Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	KT2440	4,970,678	G→A	8.5%	P346L (CCC→CTC)	flgI ←	Flagellar P‑ring protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	KT2440	4,970,678	0	G	A	8.5%	140.4 / 3.3	47	P346L (CCC→CTC)	flgI	Flagellar P‑ring protein
Reads supporting (aligned to +/- strand):  ref base G (22/21);  new base A (2/2);  total (24/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGGCGCCGCTGTCGGCACTACCGGATACCTGGCTTTTGATATTCATCCGCGCCGTCCTCAGATCACGATCAGGTCGGCCTGCAAGGCGCCGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAGCGTGGTGCCTGGGCCGAACTTGAACATCGGCTTGGCTTCCTGCTCGGCATTGACCCGCGAGCGTGGCACCACGGCAGTCTGGCCATTGGA  >  KT2440/4970548‑4970811                                                                                                                                   |                                                                                                                                      aGGCGCCGCTGTCGGCACTACCGGATACCTGGCTTTTGATATTCATCCGCGCCGTCCTCAGATCACGATCAGGTCGGCCTGCAAGGCGCCGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGgcgc                                                                                                                                   >  8:181608/1‑135 (MQ=255) aGGCGCCGCTGTCGGCACTACCGGATACCTGGCTTTTGATATTCATCCGCGCCGTCCTCAGATCACGATCAGGTCGGCCTGCAAGGCGCCGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGgcgc                                                                                                                                   >  7:202235/1‑135 (MQ=255) aGGCGCCGCTGTCGGCACTACCGGATACCTGGCTTTTGATATTCATCCGCGCCGTCCTCAGATCACGATCAGGTCGGCCTGCAAGGCGCCGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGgcgc                                                                                                                                   >  6:51866/1‑135 (MQ=255)   gcgcCGCTGTCGGCACTACCGGATACCTGGCTTTTGATATTCATCCGCGCCGTCCTCAGATCACGATCAGGTCGGCCTGCAAGGCGCCGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCt                                                                                                                                  <  4:220006/134‑1 (MQ=255)   gcgcCGCTGTCGGCACTACCGGATACCTGGCTTTTGATATTCATCCGCGCCGTCCTCAGATCACGATCAGGTCGGCCTGCAAGGCGCCGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCTg                                                                                                                                 <  6:14625/135‑1 (MQ=255)      ccgcTGTCGGCACTACCGGATACCTGGCTTTTGATATTCATCCGCGCCGTCCTCAGATCACGATCAGGTCGGCCTGCAAGGCGCCGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCTgcgc                                                                                                                              >  3:167296/1‑135 (MQ=255)           gTCGGCACTACCGGATACCTGGCTTTTGATATTCATCCGCGCCGTCCTCAGATCACGATCAGGTCGGCCTGCAAGGCGCCGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCAcc                                                                                                                         >  8:105519/1‑135 (MQ=255)           gTCGGCACTACCGGATACCTGGCTTTTGATATTCATCCGCGCCGTCCTCAGATCACGATCAGGTCGGCCTGCAAGGCGCCGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCAcc                                                                                                                         >  7:102866/1‑135 (MQ=255)                        gATACCTGGCTTTTGATATTCATCCGCGCCGTCCTCAGATCACGATCAGGTCGGCCTGCAAGGCGCCGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACcgcgc                                                                                                            <  3:86737/135‑1 (MQ=255)                             cTGGCTTTTGATATTCATCCGCGCCGTCCTCAGATCACGATCAGGTCGGCCTGCAAGGCGCCGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGAc                                                                                                        <  4:296773/134‑1 (MQ=255)                                gCTTTTGATATTCATCCGCGCCGTCCTCAGATCACGATCAGGTCGGCCTGCAAGGCGCCGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACcgcgc                                                                                                            >  1:221570/1‑127 (MQ=255)                                gCTTTTGATATTCATCCGCGCCGTCCTCAGATCACGATCAGGTCGGCCTGCAAGGCGCCGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACcgcgc                                                                                                            <  2:221570/127‑1 (MQ=255)                                gCTTTTGATATTCATCCGCGCCGTCCTCAGATCACGATCAGGTCGGCCTGCAAGGCGCCGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGACGAt                                                                                                     >  4:2130/1‑134 (MQ=255)                                  ttttGATATTCATCCGCGCCGTCCTCAGATCACGATCAGGTCGGCCTGCAAGGCGCCGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGACGAttt                                                                                                   >  5:218847/1‑134 (MQ=255)                                  ttttGATATTCATCCGCGCCGTCCTCAGATCACGATCAGGTCGGCCTGCAAGGCGCCGGCCTGTTTCAAGGCTTCGAGGAGCGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTc                                                                                                  <  7:132434/135‑1 (MQ=255)                                        tatTCATCCGCGCCGTCCTCAGATCACGATCAGGTCGGCCTGCAAGGCGCCGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAg                                                                                            <  8:131374/135‑1 (MQ=255)                                        tatTCATCCGCGCCGTCCTCAGATCACGATCAGGTCGGCCTGCAAGGCGCCGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAg                                                                                            <  6:218847/135‑1 (MQ=255)                                              tCCGCGCCGTCCTCAGATCACGATCAGGTCGGCCTGCAAGGCGCCGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAGCgtggt                                                                                      <  8:110281/135‑1 (MQ=255)                                                 gcgcCGTCCTCAGATCACGATCAGGTCGGCCTGCAAGGCGCCGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAGCGTGGTGcc                                                                                   >  8:15405/1‑135 (MQ=255)                                                   gcCGTCCTCAGATCACGATCAGGTCGGCCTGCAAGGCGCCGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAGCGTGGTGCCTg                                                                                 >  8:33130/1‑135 (MQ=255)                                                   gcCGTCCTCAGATCACGATCAGGTCGGCCTGCAAGGCGCCGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAGCGTGGTGCCTg                                                                                 <  3:117819/135‑1 (MQ=255)                                                     cGTCCTCAGATCACGATCAGGTCGGCCTGCAAGGCGCCGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGACGCTTTCATCCAGCGTGGTGCCTggg                                                                               >  4:12957/1‑135 (MQ=255)                                                     cGTCCTCAGATCACGATCAGGTCGGCCTGCAAGGCGCCGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGAGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAGCGTGGTGCCTggg                                                                               >  8:138697/1‑135 (MQ=255)                                                     cGTCCTCAGATCACGATCAGGTCGGCCTGCAAGGCGCCGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGAGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAGCGTGGTGCCTggg                                                                               >  8:135008/1‑135 (MQ=255)                                                                    aTCAGGTCGGCCTGCAAGGCGCCGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAGCGTGGTGCCTGGGCCGAACTTGAACATc                                                                >  7:104575/1‑135 (MQ=255)                                                                      cAGGTCGGCCTGCAAGGCGCCGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAGCGTGGTGCCTGGGCCGAACTTGAACATCgg                                                              >  8:178601/1‑135 (MQ=255)                                                                           cGGCCTGCAAGGCGCCGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAGCGTGGTGCCTGGGCCGAACTTGAACATCggcttgg                                                         >  3:236124/1‑135 (MQ=255)                                                                            ggCCTGCAAGGCGCCGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAGCGTGGTGCCTGGGCCGAACTTGAACATCggcttggc                                                        <  4:22693/135‑1 (MQ=255)                                                                                   aaGGCGCCGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAGCGTGGTGCCTGGGCCGAACTTGAACATCGGCTTGGCTTCCt                                                   <  3:236907/133‑1 (MQ=255)                                                                                   aaGGCGCCGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAGCGTGGTGCCTGGGCCGAACTTGAACATCGGCTTGGCTTCCt                                                   <  8:102866/133‑1 (MQ=255)                                                                                      gcgcCGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAGCGTGGTGCCTGGGCCGAACTTGAACATCGGCTTGGCTTCCTGCTCg                                              >  4:263232/1‑135 (MQ=255)                                                                                          cGGCCTGTTTCAAGGCTTCGAGGATCGCCTTCAGGTCGCCGGGCGCTGCGCCCCCCTGGTTCACCGCGCGGACGATTTCATCCAGCGTGGTGCCAGGGCCGAACTTGAACATCGGCTTGGCTTCCTGCTCGGCAt                                          >  3:50085/1‑135 (MQ=255)                                                                                          cGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAGCGTGGTGCCTGGGCCGAACTTGAACATCGGCTTGGCTTCCTGCTCGGCAt                                          >  1:249067/1‑135 (MQ=255)                                                                                               tGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAGCGTGGTGCCTGGGCCGAACTTGAACATCGGCTTGGCTTCCTGCTCGGCATTGAcc                                     >  2:217461/1‑135 (MQ=255)                                                                                               tGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAGCGTGGTGCCTGGGCCGAACTTGAACATCGGCTTGGCTTCCTGCTCGGCATTGAcc                                     <  2:264553/135‑1 (MQ=255)                                                                                                  ttCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAGCGTGGTGCCTGGGCCGAACTTGAACATCGGCGTGGCTTCCTGCTCGGCATTGACCcgc                                  <  1:52546/135‑1 (MQ=255)                                                                                                      aGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAGCGTGGTGCCTGGGCCGAACTTGAACATCGGCTTGGCTTCCTGCTCGTCATTGACCCGCGAg                               <  7:181608/134‑1 (MQ=255)                                                                                                      aGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAGCGTGGTGCCTGGGCCGAACTTGAACATCGGCTTGGCTTCCCGCTCGGCATTGACCCGCGAg                               <  3:2130/134‑1 (MQ=255)                                                                                                         cTTCGAGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAGCGTGGTGCCTGGGCCGAACTTGAACATCGGCTTGGCTTCCTGCTCGGCATTGACCCGCGAGCGTg                           >  2:100332/1‑135 (MQ=255)                                                                                                              aGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAGCGTGGTGCCTGGGCCGAACTTGAACATCGGCTTGGCTTCCTGCTCGGCATTGACCCGCGAGCGTGGcacc                      >  1:172138/1‑135 (MQ=255)                                                                                                              aGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAGCGTGGTGCCTGGGCCGAACTTGAACATCGGCTTGGCTTCCTGCTCGGCATTGACCCGCGAGCGTGGcacc                      >  8:173066/1‑135 (MQ=255)                                                                                                                   cGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAGCGTGGTGCCTGGGCCGAACTTGAACATCGGCTTGGCTTCCTGCTCGGCATTGACCCGCGAGCGTGGCACCACGGc                 <  7:173066/135‑1 (MQ=255)                                                                                                                     ccATCAGGTCGCCGAGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAGCGTGGTGCCTGGGCCGAACTTGAACATCGGCTTGGCTTCCTGCTCGGCATTGACCCGCGAGCGTGGCACCACGGCAg               <  7:138697/135‑1 (MQ=255)                                                                                                                     ccATCAGGTCGCCGAGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAGCGTGGTGCCTGGGCCGAACTTGAACATCGGCTTGGCTTCCTGCTCGGCATTGACCCGCGAGCGTGGCACCACGGCAg               <  7:135008/135‑1 (MQ=255)                                                                                                                           gggcGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAGCGTGGTGCCTGGGCCGAACTTGAACATCGGCTTGGCTTCCTGCTCGGCATTGACCCGCGAGCGTGGCACCACGGCAGTCTgg          <  4:168447/131‑1 (MQ=255)                                                                                                                           ggTCGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAGCGTGGTGCCTGGGCCGAACTTGAACATCGGCTTGGCTTCCTGCTCGGCATTGACCCGCGAGCGTGGCACCACGGCAGTCTgg          <  3:275897/134‑1 (MQ=255)                                                                                                                           ggTCGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAGCGTGGTGCCTGGGCCGAACTTGAACATCGGCTTGGCTTCCTGCTCGGCATTGACCCGCGAGCGTGGCACCACGGCAGTCTGGc         <  8:104575/135‑1 (MQ=255)                                                                                                                                   ggCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAGCGTGGTGCCTGGGCCGAACTTGAACATCGGCTTGGCTTCCTGCTCGGCATTGACCCGCGAGCGTGGCACCACGGCAGTCTGGCCATTGga  >  1:289855/1‑134 (MQ=255)                                                                                                                                   |                                                                                                                                      AGGCGCCGCTGTCGGCACTACCGGATACCTGGCTTTTGATATTCATCCGCGCCGTCCTCAGATCACGATCAGGTCGGCCTGCAAGGCGCCGGCCTGTTTCAAGGCTTCGAGGATCGCCATCAGGTCGCCGGGCGCTGCGCCCACCTGGTTCACCGCGCGGACGATTTCATCCAGCGTGGTGCCTGGGCCGAACTTGAACATCGGCTTGGCTTCCTGCTCGGCATTGACCCGCGAGCGTGGCACCACGGCAGTCTGGCCATTGGA  >  KT2440/4970548‑4970811

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑