Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,139,406	Δ1 bp	coding (1029/1644 nt)	flgK →	flagellar hook‑filament junction protein 1

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,139,406	0	T	.	100.0%	53.5 / NA	14	coding (1029/1644 nt)	flgK	flagellar hook‑filament junction protein 1
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (6/8);  total (6/8)

CTGGCATTTGCCGAGGCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGGTGACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGCCTTGCCAGCAATACCACTTTTACGGTGACGCCGG  >  NC_000913/1139284‑1139536                                                                                                                           |                                                                                                                                   cTGGCATTTGCCGAGGCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGc                                                                                                                   >  2:793957/1‑139 (MQ=255)   ggCATTTGCCGAGGCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCa                                                                                                                 >  2:1078764/1‑139 (MQ=255)                                         gATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACATTGCGAt                                                                                                                         <  1:924862/93‑1 (MQ=255)                                         gATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACATTGCGAt                                                                                                                         >  2:924862/1‑93 (MQ=255)                                         gATTTGATGCTAACGGCGATGACGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTAc                                                                           <  2:801702/139‑1 (MQ=255)                                          aTTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACa                                                                          <  1:566575/139‑1 (MQ=255)                                                         cGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGtt                                                                >  1:1099680/1‑134 (MQ=255)                                                         cGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGtt                                                                <  2:1099680/134‑1 (MQ=255)                                                                           cTTTGCTATAGGTAAGCCCGCGGGTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGGTCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGAGTACGAAATCTCGTTCGATAATAATCAGTGGCAGTTCa                                         <  2:484579/139‑1 (MQ=255)                                                                                  aTCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCcg                                                                                               <  1:757873/78‑1 (MQ=255)                                                                                  aTCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCcg                                                                                               >  2:757873/1‑78 (MQ=255)                                                                                             cgcgGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGc                                                                                                    <  1:1188103/62‑1 (MQ=255)                                                                                             cgcgGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGc                                                                                                    >  2:1188103/1‑62 (MQ=255)                                                                                                                  aaaCAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGCCTTGCCAGCAATACCACTTTTACGGTGACGCCgg  <  1:793957/139‑1 (MQ=255)                                                                                                                           |                                                                                                                                   CTGGCATTTGCCGAGGCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGGTGACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGCCTTGCCAGCAATACCACTTTTACGGTGACGCCGG  >  NC_000913/1139284‑1139536

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑