Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,165,419:1	+A	9.4%	coding (2509/3906 nt)	hrpA ←	ATP‑dependent helicase HrpA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,165,419	1	.	A	9.4%	187.4 / 15.5	53	coding (2509/3906 nt)	hrpA	ATP‑dependent helicase HrpA
Reads supporting (aligned to +/- strand):  ref base . (22/26);  new base A (3/2);  total (25/28)
Fisher's exact test for biased strand distribution p-value = 6.58e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.78e-01

GGCAACAGCGGTGCCGGCACCCGCACCGTCACACCATCACGGGGGTGGCCGGGCTCGAAGTGGTAGCTCAGCGGCAGGCGCAGATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTGGCGTCCTTTTGGCTGCCCATGCGGTACCAACTATCAAAGGTCGCCGTCTGGTGGATTTCCGCCGGCAGGCGCGCTTCATAGAAAGCGTACAGCGTTTCTTCGTCAGCCAGGA  >  NC_002947/5165280‑5165568                                                                                                                                              |                                                                                                                                                      ggCAACAGCGGTGCCGGCACCCGCACCGTCACACCATCACGGGGGTGGCCGGGCTCGAAGTGGTAGCTCAGCGGCAGGCGCAGATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCC‑CGCGAGGCCAGcgaa                                                                                                                                             <  2:10587/150‑4 (MQ=255)  gCAACAGCGGTGCCGGCACCCGCACCGTCACACCATCACGGGGGTGGCCGGGCTCGAAGTGGTAGCTCAGCGGCAGGCGCAGATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGt                                                                                                                                            >  2:1400966/1‑150 (MQ=255)   cAACAGCGGTGCCGGCACCCGCACCGTCACACCATCACGGGGGTGGCCGGGCTCGAAGTGGTAGCTCAGCGGCAGGCGCAGATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGtc                                                                                                                                           >  1:282952/1‑150 (MQ=255)   cAACAGCGGTGCCGGCACCCGCACCGTCACACCATCACGGGGGTGGCCGGGCTCGAAGTGGTAGCTCAGCGGCAGGCGCAGATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCCACCCCCGCG‑CTCGAGCACGtc                                                                                                                                           >  2:748162/1‑150 (MQ=255)    aaCAGCGGTGCCGGCACCCGCACCGTCACACCATCACGGGGGTGGCCGGGCTCGAAGTGGTAGCTCAGCGGCAGGCGCAGATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CAGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGtcc                                                                                                                                          <  2:217154/150‑1 (MQ=255)           gTGCCGGCACCCGCACCGTCACACCATCACGGGGGTGGCCGGGCTCGAAGTGGTAGCTCAGCGGCAGGCGCAGATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTcgc                                                                                                                                   <  1:982581/150‑1 (MQ=255)               cGGCACCCGCACCGTCACACCATCACGGGGGTGGCCGCGCTCGAAGTGGTAGCTCAGCGGCAGGCGCAGATCGCCCACCTGCATACTGTCGGGGTACTGTCCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCAt                                                                                                                               <  2:123041/150‑1 (MQ=255)                     ccGCACCGTCACACCATCACGGGGGTGGCCGGGCTCGAAGTGGTAGCTCAGCGGCAGGCGCAGATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATcag                                                                                                                         >  2:1417480/1‑150 (MQ=255)                      ctcACCGTCACACCATCACGGGGGTGGCCGGGCTCGAAGTTGTCGCTCAGCTGCAGTCGCAGATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCATCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATcagc                                                                                                                        <  2:1156385/148‑1 (MQ=255)                         aCCGTCACACCATCACGGGGGTGGCCGGGCTCGAAGTGGTAGCTCAGCGGCAGGCGCAGATCGCCCACCTGCATACTGTCGGGGTACTGTGCGGAAGAGCAC‑ACGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATcagcaag                                                                                                                     >  1:1156385/1‑148 (MQ=255)                         aCCGTCACACCATCACGGGGGTGGCCGGGCTCGAAGTGGTAGCTCAGCGGCAGGCGCAGATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAgg                                                                                                                     <  1:1400966/150‑1 (MQ=255)                         aCCGTCACACCATCACGGGGGTGGCCGGGCTCGAAGTGGTAGCTCAGCGGCAGGCGCAGATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCC‑CGCGAGGCCAGcgaa                                                                                                                                             <  1:966529/126‑4 (MQ=255)                         aCCGTCACACCATCACGGGGGTGGCCGGGCTCGAAGTGGTAGCTCAGCGGCAGGCGCAGATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCC‑CGCGAGGCCAGcgaa                                                                                                                                             >  2:966529/1‑123 (MQ=255)                            gTCACACCATCACGGGGGTGGCCGGGCTCGAAGTGGTAGCTCAGCGGCAGGCGCAGATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTg                                                                                                                  <  2:663865/150‑1 (MQ=255)                               acacCATCAGGGGGGTGGCCGGGCTCGAAGTGGTAGCTCAGCGGCAGGCGCAGATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGtc                                                                                                                                           <  2:284753/122‑1 (MQ=255)                               acacCATCACGGGGGTGGCCGGGCTCGAAGTGGTAGCTCAGCGGCAGGCGCAGATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGtc                                                                                                                                           >  1:284753/1‑122 (MQ=255)                               acacCATCACGGGGGTGGCCGGGCTCGAAGTGGTAGCTCAGCGGCAGGCGCAGATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTGGCg                                                                                                               <  1:979615/150‑1 (MQ=255)                                 acCATCACGGGGGTGGCCGGGCTCGAAGTGGTAGCTCAGCGGCAGGCGCAGATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTGGCGTc                                                                                                             >  2:934253/1‑150 (MQ=255)                                   cATCACGGGGGTGGCCGGGCTCGAAGTGGTAGCTCAGCGGCAGGCGCAGATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTGGCGTCCt                                                                                                           <  1:1059491/150‑1 (MQ=255)                                      cACGGGGGTGGCCGGGCTCGAAGTGGTAGCTCAGCGGCAGGCGCAGATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTGGCGTCCtttt                                                                                                        <  1:376335/150‑1 (MQ=255)                                       aCGGGGGTGGCCGGGCTCGAAGTGGTAGCTCAGCGGCAGGCGCAGATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTGGCGTCCTTTTg                                                                                                       >  2:1346482/1‑150 (MQ=255)                                                         gAAGTGGTAGCTCAGCGGCAGGCGCAGATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTGGCGTCCTTTTGGCTGCCCATGCGGTACCa                                                                                     >  2:968519/1‑150 (MQ=255)                                                                tAGCTCAGCGGCAGGCGCAGATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTGGCGTCCTTTTGGCTGCCCATGCGGTACCAACTATCa                                                                              <  1:897258/150‑1 (MQ=255)                                                                      aGCGGCAGGCGCAGATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTGGCGTCCTTTTGGCTGCCCATGCGGTACCAACTATCAAAGGTc                                                                        <  1:1305129/150‑1 (MQ=255)                                                                         ggCAGGCGCAGATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTGGCGTCCTTTTGGCTGCCCATGCGGTACCAACTATCAAAGGTCGcc                                                                     <  1:1346482/150‑1 (MQ=255)                                                                          gCAGGCGCAGATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTGGCGTCCTTTTGGCTGCCCATGCGGTACCAACTATCAAAGGTCGCCg                                                                    <  1:1417480/150‑1 (MQ=255)                                                                            aGGCGCAGATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTGGCGTCCTTTTGGCTGCCCATGCGGTACCAACTATCAAAGGTCGCCGTc                                                                  >  1:120296/1‑150 (MQ=255)                                                                                gcAGATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGc                                                                                                                                                >  1:755939/1‑68 (MQ=255)                                                                                gcAGATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGc                                                                                                                                                <  2:755939/68‑1 (MQ=255)                                                                                gcAGATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGACAGCACGTCCTCCTCGCGCCTGATAAGCAGGTTGGCGTCCTTTTGGCTTCCCATGCGGTACCAACTATCAAAGGTCGCCGTCtggt                                                              <  2:873560/150‑1 (MQ=255)                                                                                gcAGATCCCCCACCTGTAGACTGTCGGTGTACTGAGCGG‑CGGTCACTGCGCTGGCCTCGCG‑GTCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTTGCGTCCTTTTGGCTGCCCATGCGGTACCAACTATCAAAGGTCGCCGTCtggt                                                              <  2:629663/150‑1 (MQ=255)                                                                                 cAGATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTGGCGTCTTTTTGGCTGCCCATGCGGTACCAACTATCAAAGGTCGCCGTCtggtg                                                             <  1:968519/150‑1 (MQ=255)                                                                                   gATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGt                                                                                                                    >  1:567771/1‑93 (MQ=255)                                                                                   gATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGt                                                                                                                    <  2:567771/93‑1 (MQ=255)                                                                                         ccACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTGGCGTCCTTTTGGCTGCCCATGCGGTACCAACTATCAAAGGTCGcc                                                                     <  1:474756/134‑1 (MQ=255)                                                                                         ccACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTGGCGTCCTTTTGGCTGCCCATGCGGTACCAACTATCAAAGGTCGcc                                                                     >  2:474756/1‑134 (MQ=255)                                                                                          cACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTGGCGTCCTTTTGGCTGCCCATGCGGTACCAACTATCAAAGGTCGCCGTCTGGTGGATTTccgc                                                    <  1:618590/150‑1 (MQ=255)                                                                                           aCCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACGTCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTGGCGTCCTTTTGGCTGCCCATGCGGTACCAACTATCAAAGGTCGCCGTCTGGTGGATTTccgcc                                                   >  1:824948/1‑150 (MQ=255)                                                                                                 aTACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCCGGTTGGCGTCCTTTTGGCTGCCCATGCGGTACCAACTATCAAAGGTCGCCGTCTGGTGGATTTCCGCCGGCAgg                                             >  2:657000/1‑150 (MQ=255)                                                                                                  tACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTGGCGTCCTTTTGGCTGCCCATGCGGTACCAACTATCAAAGGTCGCCGTCTGGTGGATTTCCGCCGGCAGgc                                            >  1:782166/1‑150 (MQ=255)                                                                                                     tGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTGGCGTCCTTTTGGCTGCCCATGCGGTACCaa                                                                                    <  1:561705/107‑1 (MQ=255)                                                                                                     tGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTGGCGTCCTTTTGGCTGCCCATGCGGTACCaa                                                                                    >  2:561705/1‑107 (MQ=255)                                                                                                     tGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTGGCGTCCTTTTGGCTGCCCATGCGGTACCAACTATCAAAGGTCGCCGTCTGGTGGATTTCCGCCGGCAGgcgcg                                         >  1:1031954/1‑150 (MQ=255)                                                                                                        cGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTGGCGTCCTTTTGGCTGCCCATGCGGTGCCATCTATCAAAGGTCGCCGTCTGGTGGATTTCCGCCGGCAGGCGCGCtt                                      <  1:748162/150‑1 (MQ=255)                                                                                                          gggTACTGTGCGG‑CGGTCACTTCGCTGGCCTTCAG‑CGTCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTGGCGTCCTTTTGGCTGCCCATGCGGTACCAACTATCAAAGGTCGCCGTCTGGTGGATTTCCGCCGGCAGGCGCGCTTCa                                    <  2:824948/150‑1 (MQ=255)                                                                                                                              cTTCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTGGCGTCCTTTTGGCTGCCCATGCGGTACGCACTATCAAAGGTCGCCGTCTGGTGGATTTCCGCCGGCAGGCGTGCTTCATAGAAAGCGTACAGCGttt                 >  1:1022468/1‑150 (MQ=255)                                                                                                                               ttCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTGGCGTCCTTTTGGCTGCCCATGCGGTACCAACTATCAAAGGTCGCCGTCTGGTGGATTTCCGCCGGCAGGCGCGCTTCATAGAAAGCGTACa                       >  2:1311323/1‑143 (MQ=255)                                                                                                                               ttCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTGGCGTCCTTTTGGCTGCCCATGCGGTACCAACTATCAAAGGTCGCCGTCTGGTGGATTTCCGCCGGCAGGCGCGCTTCATAGAAAGCGTACa                       <  1:1311323/143‑1 (MQ=255)                                                                                                                               ttCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTGGCGTCCTTTTGGCTGCCCATGCGGTACCAACTATCAAAGGTCGCCGTCTGGTGGATTTCCGCCGGCAGGCGCGCTTCATAGAAAGCGTACAGCGTttc                >  1:829699/1‑150 (MQ=255)                                                                                                                               ttCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTGGCGTCCTTTTGGCTGCCCATGCGGTACCAACTATCAAAGGTCGCCGTCTGGTGGATTTCCGCCGGCAGGCGCGCTTCATAGAAAGCGTACAGCGTttc                >  2:1382190/1‑150 (MQ=255)                                                                                                                               cgtgCTGGCC‑CGCGAGGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTGGCGTCCTTTTGGCTGCCCATGCGGTACCAACTATCAAAGGTCGCCGTCTGGTGGATTTCCGCCGGCAGGCGCGCTTCATAGAAAGCGTACAGCGTttc                >  1:794433/4‑150 (MQ=255)                                                                                                                                gtgCTGGCC‑CGCGAGGCCAGCACGTCGTCCTCGCGCATGATCAGCAGGTTGGCGTCCTTTTGGCTGCCAATGCGGTACCAACTGTCAAAGGTCGCCGTCTGGTGGATTTCCGCCGGCAGGCGCGTTTCATTAAAAGCGTACAGCGTttct               >  2:229757/3‑150 (MQ=255)                                                                                                                                  gCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTGGCGTCCTTTTGGCTGCCCATGCGGTACCAACTATCAAAGGTCGCCGTCTGGTGGATTTCCGCCGGCAGGCGCGCTTCATAGAAAGCGTACAGCGTttcttc             <  1:934253/150‑1 (MQ=255)                                                                                                                                             g‑ggCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTGGCGTCCTTTTGGCTGCCCATGCGGTACCAACTATCAAAGGTCGCCGTCTGGTGGATTTCCGCCGGCAGGCGCGCTTCATAGAAAGCGTACAGCGTTTCTTCGTCAGCCAGGa  >  1:170592/1‑150 (MQ=255)                                                                                                                                              |                                                                                                                                                      GGCAACAGCGGTGCCGGCACCCGCACCGTCACACCATCACGGGGGTGGCCGGGCTCGAAGTGGTAGCTCAGCGGCAGGCGCAGATCGCCCACCTGCATACTGTCGGGGTACTGTGCGG‑CGGTCACTTCGCTGGCCTCGCG‑GGCCAGCACGTCCTCCTCGCGCATGATCAGCAGGTTGGCGTCCTTTTGGCTGCCCATGCGGTACCAACTATCAAAGGTCGCCGTCTGGTGGATTTCCGCCGGCAGGCGCGCTTCATAGAAAGCGTACAGCGTTTCTTCGTCAGCCAGGA  >  NC_002947/5165280‑5165568

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑