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%	225.6 / NA	55	coding (1029/1644 nt)	flgK	flagellar hook‑filament junction protein 1
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (23/32);  total (23/32)

CTGGCGCTGGCATTTGCCGAGGCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGGTGACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGCCTTGCCAGCAATACCACTTTTAC  >  NC_000913/1139278‑1139525                                                                                                                                 |                                                                                                                        cTGGCGCTGGCATTTGCCGAGGCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGAt                                                                                                              >  2:1402141/1‑139 (MQ=255)            aTTTGCCGAGGCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACgg                                                                                                   <  2:34838/139‑1 (MQ=255)                  cGAGGCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTg                                                                                             <  2:339599/139‑1 (MQ=255)                      gCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGc                                                                                         <  1:1094842/139‑1 (MQ=255)                      gCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGc                                                                                         <  1:127613/139‑1 (MQ=255)                      gCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCCGGTAAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGc                                                                                         <  1:1842566/139‑1 (MQ=255)                         ttCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTc                                                                                      <  2:1721877/139‑1 (MQ=255)                           cAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCcg                                                                                    <  1:1548148/139‑1 (MQ=255)                               acCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGt                                                                                <  2:1951785/139‑1 (MQ=255)                                          aGCCGGATTTGATGCTAACGACGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAg                                                                     >  1:1208183/1‑139 (MQ=255)                                               gATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGcc                                                                                                       <  2:267542/100‑1 (MQ=255)                                               gATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGcc                                                                                                       >  1:267542/1‑100 (MQ=255)                                               gATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTAc                                                                >  2:61657/1‑139 (MQ=255)                                               gATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTAc                                                                >  2:447283/1‑139 (MQ=255)                                                aTTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAATACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACa                                                               <  1:1402141/139‑1 (MQ=255)                                                        cTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCg                                                       <  1:61657/139‑1 (MQ=255)                                                        cTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCg                                                       <  1:447283/139‑1 (MQ=255)                                                          aaCGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGtt                                                     <  2:1554622/139‑1 (MQ=255)                                                          aaCGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGtt                                                     >  1:1461098/1‑139 (MQ=255)                                                               cGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCGGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGa                                                                        <  2:9135/115‑1 (MQ=255)                                                               cGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCGGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGa                                                                        >  1:9135/1‑115 (MQ=255)                                                                gATGCCGGTGAAGATTTCTTTACTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGataa                                               <  2:1208183/139‑1 (MQ=255)                                                                  tGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGt                                                                                                          >  1:684255/1‑78 (MQ=255)                                                                  tGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGt                                                                                                          <  2:684255/78‑1 (MQ=255)                                                                    ccGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATaataat                                           <  2:1461098/139‑1 (MQ=255)                                                                    ccGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATaataat                                           <  2:1199644/139‑1 (MQ=255)                                                                                 cTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCTGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCa                              <  1:614068/139‑1 (MQ=255)                                                                                        aTCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCcg                                                                                    >  1:1741421/1‑78 (MQ=255)                                                                                        aTCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCcg                                                                                    <  2:1741421/78‑1 (MQ=255)                                                                                         tCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGa                                                                        <  1:1703855/89‑1 (MQ=255)                                                                                         tCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGa                                                                        >  2:1703855/1‑89 (MQ=255)                                                                                           ggTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGAt                                                                                           <  1:2030579/68‑1 (MQ=255)                                                                                           ggTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGAt                                                                                           >  2:2030579/1‑68 (MQ=255)                                                                                                 cccGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAg                                                                     <  1:330164/84‑1 (MQ=255)                                                                                                 cccGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAg                                                                     >  2:330164/1‑84 (MQ=255)                                                                                                 cccGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAAtc                                                          >  2:1104601/1‑95 (MQ=255)                                                                                                 cccGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAAtc                                                          <  1:1104601/95‑1 (MQ=255)                                                                                                   cgcgGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCAccc                           >  1:1021854/1‑124 (MQ=255)                                                                                                   cgcgGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCAccc                           <  2:1021854/124‑1 (MQ=255)                                                                                                     cgGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGAtaataa                                            >  2:1102866/1‑105 (MQ=255)                                                                                                     cgGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGAtaataa                                            <  1:1102866/105‑1 (MQ=255)                                                                                                      ggTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGCCTTGCCAGCAATACCa         >  2:634967/1‑139 (MQ=255)                                                                                                           tGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGtt                                                     <  1:1704313/90‑1 (MQ=255)                                                                                                           tGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGtt                                                     >  2:1704313/1‑90 (MQ=255)                                                                                                             cAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGCCTTGCCAGCAATACCACTTTTAc  >  2:469968/1‑139 (MQ=255)                                                                                                                  cacGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGTTAACTGATGCCTCCGCGGTACTGGCGACa                                                                      <  2:1372629/66‑1 (MQ=255)                                                                                                                  cacGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCcgcg                                                                                  <  1:3302/54‑1 (MQ=255)                                                                                                                  cacGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCcgcg                                                                                  >  2:3302/1‑54 (MQ=255)                                                                                                                  cacGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGataata                                             >  2:1027053/1‑91 (MQ=255)                                                                                                                  cacGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGataata                                             <  1:1027053/91‑1 (MQ=255)                                                                                                                  cacGAAAAACAAAGG‑AACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACa                                                                      >  1:1372629/1‑66 (MQ=255)                                                                                                                       aaaaCAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGa                                                                        <  2:1063453/59‑1 (MQ=255)                                                                                                                       aaaaCAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGa                                                                        >  1:1063453/1‑59 (MQ=255)                                                                                                                       aaaaCAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCa                                   <  2:145681/96‑1 (MQ=255)                                                                                                                       aaaaCAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCa                                   >  1:145681/1‑96 (MQ=255)                                                                                                                                 |                                                                                                                        CTGGCGCTGGCATTTGCCGAGGCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGGTGACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGCCTTGCCAGCAATACCACTTTTAC  >  NC_000913/1139278‑1139525

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑