Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,674,464	T→C	13.8%	L135P (CTT→CCT)	PP_2343 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,674,464	0	T	C	13.8%	67.4 / 3.2	29	L135P (CTT→CCT)	PP_2343	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (11/14);  new base C (2/2);  total (13/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.67e-01

AATTCCAGCCTTTTCCAGCGTGGGGTAACCACGTTTGTGGAGAGAACCCTGGATCTGGTGTACAAGCAGCGGCAGTCTTTTCTCTTGGATGGCACCCTCGCCAACCTTGATGTCGGAAGAAGAAACATCGCTCGCGCGCTTGAAAAAGTGAACAGGTCGGCCCAGGTTATCTACGTGTACCAGCGACCTGAGCTGGCTTGGGAGTTTGTTCTGGCGAGAGAGAAGAAGGACGGAAGGAACATCCCGTGCTCGGAATTTGTAAGACAGTTTTACGCGGCCAAGGT  >  NC_002947/2674325‑2674608                                                                                                                                            |                                                                                                                                                 aaTTCCAGCCTTTTCCAGCGTGGGGTAACCACGTTTGTGGAGAGAACCCTGGATCTGGTGTACAAGCAGCGGCAGTCTTTTCTCTTGGATGGCACCCTCGCCAACCTTGATGTCGGAAGAAGAAACATCGCTCGCGCGCTTGAAAAAGTg                                                                                                                                        <  1:382429/150‑1 (MQ=255)         ccTTTTCCAGCGTGGGGTAACCACGTTTGTGGAGAGAACCCGGGATCTGGTGTACAAGCAGCGGCAGTCTTTTCTCTTGGATGGCACCCTCGCCAACCTTGATGTCGGAAGAAGAAACATCGCTCGCGCGCTTGAAAAAGTGAACAGGTc                                                                                                                                <  2:583720/150‑1 (MQ=255)           ttttCCAGCGTGGGGTAACCACGTTTGTGGAGAGAACCCTGGATCTGGTGTACAAGCAGCGGCAGTCTTTTCTCTTGGATGGCACCCTCGCCAACCTTGATGTCGGAAGAAGAAACATCGCTCGCGCGCCTGAAAAAGTGAACAGGt                                                                                                                                 >  2:496687/1‑147 (MQ=255)           ttttCCAGCGTGGGGTAACCACGTTTGTGGAGAGAACCCTGGATCTGGTGTACAAGCAGCGGCAGTCTTTTCTCTTGGATGGCACCCTCGCCAACCTTGATGTCGGAAGAAGAAACATCGCTCGCGCGCCTGAAAAAGTGAACAGGt                                                                                                                                 <  1:496687/147‑1 (MQ=255)           ttttCCAGCGTGGGGTAACCACGTTTGTGGAGAGAACCCTGGATCTGGTGTACAAGCAGCGGCAGTCTTTTCTCTTGGATGGCACCCTCGCCAACCTTGATGTCGGAAGAAGAAACATCGCTCGCGCGCCTGAAAAAGTGAACAGGTCgg                                                                                                                              >  2:248180/1‑150 (MQ=255)             ttCCAGCGTGGGGTAACCACGTTTGTGGAGAGAACCCTGGATCTGGTGAACAAGCAGCGGCAGTCTTTTCTCTTGGATGGCACCCTCGCCAACCTTGATGTCGGAAGAAGAAACATCGCTCGCGCGCTTGAAAAAGTGAACAGGTCGGcc                                                                                                                            <  1:824531/150‑1 (MQ=255)                cAGCGTGGGGTAACCACGTTTGTGGAGAGAACCCTGGATCTGGTGTACAAGCAGCGGCAGTCTTTTCTCTTGGATGGCACCCTCGCCAACCTTGATGTCGGAAGAAGAAACATCGCTCGCGCGCTTGAAAAAGTGAACAGGTCGGCCCAg                                                                                                                         <  2:502318/150‑1 (MQ=255)                         gTAACCACGTTTGTGGAGAGAACCCTGGATCTGGTGTACAAGCAGCGGCAGTCTTTTCTCTTGGATGGCACCCTCGCCAACCTTGATGTCGGAAGAAGAAACATCGCTCGCGCGCCTGAAAAAGTGAACAGGTCGGCCCAGGTTATCTAc                                                                                                                <  1:248180/150‑1 (MQ=255)                                        gagagaACCCTGGATCTGGTGTACAAGCAGCGGCAGTCTTTTCTCTTGGATGGCACCCTCGCCAACCTTGATGTCGGAAGAAGAAACATCGCTCGCGCGCTTGAAAAAGTGAACAGGTCGGCCCAGGTTATCTACGTGTACCAGctcagg                                                                                                 >  1:477306/1‑145 (MQ=255)                                               cccTGGATCTGGTGTACAAGCAGCGGCAGTCTTTTCTCTTGGATGGCACCCTCGCCAACCTTGATGTCGGAAGAAGAAACATCGCTCGCGCGCTTGAAAAAGTGAACAGGTCGGCCCAGGTTATCTACGTGTACCAGCGACCTGAGCTgg                                                                                          <  2:111279/150‑1 (MQ=255)                                                ccTGGATCTGGTGTACAAGCAGCGGCAGACATTTCTCTTGGATGGCACCCTCGCCAACCTTGATGTCGGAAGAAGAAAGGGCCCTCGCGCGCTTGAAAAAGTGAACAGGTCGGCCCAGGTTATCTACGTGTACCAGCGATCTGAGCTGGc                                                                                         >  1:271147/1‑150 (MQ=255)                                                        tGGTGTACAAGCAGCGGCAGTCTTTTCTCTTGGATGGCACCCTCGCCAACCTTGATGTCGGAAGAAGAAACATCGCTCGCGCGCTTGAAAAAGTGAACAGGTCGGCCCAGGTTATCTACGTGTACCAg                                                                                                       >  1:669096/1‑128 (MQ=255)                                                        tGGTGTACAAGCAGCGGCAGTCTTTTCTCTTGGATGGCACCCTCGCCAACCTTGATGTCGGAAGAAGAAACATCGCTCGCGCGCTTGAAAAAGTGAACAGGTCGGCCCAGGTTATCTACGTGTACCAg                                                                                                       <  2:669096/128‑1 (MQ=255)                                                                aaGCAGCGGCAGTCTTTTCTCTTGGATGGCAGCCTCGCCAACCTTGATGTCGGAAGAAGAAACATCGCTCGCGCGCTTGAAAAAGTGAACAGGTCGGCCCAGGTTATCTACGTGTACCAGCGACCTGAGCTGGCTTGGGAGTTTGTTCTg                                                                         >  2:526730/1‑150 (MQ=255)                                                                 agcagcGGCAGTCTTTTCTCTTGGATGGCACCCTCGCCAACCTTGATGTCGGAAGAAGAAACATCGCTCGCGCGCTTGAAAAAGTGAACAGGTCGGCCCAGGTTATCTACGTGTACCAGCGACCTGAGCTGGCTTGGGAGTTTGTTCTgg                                                                        <  2:844354/150‑1 (MQ=255)                                                                          aGTCTTTTCTCTTGGATGGCACCCTCGCCAACCTTGATGTCGGAAGAAGAAACATCGCTCGCGCGCTTGAAAAAGTGAACAGGTCGGCCCAGGTTATCTACGTGTACCAGCGACCTGAGCTGGCTTGGGAGTTTGTTCTGGCgagagaga                                                               >  2:348682/1‑150 (MQ=255)                                                                                 tctcTTGGATGGCACCCTCGCCAACCTTGATGTCGGAAGAAGAAACATCGCTCGCGCGCTTGAAAAAGTGAACAGGTCGGCCCAGGTTATCTACGTGTACCAGCGACCTGAGCTGGCTTGGGAGTTTGTTCTGGCGAGAGAGAAGAAGGa                                                        >  1:117441/1‑150 (MQ=255)                                                                                     ttGGATGGCACCCTCGCCAACCTTGATGTCGGAAGAAGAAACATCGCTCGCGCGCTTGAAAAAGTGAACAGGTCGGCCCAGGTTATCTACGTGTACCAGCGACCTGAGCTGGCTTGGGCGTTTGTTCTGGCGAGCGAGAAGAAGGACgga                                                    >  2:426710/1‑150 (MQ=255)                                                                                         aTGGCACCCTCGCCAACCTTGATGTCGGAAGAAGAAACATCGCTCGCGCGCTTGAAAAAGTGAACAGGTCGGCCCAGGTTATCTACGTGTACCAGCGACCTGAGCTGGCTTGGGAGTTTGTTCTGGCGAGAGAGAAGAAGGACggaagga                                                >  2:241096/1‑150 (MQ=255)                                                                                             cACCCTCGCCAACCTTGATGTCGGAAGAAGAAACATCGCTCGCGCGCTTGAAAAAGTGAACAGGTCGGCCCAGGTTATCTACGTGTACCAGCGACCTGAGCTGGCTTGGGAGTTTGTTCTGGCGAGAGAGAAGAAGGACg                                                      >  2:3176/1‑140 (MQ=255)                                                                                             cACCCTCGCCAACCTTGATGTCGGAAGAAGAAACATCGCTCGCGCGCTTGAAAAAGTGAACAGGTCGGCCCAGGTTATCTACGTGTACCAGCGACCTGAGCTGGCTTGGGAGTTTGTTCTGGCGAGAGAGAAGAAGGACg                                                      <  1:3176/140‑1 (MQ=255)                                                                                             cACCCTCGCCAACCTTGATGTCGGAAGAAGAAACATCGCTCGCGCGCTTGAAAAAGTGAACAGGTCGGCCCAGGTTATCTACGTGTACCAGCGACCTGAGCTGGCTTGGGAGTTTGTTCTGGCGAGAGAGAAGAAGGACGGAAGGAACAt                                            <  1:348682/150‑1 (MQ=255)                                                                                                ccTCGCCAACCTTGATGTCGGAAGAAGAAACATCGCTCGCGCGCTTGAAAAAGTGAACAGGTCGGCCCAGGTTATCTACGTGTACCAGCGACCTGAGCTGGCTTGGGAGTTTGTTCTGGCGAGAGAGAAGAAGGACGGAAGGAACATccc                                         >  1:610461/1‑150 (MQ=255)                                                                                                    gCCAACTTTGATGTCGGAAGAAGAAACATCGCTCGCGCGCTTGAAAAAGTGAACAGGTCGGCCCAGGTTATCTACGTGTACCAGCGACCTGAGCTGGCTTCGGAGTTTGTTCTGGCGAGAGAGAAGAAGGACGGAAGGAACATCCCGTGc                                     <  1:830967/150‑1 (MQ=255)                                                                                                                    gaagaagaaACATCGCTCGCGCGCTTGAAAAAGTGAACAGGTCGGCCCAGGTTATCTACGTGTACCAGCGACCTGAGCTGGCTTGGGAGTTTGTTCTGGCGAGAGAGAAGAAGGACGGAAGGAACATCCCGTGCTCGGAATTTGTAAGAc                     <  2:117441/150‑1 (MQ=255)                                                                                                                       gaagaaACATCGCTCGCGCGCTTGAAAAAGTGAACAGGTCGGCCCAGGTTATCTACGTGTACCAGCGACCTGAGCTGGCTTGGGAGTTTGTTCTGGCGAGAGAGAAGAAGGACGGAAGGAACATCCCGTGCTCGGAATTTGTAAGACAGt                  >  2:593611/1‑150 (MQ=255)                                                                                                                        aataaaCATCGCTCGCGCGCTTGAAAAAGTGAACAGGTCGGCCCAGGTTATCTACGTGTACCAGCGACCTGAGCTGGCTTGGGAGTTTGTTCTGGCGAGAGAGAAGAAGGACGGAAGGAACATCCCGTGCTCGGAATTTGTACGACAGtt                 <  2:358792/147‑1 (MQ=255)                                                                                                                                  gctcgcGCGCTTGAAAAAGTGAACAGGTCGGCCCAGGTTATCTACGTGTACCAGCGACCTGAGCTGGCTTGGGAGTTTGTTCTGGCGAGAGAGAAGAAGGACGGAAGGAACATCCCGTGCTCGGAATTTGTAAGACAGTTTTACGCGGcc       <  1:526730/150‑1 (MQ=255)                                                                                                                                       cgcgcTTGAAAAAGTGAACAGGTCGGCCCAGGTTATCTACGTGTACCAGCGACCTGAGCTGGCTTGGGAGTTTGTTCTGGCGAGAGAGAAGAAGGACGGAAGGAACATCCCGTGCTCGGAATTTGTAAGACAGTTTTACGCGGCCAAGgt  <  1:593611/150‑1 (MQ=255)                                                                                                                                            |                                                                                                                                                 AATTCCAGCCTTTTCCAGCGTGGGGTAACCACGTTTGTGGAGAGAACCCTGGATCTGGTGTACAAGCAGCGGCAGTCTTTTCTCTTGGATGGCACCCTCGCCAACCTTGATGTCGGAAGAAGAAACATCGCTCGCGCGCTTGAAAAAGTGAACAGGTCGGCCCAGGTTATCTACGTGTACCAGCGACCTGAGCTGGCTTGGGAGTTTGTTCTGGCGAGAGAGAAGAAGGACGGAAGGAACATCCCGTGCTCGGAATTTGTAAGACAGTTTTACGCGGCCAAGGT  >  NC_002947/2674325‑2674608

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: ‑