Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,947,456	(C)5→6	noncoding (70/77 nt)	metZ →	tRNA‑Met

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,947,451	1	.	C	96.0%	75.4 / ‑2.8	25	noncoding (65/77 nt)	metZ	tRNA‑Met
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base C (6/18);  total (7/18)
Fisher's exact test for biased strand distribution p-value = 2.80e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.47e-01

TCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGCATGAAAACGCGAGCGGAGTATAGTGCGCATCCACGGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑GG‑CCCCCGCAACCAATTAAAATTTGATGAAGTAAAGCAGTACGGTGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCCGGCCCCCGCAACCAATCAAATTTGAT  >  NC_000913/2947312‑2947585                                                                                                                                              |                                                                                                                                       tCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGCATGAAAACGCGAGCGGAGTATAGTGCGCATCCACGGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑gg                                                                                                                                         <  1:534820/140‑1 (MQ=255) tCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGCATGAAAACGCGAGCGGAGTATAGTGCGCATCCACGGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑gg                                                                                                                                         <  1:766295/140‑1 (MQ=255)   aTGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGCATGAAAACGCGAGCGGAGTATAGTGCGCATCCACGGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑ggtc                                                                                                                                       <  2:363598/140‑3 (MQ=255)    tGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGCATGAAAACGCGAGCGGAGTATAGTGCGCATCCACGGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑GG‑ccc                                                                                                                                     >  1:523943/1‑140 (MQ=255)         aaTCCGTGATCGGGGCAAAAAAAAGGTTGCATGAAAACGCGAGCGGAGTATAGTGCGCATCCACGGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑GG‑ccccccgc                                                                                                                                >  1:158398/1‑137 (MQ=255)           tCCGTGATCGGGGTAAAAAAAAGGTTGCATGAAAACGCGAGCGGAGTATAGTGCGCATCCACGGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑GG‑ccccccgcaa                                                                                                                              <  1:124943/140‑6 (MQ=255)                gATCGGGGTAAAAAAAAGGTTGCATGAAAACGCGAGCGGAGTATAGTGCGCATCCACGGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑GGCCCCCCGCAACCAAt                                                                                                                          <  2:640254/140‑1 (MQ=255)                      ggTAAAAAAAAGGTTGCATGAAAACGCGAGCGGAGTATAGTGCGCATCCACGGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑GGCCCCCCGCAACCAATTAAAAt                                                                                                                    >  2:534489/1‑140 (MQ=255)                          aaaaaaaGGTTGCATGAAAACGCGAGCGGAGTATAGTGCGCATCCACGGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑GGCCCCCCGCAACCAATTAAAATTtga                                                                                                                <  1:161082/140‑1 (MQ=255)                          aaaaaaaGGTTGCATGAAAACGCGAGCGGAGTATAGTGCGCATCCACGGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑GGCCCCCCGCAACCAATTAAAATTtga                                                                                                                <  2:510232/140‑1 (MQ=255)                          aaaaaaaGGTTGCATGAAAACGCGAGCGGAGTATAGTGCGCATCCACGGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑GGCCCCCCGCAACCAATTAAAATTtga                                                                                                                <  2:348024/140‑1 (MQ=255)                               aaGGTTGCATGAAAACGCGAGCGGAGTATAGTGCGCATCCACGGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑GGCCCCCCGCAACCAATTAAAATTTGATGAAg                                                                                                           <  1:601852/140‑1 (MQ=255)                               aaGGTTGCATGAAAACGCGAGCGGAGTATAGTGCGCATCCACGGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑GGCCCCCCGCAACCAATTAAAATTTGATGAAg                                                                                                           <  2:158398/140‑1 (MQ=255)                               aaGGTTGCATGAAAACGCGAGCGGAGTATAGTGCGCATCCACGGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑GGCCCCCCGCAACCAATTAAAATTTGATGAAg                                                                                                           <  1:103457/140‑1 (MQ=255)                                aGGTTGCATGAAAACGCGAGCGGAGTATAGTGCGCATCCACGGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑GGCCCCCCGCAACCAATTAAAATTTGATGAAGt                                                                                                          >  1:455671/1‑140 (MQ=255)                                  gTTGCATGAAAACGCGAGCGGAGTATAGTGCGCATCCACGGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑GGCCCCCCGCAACCAATTAAAATTTGATGAAGTaa                                                                                                        <  2:119864/140‑1 (MQ=255)                                  gTTGCATGAAAACGCGAGCGGAGTATAGTGCGCATCCACGGACGCGGGGTGGAGCAGCCTGGTAGCTCGGCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑GGCCCCCCGCAACCAATTAAAATTTGATGAAGTaa                                                                                                        >  2:165294/1‑140 (MQ=255)                                    tGCATGAAAACGCGAGCGGAGTATAGTGCGCATCCACGGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑GGCCCCCCGCAACCAATTAAAATTTGATGaaaaaaaa                                                                                                      >  2:794885/1‑134 (MQ=255)                                    tGCATGAAAACGCGAGCGGAGTATAGTGCGCATCCACGGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑GGCCCCCCGCAACCAATTAAAATTTGATGAAGTAAAg                                                                                                      <  1:606481/140‑1 (MQ=255)                                    tGCATGAAAACGCGAGCGGAGTATAGTGCGCATCCACGGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑GGCCCCCCGCAACCAATTAAAATTTGATGAAGTAAAg                                                                                                      <  2:455671/140‑1 (MQ=255)                                                 gAGCGGAGTATAGTGCGCATCCACGGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑GGCCCCCCGCAACCAATTAAAATTTGATGAAGTAAAGCAGTACGGTGAcg                                                                                         <  1:165294/140‑1 (MQ=255)                                                 gAGCGGAGTATAGTGCGCATCCACGGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑GGCCCCCCGCAACCAATTAAAATTTGATGAAGTAAAGCAGTACGGTGAcg                                                                                         <  2:794161/140‑1 (MQ=255)                                                     ggAGTATAGTGCGCATCCACGGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑GGCCCCCCGCAACCAATTAAAATTTGATGAAGTAAAGCAGTACGGTGACGCggg                                                                                     <  1:534489/140‑1 (MQ=255)                                                      gAGTATAGTGCGCATCCACGGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑GGCCCCCCGCAACCAATTAAAATTTGATGAAGTAAAGCAGTACGGTGACGCgggg                                                                                    <  2:163561/140‑1 (MQ=255)                                                           taGTGCGCATCCACGGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑GGCCCCCCGCAACCAATTAAAATTTGATGAAGTAAAGCAGTACGGTGACGCGGGGTGGag                                                                               <  1:291546/140‑1 (MQ=255)                                                            aGTGCGCATCCACGGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑GGCCCCCCGCAACCAATTAAAATTTGATGAAGTAAAGCAGTACGGTGACGCGGGGTGGagc                                                                              <  2:342528/140‑1 (MQ=255)                                                              tGCGCATCCACGGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑GGCCCCCCGCAACCAATTAAAATTTGATGAAGTAAAGCAGTACGGTGACGCGGGGTGGagcag                                                                            <  1:604601/140‑1 (MQ=255)                                                                 gcATCCACGGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑GGCCCCCCGCAACCAATTAAAATTTGATGAAGTAAAGCAGTACGGTGACGCGGGGTGGag                                                                               <  1:364971/134‑1 (MQ=255)                                                                 gcATCCACGGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑GGCCCCCCGCAACCAATTAAAATTTGATGAAGTAAAGCAGTACGGTGACGCGGGGTGGag                                                                               >  2:364971/1‑134 (MQ=255)                                                                   aTCCACGGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑GGCCCCCCGCAACCATTTAAATTTTGGTGAAAAAAACCAGAACGGTGACGCGGGGAGAAACATCCTgg                                                                       >  2:369367/1‑140 (MQ=14)                                                                                                     cgtcgGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑GGCCCCCCGCAACCAATTAAAATTTGATGAAGTAAAGCAGTACGGGGACGCGGGGGGGAGCAGCCTGGTAGCTTGTCTTGTTCACAACCCGAGGGTCCTCgg                                     >  2:334346/1‑140 (MQ=14)                                                                                                                              tcgGTTCAAAACCAGA‑CCCCCGCAACCAATTAAAATTCGATGAAGTAAAGCAGTCCGGTGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCCGGCCCCCGCAACCAAt            <  2:523943/140‑1 (MQ=14)                                                                                                                                     aaaTCC‑GG‑‑CCCCGCAACCAATTAAAATTTGATGAAGTAAAGCAGTACGGTGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCCGGCCCCCGCAACCAATTAAAtaaga   >  1:877936/1‑136 (MQ=255)                                                                                                                                        tCC‑GGCCCCCCGCAACCAATTAAAATTTGATGAAGTAAAGCAGTACGGTGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCCGGCCCCCGCAACCAATCAAATTtgat  <  1:233571/140‑1 (MQ=255)                                                                                                                                              |                                                                                                                                       TCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGCATGAAAACGCGAGCGGAGTATAGTGCGCATCCACGGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCC‑GG‑CCCCCGCAACCAATTAAAATTTGATGAAGTAAAGCAGTACGGTGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCCGGCCCCCGCAACCAATCAAATTTGAT  >  NC_000913/2947312‑2947585

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑