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%	238.7 / NA	57	coding (1029/1644 nt)	flgK	flagellar hook‑filament junction protein 1
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (27/30);  total (27/30)

GGACAACTGGCGCTGGCATTTGCCGAGGCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGGTGACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGCCTTGCCAGCAATACCACTTTTACGGTGACGC  >  NC_000913/1139272‑1139533                                                                                                                                       |                                                                                                                                ggACAACTGGCGCTGGCATTTGCCGAGGCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGt                                                                                                                            >  2:591690/1‑139 (MQ=255)     aaCTGGCGCTGGCATTTGCCGAGGCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCg                                                                                                                        <  1:612866/139‑1 (MQ=255)       cTGGCGCTGGCATTTGCCGAGGCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGAt                                                                                                                      <  1:126637/139‑1 (MQ=255)        tGGCGCTGGCATTTGCCGAGGCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATc                                                                                                                     >  1:1305243/1‑139 (MQ=255)                          aGGCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGt                                                                                                                            >  1:1180338/1‑114 (MQ=255)                          aGGCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGt                                                                                                                            <  2:1180338/114‑1 (MQ=255)                                 cAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGc                                                                                                                >  2:1241931/1‑119 (MQ=255)                                 cAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGc                                                                                                                <  1:1241931/119‑1 (MQ=255)                                 cAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCcg                                                                                            <  1:1301035/139‑1 (MQ=255)                                      cccAACACAAAGCCGGATTTGATGCTAACGGCGATGCCAGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTa                                                                                       <  2:1178649/139‑1 (MQ=255)                                         aaCACAAAGCCGGATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGAt                                                                                                                      <  2:725320/105‑1 (MQ=255)                                         aaCACAAAGCCGGATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGAt                                                                                                                      >  1:725320/1‑105 (MQ=255)                                                     gATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTAc                                                                        >  2:941008/1‑139 (MQ=255)                                                                aaCGGGGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGtt                                                             <  1:1255392/139‑1 (MQ=255)                                                                aaCGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGtt                                                             <  1:591690/139‑1 (MQ=255)                                                                 aCGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTc                                                            >  2:338021/1‑139 (MQ=255)                                                                    gCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGat                                                         <  1:1199186/139‑1 (MQ=255)                                                                       aTGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCcgcg                                                                                          <  1:10972/103‑1 (MQ=255)                                                                       aTGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCcgcg                                                                                          >  2:10972/1‑103 (MQ=255)                                                                       aTGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGataat                                                      >  2:582762/1‑139 (MQ=255)                                                                        tGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGa                                                                                                    >  1:696896/1‑92 (MQ=255)                                                                        tGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGa                                                                                                    <  2:696896/92‑1 (MQ=255)                                                                        tGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACa                                                                              >  2:333898/1‑114 (MQ=255)                                                                        tGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACa                                                                              <  1:333898/114‑1 (MQ=255)                                                                                     ttCTTTGCTATCGGTAAGTCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGGAGGt                                        >  1:943409/1‑139 (MQ=255)                                                                                       cTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCa                                      <  1:338021/139‑1 (MQ=255)                                                                                          tGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCg                                                               <  1:1084683/111‑1 (MQ=255)                                                                                          tGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCg                                                               >  2:1084683/1‑111 (MQ=255)                                                                                          tGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGa                                                          <  1:781734/116‑1 (MQ=255)                                                                                          tGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGa                                                          >  2:781734/1‑116 (MQ=255)                                                                                             tATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGc                                                                                                                <  1:568676/59‑1 (MQ=255)                                                                                             tATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGc                                                                                                                >  2:568676/1‑59 (MQ=255)                                                                                                 ggTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGc                                                                                                                <  2:549197/55‑1 (MQ=255)                                                                                                 ggTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGc                                                                                                                >  1:549197/1‑55 (MQ=255)                                                                                                  gTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGCCTTGcc                           <  1:319351/139‑1 (MQ=255)                                                                                                    aaGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATaataat                                                   <  2:1206638/113‑1 (MQ=255)                                                                                                    aaGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATaataat                                                   >  1:1206638/1‑113 (MQ=255)                                                                                                    aaGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCTGGTCACCCGCCTTGCCAg                         <  1:941008/139‑1 (MQ=255)                                                                                                       cccGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGCCTTGc                            <  2:1199260/133‑1 (MQ=255)                                                                                                       cccGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGCCTTGc                            >  1:1199260/1‑133 (MQ=255)                                                                                                        ccGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGTCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGCCTTGCCAGCAAt                     <  2:1305243/139‑1 (MQ=255)                                                                                                         cgcgGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCg                                                               >  1:321075/1‑96 (MQ=255)                                                                                                         cgcgGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCg                                                               <  2:321075/96‑1 (MQ=255)                                                                                                         cgcgGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGCCTTGCCAGCAATa                    >  2:256368/1‑139 (MQ=255)                                                                                                           cgGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGa                                                                                <  2:1399720/77‑1 (MQ=255)                                                                                                           cgGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGa                                                                                >  1:1399720/1‑77 (MQ=255)                                                                                                           cgGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGtt                                                             >  1:419134/1‑96 (MQ=255)                                                                                                           cgGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGtt                                                             <  2:419134/96‑1 (MQ=255)                                                                                                                        cacGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGAtaataa                                                    <  2:1128474/92‑1 (MQ=255)                                                                                                                        cacGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGAtaataa                                                    >  1:1128474/1‑92 (MQ=255)                                                                                                                        cacGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGt                                               <  2:676423/97‑1 (MQ=255)                                                                                                                        cacGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGt                                               >  1:676423/1‑97 (MQ=255)                                                                                                                        cacGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGCCTTGCCAGc                        >  1:1182353/1‑120 (MQ=255)                                                                                                                        cacGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGCCTTGCCAGc                        <  2:1182353/120‑1 (MQ=255)                                                                                                                           gAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGCCTTGCCAGCAATACCACTTTTACGGTGACGc  >  1:541091/1‑139 (MQ=255)                                                                                                                             aaaaCAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATaataat                                                   >  1:221362/1‑88 (MQ=255)                                                                                                                             aaaaCAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATaataat                                                   <  2:221362/88‑1 (MQ=255)                                                                                                                                       |                                                                                                                                GGACAACTGGCGCTGGCATTTGCCGAGGCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGGTGACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGCCTTGCCAGCAATACCACTTTTACGGTGACGC  >  NC_000913/1139272‑1139533

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑