATATCAAACTGGAATACCACGAAGTTACGGACCCGTATACGAAAGAAAAATACTTCGAATATTCCCATGACGGCAAACTGATGGGACGGCTGCTGATACCGTCAAACCCTGATAACCGGGAATAAAAACAACGAGAAAGGAGACATAAATGAAAATACGTTCACTAAGCCGGTTTGTACTGGCAA  >  NC_000913/2770996‑2771184

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑