Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	295,643	C→T	intergenic (‑64/+53)	yagN ← / ← intF	protein YagN/putative phage integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	295,643	0	C	T	100.0%	27.3 / NA	12	intergenic (‑64/+53)	yagN/intF	protein YagN/putative phage integrase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (4/8);  total (4/8)

ATGCGACAGACTTGCGAAGAGCTGAGTATGTTCCTTTGAGATACTCGACAACCTCTTCCATGGACGCAGGATCGTTAAAGGATTGAGTTGTTTTACTTGAATTAATACACCAGCGAGCTCTGATAGCTGCCAGAGTGGGTTCTATGGATACAGTTGCTGGGGTTGCCATTGGCTTATCTCCTGTGTAGTTGCTGTATCATTGACTAAACTGTGTATTACGATACATGAAAATCTATCTTGATCAATAGTTGATGATATTTTGTAATATGTTGATTTTTAATGGAATCAACGCATATCAACGTTGTTTTTTATGGTAATACCTGCTTCATTTAAGATCCATGTCTCAATTTTCTCGTGCCATTTTCGTAACAGATCTAACGGACGACGGCGATAGTGTTTTTCGGCAAGAGCGCTGGGTTTGTGTCCCATAATTTGAGCAACAATACCAGTGGGAACTTCAAC  >  NC_000913/295411‑295872                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                      aTGCGACAGACTTGCGAAGAGCTGAGTATGTTCCTTTGAGATACTCGACAACCTCTTCCATGGACGCAGGATCGTTAAAGGATTGAGTTGTTTTACTTGAATTAATACACCAGCGAGCTCTGATAGCTGCCAGAGTGGGTTCTATGGATACAGTTGCTGGGGTTTCCATTGGCGTATCTCCGGTGTAGTTGCTGTATCAGTGACTAAACTGTGGAATACGATACATGAAAATTTAGCTTGATCAATAGTtg                                                                                                                                                                                                                     <  1:66286/251‑1 (MQ=255)                                                                      gATCGTTAAAGGATTGAGTTGTTTTACTTGAATTAATACACCAGCGAGCTCTGATAGCTGCCAGAGTGGGTTCTATGGATACAGTTGCTGGGGTTGCCATTGGCTTATCTCCTGTGTAGTTGCTGTATCATTGACTAAACTGTGTATTACGATACATGAAAATTTATCTTGATCAATAGTTGATGATATTTTGTAATATGTTGATTTTTAATGGAATCAACGCATATCAACGTTGTTTTTTATGGTAATAc                                                                                                                                                >  1:52021/1‑251 (MQ=255)                                                                                                                                         gngTTCTATGGATACAGTTGCTGGGGTTGCCATTGGCTTATCTCCTGTGTAGTTGCTGTATCATTGACTAAACTGTGTATTACGATACATGAAAATTTATCTTGATCAATAGTTGATGATATTTTGTAATATGTTGATTTTTAATGGAATCAACGCATATCAACGTTGTTTTTTATGGTAATACCTGCTTCATTTAAGATCCATGTCTCAATTTTCTCGTGCCATTTTCGTAACAGATCTAACGGacgacg                                                                             >  1:132068/1‑251 (MQ=255)                                                                                                                                                    aTACAGTTGCTGGGGTTGCCATTGGCTTATCTCCTGTGTAGGTGCTGTATCATTGACTAAACTGTGTATTACGATACATGAAAATTTATCTTg                                                                                                                                                                                                                                <  1:94085/93‑1 (MQ=255)                                                                                                                                                        aGTTGCTGGGGTTGCCATTGGCTTATCTCCTGTGTAGTTGCTGTATCATTGACTAAACTGTGTATTACGATACATGAAAATTTATCTTGATCAATAGTTGATGATATTTTGTAATATGTTGATTTTTAATGGAATCAACGCATATCAACGTTGTTTTTTATGGTAATACCTGCTTCATTTAAGATCCATGTCTCAATTTTCTCGTGCCATTTTCGTAACAGATCTAACGGACGACGGCGATAGTGTTTTTc                                                              <  1:158879/251‑1 (MQ=255)                                                                                                                                                                      ccATTGGCTTATCTCCTGTGTAGTTGCTGTATCATTGACTAAACTGTGTATTCCGATACATGAAAATTTATCTTGATCAATAGTTGATGATATTTTGTAATATGTTGATTTTTAATGGAATCAACGCATATCGNCGTNNnnntt                                                                                                                                                           >  2:101334/1‑144 (MQ=255)                                                                                                                                                                      ccATTGGCTTATCTCCTGTGTAGTTGCTGTATCATTGACTAAACTGTGTATTACGATACATGAAAATTTATCTTGATCAATAGTTGATGATAGTTTGTAATATGTTGAGTTTTAATGGAATCAACGCATATCGACGTTGTTTTTTATGGTAAGACCTGCTTCATGTAAGATCCATGTCTCAATTTTCTCGTGCCATTTTCGTAACAGATCTAACGGACGACGGCGATAGTGTTTTTCGGcn                                                          <  1:101334/241‑2 (MQ=255)                                                                                                                                                                           ggCTTATCTCCTGTGTAGTTGCTGTATCATTGACTAAACTGTGTATTACGATACATGAAAATTTATCTTGATCAATAGTTGATGATATTTTGTAATATGTTGATTTTTAATGGAATCAACGCATATCAACGTTGGTTTTTATGGTAAGACCTGCTTCATTTAAGATCCATGTCTCAAGTGTCTCGTGCCATTTTCGTAACAGATCTAACGGACGACGGCGATAGTGTTTTTCGGCAAGAGCGCTGGGTTtg                                           <  1:111876/251‑1 (MQ=255)                                                                                                                                                                                              tgcttgaTCATTTACTAAACTGTGTATTACGATACATGAAAATTTATCTTGATCAATAGTTTATTATATTGTGTAATAGGTTGATTTTTAATGGACGCAGCGCATATCAACGTTGTTTTTTATGGTAATACCTGCTTCATTTAAGATCCATGTCTCAATTTTCTCGTGCCATGTTCGTAACAGATCTAACGGACGACTTCCATAGTGTTTCTCGGCAAGAGCGCTGGGTTTGTGTCCCATAATTTGAGca                         <  1:107653/244‑1 (MQ=255)                                                                                                                                                                                                            ntataCTGTGTATTACGATACATGAAAATTTATATTGATCAATAGTTGATGATATTTTGTAATATGTTGATTTTTAATGGAGTCAACGCATATCAACGTTGTTTTTTATGGTAATACCTGCTTCATTTAAGATCCATGTCTCAATTTTCTCGTGCCATTTTCGTAACAGATCTAACGGACGACGGCGATAGTGTTTTTCGGCAAGAGCGCTGGGTTTGTGTCCCATAATTTg                             >  1:15344/5‑232 (MQ=255)                                                                                                                                                                                                                     gtATTACGATACATGAAAATTTATCTTGATCAATAGTTGATGATATTTTGTAATATGTTGATTTTTAATGGAATCAACGCATATCAACGTTGTTTTTTATGGTAATACCTGCTTCATTTAAGATCCATGTCTCAATTTTCTCGTGCCATTTTCGTAACAGATCTAACGGACGACGGCGATAGTGTTTTTCGGCAAGAGCGCTGGGTTTGTGTCCCATAATTTGAGCAACAATACCAGTGGGAACTTCaan  <  1:48841/250‑2 (MQ=255)                                                                                                                                                                                                                                cATGAAAATTTATCTTGATCAATAGTTGATGATATTTTGTAATATGTTGATTTTTAATGGAATCAACGCATATCAACGTTGTTTTTTATGGTAATACCTGCTTCATTTAAGATCCAGGGCTCAATTTTCTCGTGCCATTTTCGTAACAGATCTAACGGACGACGGCGATAgtgt                                                                   <  1:68760/174‑1 (MQ=255)                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                      ATGCGACAGACTTGCGAAGAGCTGAGTATGTTCCTTTGAGATACTCGACAACCTCTTCCATGGACGCAGGATCGTTAAAGGATTGAGTTGTTTTACTTGAATTAATACACCAGCGAGCTCTGATAGCTGCCAGAGTGGGTTCTATGGATACAGTTGCTGGGGTTGCCATTGGCTTATCTCCTGTGTAGTTGCTGTATCATTGACTAAACTGTGTATTACGATACATGAAAATCTATCTTGATCAATAGTTGATGATATTTTGTAATATGTTGATTTTTAATGGAATCAACGCATATCAACGTTGTTTTTTATGGTAATACCTGCTTCATTTAAGATCCATGTCTCAATTTTCTCGTGCCATTTTCGTAACAGATCTAACGGACGACGGCGATAGTGTTTTTCGGCAAGAGCGCTGGGTTTGTGTCCCATAATTTGAGCAACAATACCAGTGGGAACTTCAAC  >  NC_000913/295411‑295872

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑