Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,970,038	T→G	9.8%	T84P (ACT→CCT)	fliC ←	flagellin

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,970,038	0	T	G	9.8%	105.2 / 4.7	41	T84P (ACT→CCT)	fliC	flagellin
Reads supporting (aligned to +/- strand):  ref base T (18/19);  new base G (2/2);  total (20/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.76e-01

ACCGAAAGTGGTGGTGTTAGCAATACGGGTGAGCTCGCCCGACAGCGCGGTAAACTCCTGCTGCATGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCACGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCTGCGGCGTCGTCTTTGGCACTGTTGATTTTCAGGC  >  NC_002947/4969889‑4970184                                                                                                                                                      |                                                                                                                                                   aCCGAAAGTGGTGGTGTTAGCAATACGGGTGAGCTCGCCCGACAGCGCGGTAAACTCCTGCTGCATGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCACGCATACGCTGCATGATGTTGCCTGAAGt                                                                                                                                                    >  2:966230/1‑150 (MQ=255)   cGAAAGTGGTGGTGTTAGCAATACGGGTGAGCTCGCCCGACAGCGCGGTAAACTCCTGCTGCATGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCACGCATACGCTGCATGATGTTGCCTGAAGTCg                                                                                                                                                  <  1:905122/150‑1 (MQ=255)          ggtggtgTTAGCAATACGGGTGAGCTCGCCCGACAGCGCGGTAAACTCCTGCTGCATGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCACGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGgc                                                                                                                                           <  1:946623/150‑1 (MQ=255)            tggtgTTAGCAATACGGGTGAGCTCGCCCGACAGCGCGGTAAACTCCTGCTGCATGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCACGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGgcgc                                                                                                                                         <  1:1154940/150‑1 (MQ=255)                 ttAGCAATACGGGTGAGCTCGCCCGACAGCGCGGTAAACTCCTGCTGCATGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCACGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTca                                                                                                                                    >  1:413151/1‑150 (MQ=255)                  tAGCAATACGGGTGAGCTCGCCCGACAGCGCGGTAAACTCCTGCTGCATGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCACGCATACGCTGCATGATGTTGCCTGAAGGCGCCATGGCGACTTcag                                                                                                                                   <  2:934753/150‑1 (MQ=255)                   aGCAATACGGGTGAGCTCGCCCGACAGCGCGGTAAACTCCTGCTGCATGGAGGCGGGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCACGCATACGCTGCATGATGTTGCCTGAAGGCGCCATGGCGACTTcagg                                                                                                                                  <  1:127185/150‑2 (MQ=255)                    gCAATACGGGTGAGCTCGCCCGACAGCGCGGTAAACTCCTGCTGCATGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCACGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTcagca                                                                                                                                 <  1:600549/150‑1 (MQ=255)                                  cTCGCCCGACAGCGCGGTAAACTCCTGCTGCATGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCACGCATACGCTGCATGATGTTGCCTGAAGTCGCAATGgc                                                                                                                                           >  2:858828/1‑126 (MQ=255)                                  cTCGCCCGACAGCGCGGTAAACTCCTGCTGCATGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCACGCATACGCTGCATGATGTTGCCTGAAGTCGCAATGgc                                                                                                                                           <  1:858828/126‑1 (MQ=255)                                   tCGCCCGACAGCGCGGTAAACTCCTGCTGCATGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCACGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATagag                                                                                                                  >  1:1200816/1‑150 (MQ=255)                                               gcgGTAAACTCCTGCTGCATGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCACGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTg                                                                                                      <  1:966230/150‑1 (MQ=255)                                                       cTCCTGCTGCATGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCACGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCtt                                                                                              >  2:706725/1‑150 (MQ=255)                                                                cATGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCACGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCaa                                                                                                                       <  2:1179648/116‑1 (MQ=255)                                                                cATGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCACGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCaa                                                                                                                       >  1:1179648/1‑116 (MQ=255)                                                                 aTGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCACGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTgcg                                                                                                                          <  1:206480/112‑1 (MQ=255)                                                                 aTGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCACGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTgcg                                                                                                                          >  2:206480/1‑112 (MQ=255)                                                                  tGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCACGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGttt                                                                                                                             <  2:618936/108‑1 (MQ=255)                                                                  tGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCACGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGttt                                                                                                                             >  1:618936/1‑108 (MQ=255)                                                                   ggAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCACGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCt                                                                                  >  1:174779/1‑150 (MQ=255)                                                                                   tCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCACGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCtttgatttga                                                                  <  1:1062860/150‑1 (MQ=255)                                                                                   tCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCACGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCtttgatttga                                                                  <  2:1200816/150‑1 (MQ=255)                                                                                       tGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCACGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTgg                                                              >  1:534655/1‑150 (MQ=255)                                                                                             aGCCGTTCGCCGATTGCAGGGCCAGTTCACGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGAc                                                        <  2:534655/150‑1 (MQ=255)                                                                                              gCCGTTCGCCGATTGCAGGGCCAGTTCACGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACg                                                       >  2:931651/1‑150 (MQ=255)                                                                                               ccGTTCGCCGATTGCAGGGCCAGTTCACGCATACGCTGCATGATGTTGCCTAAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCtttgatttga                                                                  >  2:1205050/1‑138 (MQ=255)                                                                                               ccGTTCGCCGATTGCAGGGCCAGTTCACGCATACGCTGCATGATGTTGCCTAAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCtttgattcga                                                                  <  1:1205050/138‑1 (MQ=255)                                                                                                        gATTGCAGGGCCAGTTCACGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATc                                             >  2:768760/1‑150 (MQ=255)                                                                                                                 gCCAGTTCACGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCt                                    <  2:228398/150‑1 (MQ=255)                                                                                                                  ccAGTTCACGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCTg                                   >  1:494709/1‑150 (MQ=255)                                                                                                                         aCGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCTGCGGcgtc                            <  2:413151/150‑1 (MQ=255)                                                                                                                               aCGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGttt                                                                                                                             <  2:957689/47‑1 (MQ=255)                                                                                                                               aCGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGttt                                                                                                                             >  1:957689/1‑47 (MQ=255)                                                                                                                                 gCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCTGCGGCGTCGTCTTTgg                    >  2:252722/1‑150 (MQ=255)                                                                                                                                      atgatgTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCTGCGGCGTCGTCTTTGGCACTg               >  2:1132529/1‑150 (MQ=255)                                                                                                                                              tgcTGAAGGCGCCATGGCGACTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCTGCGGCGTCGTCTTTGGCACTGTTGAtttt       >  2:779004/3‑150 (MQ=255)                                                                                                                                               tgcgatctCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATCCCCTCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCTGCGGCGTCGTCTTTGGCACTGTTGATTTTc      <  2:337779/143‑1 (MQ=255)                                                                                                                                                cTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCTGCGGCGTCGTCTTTGGCACTGTTGATTTTCa     <  2:494709/150‑1 (MQ=255)                                                                                                                                                cTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCTGCGGCGTCGTCTTTGGCACTGTTGATTTTCa     >  1:1175960/1‑150 (MQ=255)                                                                                                                                                 tGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCtt                                                                          <  2:98350/80‑1 (MQ=255)                                                                                                                                                 tGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCtt                                                                          >  1:98350/1‑80 (MQ=255)                                                                                                                                                 tGAAGGCGCCATGGCGACTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCTGCGGCGTCGTCTTTGGCACTGTTGATTTTCAg    >  1:1164619/1‑150 (MQ=255)                                                                                                                                                   aaGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCTGCGGCGTCGTCTTTGGCACTGTTGATTTTCAGGc  <  1:931651/150‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                   ACCGAAAGTGGTGGTGTTAGCAATACGGGTGAGCTCGCCCGACAGCGCGGTAAACTCCTGCTGCATGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCACGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCTGCGGCGTCGTCTTTGGCACTGTTGATTTTCAGGC  >  NC_002947/4969889‑4970184

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑