Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	KT2440	1,630,540	A→C	36.1%	L419R (CTG→CGG)	czcS ←	Sensor protein CzcS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	KT2440	1,630,540	0	A	C	36.1%	20.9 / 4.7	34	L419R (CTG→CGG)	czcS	Sensor protein CzcS
Reads supporting (aligned to +/- strand):  ref base A (8/13);  new base C (8/5);  total (16/18)
Fisher's exact test for biased strand distribution p-value = 2.91e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCATGATCGACTTCACGATCGCCAACCCCAACCCGGTCCCGCCCTCCAGCCGCGAACGCCCCGAACCTACCCGGTAAAA‑CCGCTCGAACAAGCGCGACTGGTGCTCTGCAGGCACACCCGGACCCTGGTTCTCCACGGATAGAATGACTTCGCTGCCCGAGCGTTCGATGCGCAGAG  >  KT2440/1630408‑1630669                                                                                                                                     |                                                                                                                                   gcCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCATGATCGACTTCACGATCGCCAACCCCAACCCGGTCCCGCCCTCCCGcc                                                                                                                                 >  4:239557/1‑136 (MQ=255)   cGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCATGATCGACTTCACGATCGCCAACCCCAACCCGGTCCCGCCCTCCAGCcg                                                                                                                                <  2:226990/135‑1 (MQ=255)   cGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCATGATCGACTTCACGATCGCCAACCCCAACCCGGTCCCGCCCTCCAGCcg                                                                                                                                <  8:252459/135‑1 (MQ=255)    gATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCATGATCGACTTCACGATCGCCAACCCCAACCCGGTCCCGCCCTCCAGCcgc                                                                                                                               <  1:24029/135‑1 (MQ=255)      tCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCATGATCGACTTCACGATCGCCAACCCCAACCCGGTCCCGCCCTCCCGCcgcgca                                                                                                                            >  4:72319/1‑134 (MQ=255)         cTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCATGATCGACTTCACGATCGCCAACCCCAACCCGGTCCCGCCCTCCAGCCGCGAAc                                                                                                                           <  6:40893/134‑1 (MQ=255)                 gAAACACCAGGTTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCATGATCGACTTCACGATCGCCAACCCCAACCCGGTCCCGCCCTCCAGCCGCGAACGCCCCGAAc                                                                                                                  <  1:226607/135‑1 (MQ=255)                 gAAACACCAGGGTACACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCATGATCGACTTCACGATCGCCAACCCCAACCCGGTCCCGCCCTCCAGCCGCGAACGCCCCGAAc                                                                                                                  <  2:59231/135‑1 (MQ=255)                           ggTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCATGATCGACTTCACGATCGCCAACCCCCACCCCGTCCCCCCCACCCCCCCCGCACGCCCCCACCCAAccccgg                                                                                                         >  8:330631/1‑131 (MQ=255)                                aCCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCATGATCGACTTCACGATCGCCAACCCCCACCCCGTCCCGCCCGCCCGCCGCGCACCCCCCGAACCAACCCCGGAAAA‑cc                                                                                                  >  8:109051/1‑135 (MQ=255)                                   gggTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCATGATCGACTTCACGATCGCCAACCCCCACCCGGTCCCGCCCTCCAGCCGCGCACGCCCCGAACCTACCCGGGAAAA‑CCGCt                                                                                               >  8:309238/1‑135 (MQ=255)                                        ggCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCATGATCGACTTCACGATCGCCAACCCCAACCCGGTCCCGCCCTCCAGCCGCGCACGCCCCGAACCTACCCGGTAAAA‑CCGCTCGaa                                                                                           >  5:325683/1‑134 (MQ=255)                                            ccAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCATGATCGACTTCACGATCGCCACCCCCCACCCGGTCCCGCCCGCCCGCCGCGAACCCCCCCCACCGACCCCGGAAAA‑CCGCGCCAACAAgc                                                                                      >  5:348363/1‑135 (MQ=255)                                                 gggCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCATGATCGACTTCACGATCGCCAACCCCAACCCGGTCCCGCCCTCCAGCCGCGAACGCCCCGAACCTACCCGGTAAAA‑CCGCTCGAACAAGCGCGAc                                                                                 >  8:3744/1‑135 (MQ=255)                                                       ctgctgACCTCGACCCGCCCGCCATGCAACTGCATGATCGACTTCACGATCGCCACCCCCAACCCGGTCCCCCCCACCAGCCCCGCACGCCCCGCACCTACCCCGGAAAA‑CCGCGCGCACCAGCCCGCCAGGTGc                                                                           >  5:347099/1‑135 (MQ=255)                                                        tgctgACCTCGACCCGCCCGCCATGCAACTGCATGATCGACTTCACGATCGCCAACCCCCCCCCGGTCCCGCCCTCCAGCCGCGCACCCCCCGCCCCTACCCGGGAAAA‑ACGCGCGCACCAGCGCGGCGGGTGcg                                                                          >  7:343573/1‑134 (MQ=255)                                                              ccgccccccccccgCCATCCAACTGCATGACCGACGACCCCAGCCCCAACCCCAACCCGCCCCCCCCCCCCCGCCCCCCCCCCCCCCAACCAACCCGGAAAAA‑CCGCTCGAACACCCGCGACTGGTGCTCTGc                                                                      <  2:321953/127‑1 (MQ=255)                                                              ccTCCACCCGCCCCCCATGCAACTGCATGAGCGCCTTCACGATCGCCAACCCCCCCCCGGTCCCGCCCTCCAGCCGCCACCGCCCCGAACCTCCCCGGTAAAA‑CCGCTCTAACAAGCGCGACTGGTGCTCTGc                                                                      <  8:357401/133‑1 (MQ=255)                                                                                   aCTTCATGTTCGACTTCACGATCGCCAACCCCAACCCGGTCCCGCCCTCCAGCCGCGAACGCCCCGAACCTACCCGGTAAAA‑CCGCTCGAACAAGCGCGACTGGTGCTCTGCAGGCACACCCGGACCCTGGTtct                                               <  6:348363/135‑1 (MQ=255)                                                                                     tccATGACCGCCTTCACGAGCGCCACCCCCACCCCGGCCCCGCCCGCCCGCCGCGACCGCCCCGAACCACCCCGGAAAAC‑CCGCTCGACCACCCGCGACTGGTGCTCTGCAGGCACACCCGGACCCTGGTTCTcc                                             <  7:157802/133‑1 (MQ=255)                                                                                     tGCATGATCGACTTCACGAGCGCCAACCCCACCCCGGTCCCCCCCTCCACCCGCGAACGCCCCGAACATACCGGGTAAAA‑CCGCTCGAACAAGCGCGACTGGTGCTCTGCAGGCACACCCGGACCCTGGTTCTcc                                             <  5:77910/135‑1 (MQ=255)                                                                                          gATCGACTTCACGATCGCCAACCCCAACCCGGTCCCGCCCTCCCGCCGCGCACGCCCCGCACCGACCCGGGAAAA‑CCGCGCGCACCAGCGCGCCTGGGGCTCTGCAGGCACCCCCGGCCCCGGGTTCTCCCCgg                                         >  5:192098/1‑134 (MQ=255)                                                                                          gATCGACTTCACGATCGCCAACCCCAACCCGGTCCCGCCCTCCCGCCGCGAACGCCCCGAACCTACCCGGTAAAA‑CCGCACGAACAAGCGCGACTGGTGCTCTGCAGGCCCCCCCGGCCCCGGGTTCGGCACgg                                         >  7:196388/1‑134 (MQ=255)                                                                                          gATCGACTTCACGATCGCCAACCCCAACCCGGTCCCGCCCTCCAGCCGCGAACGCCCCGAACCTACCCGGTAAAA‑CCGCTCGAACAAGCGCGACTGGTGCTCTGCAGGCACACCCGGACCCTGGTTCTCCACgg                                         >  7:246631/1‑134 (MQ=255)                                                                                                                  caacccGGTCCCGCCCTCCAGCCGCGAACGCCCCGAACCTACCCGGTAAAA‑CCGCTCGAACAAGCGCGACTGGTGCTCTGCAGGCACACCCGGACCCTGGTTCTCCACGGATAGAATGACTTCGCTGCCCGAGCGt               <  3:72319/136‑1 (MQ=255)                                                                                                                    ccccGGTCCCGCCCCCCAGCCGCCAACGCCCCGAACCAACCCGGTAAAA‑CCGCTCGAACAAGCGCGACTGGTGCTCTGCAGGCACACCCGGACCCTGGTTCTCCACGGATAGAATGACTTCGCTGCCCGAGCGTTc             <  4:82105/135‑1 (MQ=255)                                                                                                                       cGGTCCCGCCCTCCCGCCGCGAACGCCCCGCACCGACCCCGTAAAA‑CCGCTCGCACAAGCGCGCCTGGTGCTCGGCAGGCCCACCCGGACCCTGGGTCTCCACGGATAGAATGCCTTCGCTTGCCGCGCGTTCGAt          >  3:179008/1‑136 (MQ=255)                                                                                                                         cacccGCCCACCACCCGCAACCGCCCCGAA‑CAACCCCGTAAAACCCGCCCCAACAAGAGCGACTGGTGCTCTGCAGGCACACCCGGACCCTGGTTCTCCACGGATAGAATGACTTCGCTGCCCGAGCGTTCGATg         <  6:248728/133‑1 (MQ=255)                                                                                                                          gcccGCCCCCCCGCCGCCAACGCCCCGAACCTACCCGGAAAAA‑CCGCTCGAACACGCGCGACTGGTGCTCTGCAGGCACACCCGGACCCTGGTTCTCCACGGATAGAATGACTTCGCTGCCCGAGCGTTCGATgc        <  7:109051/134‑1 (MQ=255)                                                                                                                             cGCCCTCCAGCCGCGAACGCCCCGAACCTACCCGGTAAAA‑CCGCTCGAACAAGCGCGACTGGTGCTCTGCAGGCACCCCCGGACCCTGGTTCTCCACGGATAGAATGACTTCGCTGCCCGAGCGGTCGATGCGCag    >  3:98691/1‑136 (MQ=255)                                                                                                                             cGCCCTCCAGCCGCGAACGCCCCGAACCTACCCGGTAAAA‑CCGCTCGAACAAGCGCGACTGGTGCTCTGCAGGCACACCCGGACCCTGGTTCTCCACGGATAGAATGACTTCGCTGCCCGAGCGTTCGATGCGCa     >  2:26705/1‑135 (MQ=255)                                                                                                                               ccccccCGCCGCCACCCCCCCTAACCTCCCCGTTAAAC‑CCGCTCCAACACGCGCGACTGGTGCTCTGCAGGCACACCCGGACCCTGGTTCTCCACGGATAGAATGACTTCGCTGCCCGAGCGTTCGATGCGCagag  <  3:237855/136‑1 (MQ=255)                                                                                                                               ccccccAGCCCCGACCGCCCCGAACCTACCCGGAAAAC‑CCGCTCGACACGGCGCGACTGCTGCTCTGCAGGCACACCCGGACCCTGGTGCTCCACGGATAGAATGACTTCGCTGCCCGAGCGTTCGATGCGCagag  <  3:272053/136‑1 (MQ=255)                                                                                                                                ccTCCCGCCGCGAACGCCCCGAACCTACCCGGTAAAA‑CCGCTCGAACACGCGCGACTGGTGCTCTGCAGGCACACCCGGACCCTGGTTCTCCACGGATAGAATGACTTCGCTGCCCGAGCGTTCGATGCGCagag  <  7:3744/135‑1 (MQ=255)                                                                                                                                     |                                                                                                                                   GCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCATGATCGACTTCACGATCGCCAACCCCAACCCGGTCCCGCCCTCCAGCCGCGAACGCCCCGAACCTACCCGGTAAAA‑CCGCTCGAACAAGCGCGACTGGTGCTCTGCAGGCACACCCGGACCCTGGTTCTCCACGGATAGAATGACTTCGCTGCCCGAGCGTTCGATGCGCAGAG  >  KT2440/1630408‑1630669

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑