Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	3,781,051	C→G	14.3%	intergenic (+34/‑164)	lldD → / → trmL	L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,781,051	0	C	G	14.3%	120.4 / 12.1	42	intergenic (+34/‑164)	lldD/trmL	L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent
Reads supporting (aligned to +/- strand):  ref base C (20/16);  new base G (3/3);  total (23/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.69e-01

GCTGACTGGCGCGAAATCGATCAGCGAAATTACGCAAGATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCC  >  NC_000913/3780906‑3781197                                                                                                                                                  |                                                                                                                                                   gCTGACTGGCGCGAAATCGATCAGCGAAATTACGCAAGATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAg                                                                                                                                                  <  4:81038/148‑1 (MQ=255) gCTGACTGGCGCGAAATCGATCAGCGAAATTACGCAAGATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAg                                                                                                                                                  >  3:81038/1‑148 (MQ=255)   tGACTGGCGCGAAATCGATCAGCGAAATTACGCAAGATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGGga                                                                                                                                               >  2:17800/1‑149 (MQ=255)      cTGGCGCGAAATCGATCAGCGAAATTACGCAAGATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTGAGGGagag                                                                                                                                            <  2:45105/149‑1 (MQ=255)      cTGGCGCGAAATCGATCAGCGAAATTACGCAAGATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGGGagag                                                                                                                                            <  4:45469/149‑1 (MQ=255)      cTGGCGCGAAATCGATCAGCGAAATTACGCAAGATTCGCTGGTGCAGGGGCTGGGTAAAGAGCTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGGGagag                                                                                                                                            <  3:15885/149‑1 (MQ=255)       tGGCGGGAAATCGATCAGCGAAATTACGCAAGATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTGAGGGAGAgg                                                                                                                                           <  4:35112/149‑1 (MQ=255)        ggCGCGAAATCGATCAGCGAAATTACGCAAGATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGGGAGAggg                                                                                                                                          <  1:71413/149‑1 (MQ=255)          cgcgAAATCGATCAGCGAAATTACGCAAGATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGGGAGAGGGGa                                                                                                                                        <  1:33481/149‑1 (MQ=255)             gAAATCGATCAGCGAAATTACGCAAGATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTGAGGGAGAgggttagg                                                                                                                                     <  4:28875/149‑6 (MQ=255)                                    aaGATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTc                                                                                                              >  2:41498/1‑149 (MQ=255)                                     aGATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCa                                                                                                             <  2:57195/149‑1 (MQ=255)                                      gATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCAc                                                                                                            >  4:18834/1‑149 (MQ=255)                                      gATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCAc                                                                                                            <  3:18834/149‑1 (MQ=255)                                                    ggggCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACAcc                                                                                              <  4:59383/149‑1 (MQ=255)                                                             tAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCttt                                                                                     >  2:79053/1‑149 (MQ=255)                                                               aaGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCttttt                                                                                   <  4:66993/149‑1 (MQ=255)                                                               aaGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCttttt                                                                                   >  1:76371/1‑149 (MQ=255)                                                                  agTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTtc                                                                                >  4:4285/1‑149 (MQ=255)                                                                               aCTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAgg                                                                                                                                                 >  2:25628/1‑71 (MQ=255)                                                                               aCTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAgg                                                                                                                                                 <  1:25628/71‑1 (MQ=255)                                                                                  ggCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCgg                                                                <  4:19601/149‑1 (MQ=255)                                                                                     tCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGga                                                             >  3:79535/1‑149 (MQ=255)                                                                                       ccATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGgaga                                                           <  4:23082/149‑1 (MQ=255)                                                                                        cATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGagag                                                          <  3:67431/149‑1 (MQ=255)                                                                                                     aaTGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAgg                                             <  1:81271/149‑1 (MQ=255)                                                                                                           gCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGGGCGGGGaaaa                                       >  1:34208/1‑149 (MQ=255)                                                                                                                        cgcCCCCTCACCCTAACCCTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTc                          >  2:50729/1‑149 (MQ=255)                                                                                                                                 aCCCTAACCCTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAggg                                            >  1:72417/1‑122 (MQ=255)                                                                                                                                 aCCCTAACCCTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAggg                                            <  2:72417/122‑1 (MQ=255)                                                                                                                                   ccTAACCCTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAGGGCCGCACTGCTCACCAATTTTCt               >  4:32957/1‑149 (MQ=255)                                                                                                                                   ccTAACCCTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCt               >  2:64628/1‑149 (MQ=255)                                                                                                                                    cTAACCCTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTg              >  4:52052/1‑149 (MQ=255)                                                                                                                                      tccccTCTCCCTGAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCt            >  1:53985/3‑149 (MQ=255)                                                                                                                                      tccccTCTCCCTGAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCt            >  3:87757/3‑149 (MQ=255)                                                                                                                                       aCCCTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTa           >  1:63375/1‑149 (MQ=255)                                                                                                                                          ctctCCCTGAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATcc        >  1:63581/1‑149 (MQ=255)                                                                                                                                           tctcCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCt       >  1:8679/1‑149 (MQ=255)                                                                                                                                             tcCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGc     >  2:34800/1‑149 (MQ=255)                                                                                                                                                cTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGaca                                                                                                <  4:41426/55‑1 (MQ=255)                                                                                                                                                cTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGaca                                                                                                >  3:41426/1‑55 (MQ=255)                                                                                                                                                cTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGcccc  >  4:68446/1‑149 (MQ=255)                                                                                                                                                  |                                                                                                                                                   GCTGACTGGCGCGAAATCGATCAGCGAAATTACGCAAGATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCC  >  NC_000913/3780906‑3781197

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑