Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	4,183,378	T→C	31.0%	S712P (TCC→CCC)	rpoB →	RNA polymerase subunit beta

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,183,378	0	T	C	31.0%	36.4 / 23.7	29	S712P (TCC→CCC)	rpoB	RNA polymerase subunit beta
Reads supporting (aligned to +/- strand):  ref base T (10/10);  new base C (5/4);  total (15/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.40e-01

GCCGTAGCAAAGGCGAATCCAGCTTGTTCAGCCGCGACCAGGTTGACTACATGGACGTATCCACCCAGCAGGTGGTATCCGTCGGTGCGTCCCTGATCCCGTTCCTGGAACACGATGACGCCAACCGTGCATTGATGGGTGCGAACATGCAACGTCAGGCCGTTCCGACTCTGCGCGCTGATAAGCCGCTGGTTGGTACTGGTATGGAACGTGCTGTTGCCGTTGACTCCGGTGTAACTGCGGTAGCTAAACGTGGTGGTGTCGTTCAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGAAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGAACACCTGTATCAACCAGATGCCGTGTGTGTCTCTGGGTGAACCGGTTGAACGTGGCGACGTGCTGGCAGACGGTCCGTCCACCGA  >  NC_000913/4183151‑4183613                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                            gCCGTAGCAAAGGCGAATCCAGCTTGTTCAGCCGCGACCAGGTTGACTACATGGACGTATCCACCCAGCAGGTGGTATCCGTCGGTGCGTCCCTGATCCCGTTCCTGGAACACGATGACGCCAACCGTGCATTGATGGGTGCGAACATGCAACGTCAGGCCGTTCCGACTCTGCGCGCTGATAAGCCGCTGGTTGGTACTGGTATGGAACGTGCTGTTGCCGTTGACTCCGGTTTAACTGCGGTAGCTAAACGTGGTGGTGTCGTTCAGTACGTg                                                                                                                                                                                              >  1:235759/1‑275 (MQ=255)  cctggtaaaaGGTGACTCCAGTGTGTGCAGCCCGTACCCGGTTGACTACATGGACGTATCCACCCAGCAGGTGGTATCCGTCGGTGCGTCCCTGATCCCGTTCCTGGAACACGATGACGCCAACCGTGCATTGATGGGTGCGAACATGCAACGTCAGGCCGTTCCGACTCTGCGCGCTGATAAGCCGCTGGTTGGTACTGGTATGGAACGTGCTGTTGCCGTTGACTCCGGTGTAACTGCGGTAGCTAAACGTGGTGGTGTCGTTCAGTACGTg                                                                                                                                                                                              <  2:235759/267‑1 (MQ=255)                                     acccgtttGACTACATGGACGTATCCACCCGGCAGGTGGTATCCGTCGGTGCGTCCCTGATCCCGTTCCTGGAACACGATGACGCCAACCGTGCATTGATGGGTGCGAACATGCAACGTCAGGCCGTTCCGACTCTGCGCGCTGATAAGCCGCTGGTTGGTACTGGTATGGAACGTGCTGTTGCCGTTGACTCCGGTGTAACTGCGGTAGCTAAACGTGGTGGTGTCGTTCAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGAc                                                                                                                                                          <  1:98296/269‑1 (MQ=255)                                              aCTACATGGACGTATCCACCCAGCAGGTGGTATCCGTCGGTGCGTCCCTGATCCCGTTCCTGGAACACGATGACGCCAACCGTGCATTGATGGGTGCGAACATGCAACGTCAGGCCGTTCCGACTCTGCGCGCTGATAAGCCGCTGGTTGGTACTGGTATGGAACGTGCTGTTGCCGTTGACTCCGGTGTAACTGCGGTAGCTAAACGGGGTGGTGTCGTTCAGTACGTGGATGCTTCCCGTAACGTTATCAAAATTAACAATGACgagacttac                                                                                                                                                 >  2:98296/1‑270 (MQ=255)                                                          tATCCACCCAGCAGGTGGTATCCGTCGGTGCGTCCCTGATCCCGTTCCTGGAACACGATGACGCCAACCGTGCATTGATGGGTGCGAACATGCAACGTCAGGCCGTTCCGACTCTGCGCGCTGATAAGCCGCTGGTTGGTACTGGTATGGAACGTGCTGTTGCCGTTGACCCCGGTGTAACTGCGGTAGCTAAACGTGGTGGTGTCGt                                                                                                                                                                                                        >  2:278886/1‑208 (MQ=255)                                                              cACCCAGCAGGTGGTATCCGTCGGTGCGTCCCTGATCCCGTTCCTGGAACACGATGACGCCAACCGTGCATTGATGGGTGCGAACATGCAACGTCAGGCCGTTCCGACTCTGCGCGCTGATAAGCCGCTGGTTGGTACTGGTATGGAACGTGCTGTTGCCGTTGACCCCGGTGTAACTGCGGTAGCTAAACGTGGTGGTGTCGTTCAg                                                                                                                                                                                                    <  1:278886/208‑1 (MQ=255)                                                                           gtATCCGTCGGTGCGTCCCTGATCCCGTTCCTGGAACACGATGACGCCAACCGTGCATTGATGGGTGCGAACATGCAACGTCAGGCCGTTCCGACTCTGCGCGCTGATAAGCCGCTGGTTGGTACTGGTATGGAACGTGCTGTTGCCGTTGACTCCGGTGTAACTGCGGTAGc                                                                                                                                                                                                                          >  1:303626/1‑173 (MQ=255)                                                                               ccGTCGGTGCGTCCCTGATCCCGTTCCTGGAACACGATGACGCCAACCGTGCATTGATGGGTGCGAACATGCAACGTCAGGCCGTTCCGACTCTGCGCGCTGATAAGCCGCTGGTTGGTACTGGTATGGAACGTGCTGTTGCCGTTGACTCCGGTGTAACTGCGGTAGCTaaa                                                                                                                                                                                                                      <  2:303626/173‑1 (MQ=255)                                                                                                                                          ggTGCGAACATGCAACGTCAGGCCGTTCCGACTCTGCGCGCTGATAAGCCGCTGGTTGGTACTGGTATGGAACGTGCTGTTGCCGTTGACCCCGGTGTAACTGCGGTAGCTAAACGTGGTGGTGTCGTTCAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGAAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGAACACCt                                                                                 >  1:309091/1‑247 (MQ=255)                                                                                                                                                           tCAGGCCGTTCCGACTCTGCGCGCTGATAAGCCGCTGGTTGGTACTGGTATGGAACGTGCTGTTGCCGTTGACTCCGGTGTAACTGCGGTAGCTAAACGTGGTGgtgt                                                                                                                                                                                                           >  1:312003/1‑108 (MQ=255)                                                                                                                                                               gCCGTTCCGACTCTGCGCGCTGATAAGCCGCTGGTTGGTACTGGTATGGAACGTGCTGTTGCCGTTGACTCCGGTGTAACTGCGGTAGCTAAACGTGGTGGTGTCGtg                                                                                                                                                                                                       <  2:312003/108‑2 (MQ=255)                                                                                                                                                                   ttCCGACTCTGCGCGCTGATAAGCCGCTGGTTGGTACTGGTATGGAACGTGCTGTTGCCGTTGACTCCGGTGTAACTGCGGTAGCTAAACgtggtg                                                                                                                                                                                                               >  2:230126/1‑96 (MQ=255)                                                                                                                                                                       gACTCTGCGCGCTGATAAGCCGCTGGTTGGTACTGGTATGGAACGTGCTGTTGCCGTTGACTCCGGTGTAACTGCGGTAGCTAAACGTGGTGgtgt                                                                                                                                                                                                           <  1:230126/96‑1 (MQ=255)                                                                                                                                                                              cgcgcTGATAAGCCGCTGGTTGGTACTGGTATGGAACGTGCTGTTGCCGTTGACTCCGGTGTAACTGCGGTAGCTAAACGTGGTGGTGTCGTTCAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGAAGCAGGTATCGACATCTACAACCTGACCAAAt                                                                                                         >  2:167769/1‑187 (MQ=255)                                                                                                                                                                                  cTGATAAGCCGCTGGTTGGTACTGGTATGGAACGTGCTGTTGCCGTTGACTCCGGTGTAACTGCGGTAGCTAAACGTGGTGGTGTCGTTCAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGAAGCAGGTATCGACATCTACAACCTGACCAAATacac                                                                                                     <  1:167769/187‑1 (MQ=255)                                                                                                                                                                                             cTGGTTGGTACTGGTATGGAACGTGCTGTTGCCGTTGACCCCGGTGTAACTGCGGTAGCTAAACGTGGTGGTGTCGTTCAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGAAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGAACACCTGTATCAACCAGATGCCGTGTGTGTCTCTGGGTGAACCGGTTGAACGTGGCGACGTGCTGGCAGACGGTCCGTCCACCGa  >  1:282052/1‑275 (MQ=255)                                                                                                                                                                                                               gAACGTGCTGTTGCCGTTGACTCCGGTGTAACTGCGGTAGCTAAACGTGGTGgtgt                                                                                                                                                                                                           >  1:350371/1‑56 (MQ=255)                                                                                                                                                                                                               gAACGTGCTGTTGCCGTTGACTCCGGTGTAACTGCGGTAGCTAAACGTGGTGGTGTCGTTCAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACg                                                                                                                                                               >  1:197122/1‑100 (MQ=255)                                                                                                                                                                                                                   gTGCTGTTGCCGTTGACTCCGGTGTAACTGCGGTAGCTAAACGTGGTGGTGTCGtt                                                                                                                                                                                                       <  2:350371/56‑1 (MQ=255)                                                                                                                                                                                                                   gTGCTGTTGCCGTTGACTCCGGTGTAACTGCGGTAGCTAAACGTGGTGGTGTCGTTCAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGa                                                                                                                                                           <  2:197122/100‑1 (MQ=255)                                                                                                                                                                                                                    tGCTGTTGCCGTTGACTCCGGTGTAACTGCGGTAGCTAAACGTGGTGGTGTCGTTCAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGAAGCa                                                                                                                                     >  1:347027/1‑121 (MQ=255)                                                                                                                                                                                                                    tGCTGTTGCCGTTGACTCCGGTGTAACTGCGGTAGCTAAACGTGGTGGTGTCGTTCAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGAAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTaa                                                                                            >  2:354735/1‑162 (MQ=255)                                                                                                                                                                                                                    tGCTGTTGCCGTTGACCCCGGTGTAACTGCGGTAGCTAAAc                                                                                                                                                                                                                     >  2:146575/1‑41 (MQ=255)                                                                                                                                                                                                                    tGCTGTTGCCGTTGACCCCGGTGTAACTGCGGTAGCTAAACGTGGTGGTGTCGTTCAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGAAGCAGGTATCGACATCTACAACCTGACCAAAt                                                                                                         >  2:199899/1‑149 (MQ=255)                                                                                                                                                                                                                        gtggCCGTTGACCCCGGTGTAACGGCGGTAGCTAAACGTGGTGGTGTCGTTCAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACTAAGACGATATGTATCTGGGTGAAGCAGGTATCGACATCTACaa                                                                                                                    <  1:170043/131‑1 (MQ=255)                                                                                                                                                                                                                        gTTGCCGTTGACTCCGGTGTAACTGCGGTAGCTAAACGTGGTGGTGTCGTTCAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGAAGCAGGTa                                                                                                                                 <  2:347027/121‑1 (MQ=255)                                                                                                                                                                                                                        gTTGCCGTTGACTCCGGTGTAACTGCGGTAGCTAAACGTGGTGGTGTCGTTCAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGAAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAg                                                                                        <  1:354735/162‑1 (MQ=255)                                                                                                                                                                                                                        gTTGCCGTTGACCCCGGTGTAACTGCGGTAGCTAAACgtgg                                                                                                                                                                                                                 <  1:146575/41‑1 (MQ=255)                                                                                                                                                                                                                        gTTGCCGTTGACCCCGGTGTAACTGCGGTAGCTAAACGTGGTGGTGTCGTTCAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGAAGCAGGTATCGACATCTACAACCTGACCAAATacac                                                                                                     <  1:199899/149‑1 (MQ=255)                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                            GCCGTAGCAAAGGCGAATCCAGCTTGTTCAGCCGCGACCAGGTTGACTACATGGACGTATCCACCCAGCAGGTGGTATCCGTCGGTGCGTCCCTGATCCCGTTCCTGGAACACGATGACGCCAACCGTGCATTGATGGGTGCGAACATGCAACGTCAGGCCGTTCCGACTCTGCGCGCTGATAAGCCGCTGGTTGGTACTGGTATGGAACGTGCTGTTGCCGTTGACTCCGGTGTAACTGCGGTAGCTAAACGTGGTGGTGTCGTTCAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGAAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGAACACCTGTATCAACCAGATGCCGTGTGTGTCTCTGGGTGAACCGGTTGAACGTGGCGACGTGCTGGCAGACGGTCCGTCCACCGA  >  NC_000913/4183151‑4183613

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑