Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,414,988	T→A	13.8%	Y62* (TAT→TAA) ‡	PP_2115 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,414,988	0	T	A	13.8%	67.6 / 3.9	29	Y62* (TAT→TAA) ‡	PP_2115	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (11/14);  new base A (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 = 8.56e-01

CTCCTGAAGTCGCGAAGATCAAGATCAAGATCAAGATCAAGATCAAGATCAAGATCAAGATCAAGATCAAGATCAAGATCGAGATCAAGATCAAGATCGAGATCAAGAGCGCTGGGTTTGAAAGCCGTGCTTGGACCGCGTCGCGCTATGCGCGACAATAGCGATCAT‑TTTCGGAGCCCCCCATGACCGATTTCACCCCCGACGCCATCCTCGATGCCACCGGCCTGAACTGCCCGGAACCGGTGATGATGCTGCACCAGCACGTACGCAAC  >  NC_002947/2414840‑2415111                                                                                                                                                     |                                                                                                                             ctcctGAAGTCGCGAAGATCAAGATCAAGATCAAGATCAAGATCAAGATCAAGATCAAGATCAAGATCAAGATCAAGATCGAGATCAAGATCAAGATCGAGATCAAGAGCGCTGGGTTTGAAAGCCGTGCTTGGACCGCGTCGCGCTAt                                                                                                                              <  8:116848/149‑1 (MQ=255)             cgAAGATCAAGATCAAGATCAAGATCAAGATCAAGATCAAGATCAAGATCAAGATCAAGATCAAGATCGAGATCAAGATCAAGATCGAGATCAAGAGCGCTGGGTTTGAAAGCCGTGCTTGGACCGCGTCGCGCATAGCGCGAcgcg                                                                                                                    >  6:127066/1‑144 (MQ=255)             cgAAGATCAAGATCAAGATCAAGATCAAGATCAAGATCAAGATCAAGATCAAGATCAAGATCAAGATCGAGATCAAGATCAAGATCGAGATCAAGAGCGCTGGGTTTGAAAGCCGTGCTTGGACCGCGTCGCGCATAGCGCGAcgcg                                                                                                                    <  5:127066/147‑4 (MQ=255)                                    atcaagatcaagatcaagatcaagatcaagatcaagatcaagatcGAGATCAAGATCAAGATCGAGATCAAGAGCGCTGGGTTTGAAAGCCGTGCTTGGACCGCGTCGCGCTATGCGCGACAATAGCGATCAT‑TTTCGGAGCCCCCCAt                                                                                          >  7:10451/1‑149 (MQ=255)                                               gatcaagatcaagatcaagatcaagatcaagatcGAGATCAAGATCAAGATCGAGATCAAGAGCGCTGGGTTTGAAAGCCGTGCTTGGACCGCGTCGCGCTATGCGCGACAATAGCGATCAT‑TTTCGGAGCCCCCCATGACCGATTTCa                                                                               >  8:180242/1‑149 (MQ=255)                                                atcaagatcaagatcaagatcaagatcaagatcGAGATCAAGATCAAGATCGAGATCAAGAGCGCTGGGTTTGAAAGCCGTGCTTGGACCGCGTCGCGCATAGCGCGAcgcg                                                                                                                    <  4:55197/112‑4 (MQ=25)                                                atcaagatcaagatcaagatcaagatcaagatcGAGATCAAGATCAAGATCGAGATCAAGAGCGCTGGGTTTGAAAGCCGTGCTTGGACCGCGTCGCGCATAGCGCGAcgcg                                                                                                                    >  3:55197/1‑109 (MQ=25)                                                    agatcaagatcaagatcaagatcaagatcGAGATCAAGATCAAGATCGAGATCAAGAGCGCTGGGTTTGAAAGCCGTGCTTGGACCGCGTCGCGCTATGCGCGACAATAGAGATCAT‑TTTCGGAGCCCCCCATGCCCGAGTTCAccccc                                                                          >  4:53290/1‑149 (MQ=255)                                                     gatcaagatcaagatcaagatcaagatcGAGATCAAGATCAAGATCGAGATCAAGAGCGCTGGGTTTGAAAGCCGTGCTTGGACCGCGTCGCGCTATGCGCGACAATAGCGATCAT‑TTTCGGAGCCCCCCATGACCGATTTCACCCCCg                                                                         >  2:21932/1‑149 (MQ=255)                                                               aagatcaagatcaagatcGAGATCAAGATCAAGATCGAGATCAAGAGCGCTGGGTTTGAAAGCCGTGCTTGGACCGCGTCGCGCTATGCGCGACAATAGCGATCAT‑TTTCGGAGCCCCCCATGACCGATTTCACCCCCGACGCCATCCt                                                               <  4:195980/149‑1 (MQ=255)                                                                  atcaatatcaagatcgagatcaagatcaagatcgacATCAAGAGCTCTGGGTTTGAAAGCCGTCCTTGGACCGCGTCGAGCTATGCGCGACAATAGAGATCAT‑TATCGAAGCCCCCAATGACCGAATTAAACCCACACGCAATCCTCGa                                                            >  8:199449/1‑149 (MQ=255)                                                                  atcaagatcaagatcgagatcaagatcaagatcgagATCAAGAGCGCTGGGTTTGAAAGCCGTGCTTGGACCGCGTCGCGCTATGCGCGACAATAGCGATCAT‑TTTCGGAGCCCCCCATGACCGATTTCACCCCCGACGCCATCCTCGa                                                            >  6:145505/1‑149 (MQ=255)                                                                   tcaagatcaagatcgagatcaagatcaagatcgagaTCAAGAGCGCTGGGTTTGAAAGCCGTGCTTGGACCGCGTCGCGCTATGCGCGACAATAGCGATCAT‑TTTCGGAGCCCCCCATGACCGATTTCACCCCCGACGCCATCCTCGAt                                                           >  2:77283/1‑149 (MQ=255)                                                                      agatcaagatcgagatcaagatcaagatcgagatcaAGAGCGCTGGGTTTGAAAGCCGTGCTTGGACCGCGTCGCGCTATGCGCGACAAt                                                                                                                    <  5:165436/90‑1 (MQ=255)                                                                      agatcaagatcgagatcaagatcaagatcgagatcaAGAGCGCTGGGTTTGAAAGCCGTGCTTGGACCGCGTCGCGCTATGCGCGACAAt                                                                                                                    >  6:165436/1‑90 (MQ=255)                                                                            agatcgagatcaagatcaagatcgagatcaagaGCGCTGGGTTTGAAAGCCGTGCTTGGACCGCGTCGCGCTATGCGCGACAATAGCGATCAT‑TTTCGGAGCCCCCCATGACCGATTTCACCCCCGACGCCATCCTCGATGCCACCGGc                                                  >  6:112235/1‑149 (MQ=255)                                                                                  agatcaagatcaagatcgagatcaagaGCGCTGGGTTTGAAAGCCGTGCTTGGACCGCGTCGCGCTATGCGCGACAATAGCGATCATCATTCGGAGCCCCCCATGACCGATTTCACCCCCGACGCCATCCTCGATGCCACCGGCCTGaa                                             <  1:77283/149‑1 (MQ=255)                                                                                    atcaagatcaagatcgagatcaagaGCGCTGGGTTTGAAAGCCGTGCTTGGACCGCGTCGCGCTATGCGCGACAATAGCGATCAT‑TTTCGGAGCCCCCCATGACCGATTTCACCCCCGACGCCATCCTCGAt                                                           <  3:109619/132‑1 (MQ=255)                                                                                    atcaagatcaagatcgagatcaagaGCGCTGGGTTTGAAAGCCGTGCTTGGACCGCGTCGCGCTATGCGCGACAATAGCGATCAT‑TTTCGGAGCCCCCCATGACCGATTTCACCCCCGACGCCATCCTCGAt                                                           >  4:109619/1‑132 (MQ=255)                                                                                       aagatcaagatcgagatcaagaGCGCTGGGTTTGAAAGCCGTGCTTGGACCGCGTCGCGCTATGCGCGACAATAGCGATCAT‑TTTCGGAGCCCCCCATGACCGATTTCACCCCCGACGCCATCCTCGATGCCACCGGCCTGAACTGccc                                       <  8:10451/149‑1 (MQ=255)                                                                                       aagatcaagatcgagatcaagaGCGCTGGGTTTGAAAGCCGTGCTTGGACCGCGTCGCGCTATGCGCGACAATAGCGATCAT‑TTTCGGAGCCCCCCATGACCGATTTCACCCCCGACGCCATCCTCGATGCCACCGGCCTGAACTGccc                                       <  7:180242/149‑1 (MQ=255)                                                                                                   gagatcaagaGCGCTGGGTTTGAAAGCCGTGCTTGGACCGCGTCGCGCTATGCGCGACAATAGCGATCAT‑TTTCGGAGCCCCCCATGACCGATTTCACCCCCGACGCCATCCTCGATGCCACCGGCCTGAACTGCCCGGAACCGGtgat                           <  7:199449/149‑1 (MQ=255)                                                                                                   gagatcaagaGCGCTGGGTTTGAAAGCCGTGCTTGGACCGCGTCGCGCTATGCGCGACAATAGCGATCAT‑TTTCGGAGCCCCCCATGACCGATTTCACCCCCGACGCCATCCTCGATGCCACCGGCCTGAACTGCCCGGAACCGGtga                            <  5:145505/148‑1 (MQ=255)                                                                                                   gagatcaagaGCGCTGGGTTGGAAAGCCGTGCTTGGACCGCGTCGCGCTATGCGCGACAATAGCGATCAT‑TTTCGGAGCCCCCCATGACCGATTTCACCCCCGACGCCATCCTCGATGCCACCGGCCTGAACTGCCCGGAACCGGtgat                           <  1:180652/149‑1 (MQ=255)                                                                                                               gcTGGGTTTGAAAGCCGTGCTTGGACCGCGTCGCGCTATGCGCGACAATAGCGATCAT‑TTTCGGAGCCCCCCATGACCGATTTCACCCCCGACGCCATCCTCGATGCCACCGGCCTGAACTGCCCGGAACCGGTGATGATGCTGCACCa               <  1:21932/149‑1 (MQ=255)                                                                                                                   ggTTTGAAAGCGGTGCTTGGACCGCGTCGCGCTATGAGCGACAATAGCGATCAT‑TTTCGGAGCCCCCCATGACCGATTTCACCCCCGACGCCATCCTCGATGCCACCGGCCTGAACTGCCCGGAACCGGTGATGATGCTGCACCAGc             <  6:230419/147‑1 (MQ=255)                                                                                                                     tttGAAAGCCGTGCTTGGACCGCGTCGCGCTATGCGCGACAATAGCGATCAT‑TTTCGGAGCCCCCCATGACCGATTTCACCCCCGACGCCATCCTCGATGCCACCGGCCTGAACTGCCCGGAACCGGTGATGATGCTGCACCAGCACGt         <  1:44607/149‑1 (MQ=255)                                                                                                                           aGCCGTGCTTGGACCGCGTCGCGCTATGCGCGACAATAGCGATCAT‑TTTCGGAGCCCCCCATGACCGATTTCACCCCCGACGCCATCCTCGATGCCACCGGCCTGAACTGCCCGGAACCGGTGATGATGCTGCACCAGCACGTACGCaa   <  5:112235/149‑1 (MQ=255)                                                                                                                            gCCGTGCTTGGACCGCGTCGCGCTATGCGCGACAATAGCGATCAT‑TTTCGGAGCCGCCGATGACCGAGGTCACCCCCGACGCCAGCCTCGCGGCCGCCGGCCTGAGCGGCCCGGAGGCGGGGCTGATGCTGCGGCGGCCCGTACGCagc  >  8:112840/1‑147 (MQ=255)                                                                                                                            gCCGTGCTTGGACCGCGTCGCGCTATGCGCGACAATAGCGATCAT‑TTTCGGAGCCCCCCATGACCGATTTCACCCCCGACGCCATCCTCGATGCCACCGGCCTGAACTGCCCGGAACCGGTGATGATGCTGCACCAGCACGTACGCAAc  <  3:53290/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                             CTCCTGAAGTCGCGAAGATCAAGATCAAGATCAAGATCAAGATCAAGATCAAGATCAAGATCAAGATCAAGATCAAGATCGAGATCAAGATCAAGATCGAGATCAAGAGCGCTGGGTTTGAAAGCCGTGCTTGGACCGCGTCGCGCTATGCGCGACAATAGCGATCAT‑TTTCGGAGCCCCCCATGACCGATTTCACCCCCGACGCCATCCTCGATGCCACCGGCCTGAACTGCCCGGAACCGGTGATGATGCTGCACCAGCACGTACGCAAC  >  NC_002947/2414840‑2415111

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑