Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,241,311	C→T	14.3%	intergenic (+58/‑223)	gltX → / → PP_t25	glutamate‑‑tRNA ligase/tRNA‑Ala

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,241,311	0	C	T	14.3%	83.0 / 5.5	40	intergenic (+58/‑223)	gltX/PP_t25	glutamate‑‑tRNA ligase/tRNA‑Ala
Reads supporting (aligned to +/- strand):  ref base C (11/19);  new base T (3/2);  total (19/21)
Fisher's exact test for biased strand distribution p-value = 3.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.88e-01

CCGCCTGCGCCAGGCTCTGGACCTGCTGGGTGGGGTGTCGAAGAAAGAAAACAAAGAGTGGGAAAAGCTGTTGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATCTGTGAAAAAATTTTTGAATATTTTTGAAAATTAGTTTGACAGCCCTGCAATCCGAACTTAATAT  >  NC_002947/2241166‑2241458                                                                                                                                                   |                                                                                                                                                    ccGCCTGCGCCAGGCTCTGGACCTGCTGGGTGGGGTGTCGAAGAAAGAAAACAAAGAGTGGGAAAAGCTGTTGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTCAat                                                                                                                                                  <  7:234743/149‑1 (MQ=255)  cGCCTGCGCCAGGCTCTGGACCTGCTGGGTGGGGTGTCGAAGAAAGAAAACAAAGAGTGGGAAAAGCTGTTGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTCAata                                                                                                                                                 >  5:208003/1‑149 (MQ=255)   gCCTGCGCCAGGCTCTGGACCTGCTGGGTGGGGTGTCGAAGGAAGAAAACAAAGAGTGGGAAAAGCTGTTGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATACAATGGTAAATTCAata                                                                                                                                                 >  2:73433/1‑148 (MQ=255)     cTGCGCCAGGCTCTGGACCTGCTGGGTGGGGTGTCGAAGAAAGAAAACAAAGAGTGGGAAAAGCTGTTGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTCAATATCg                                                                                                                                              <  6:208003/149‑1 (MQ=255)        cgcCAGGCTCTGGACCTGCTGGGTGGGGTGTCGAAGAAAGAAAACAAAGAGTGGGAAAAGCTGTTGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTCAATATCGCa                                                                                                                                            <  5:104561/148‑1 (MQ=255)        cgcCAGGCTCTGGACCTGCTGGGTGGGGTGTCGAAGAAAGAAAACAAAGAGTGGGAAAAGCTGTTGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTCAATATCGCa                                                                                                                                            <  7:109135/148‑1 (MQ=255)         gcCAGGCTCTGGACCTGCTGTGTGGGTTGTAGAAGAAAGAAAACAAAGAGTTGGAAATTCTGTTGGCTTCCATAGCATGATTCAGCTTTGCACCTAAACAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTCAATATCGCAtt                                                                                                                                          <  5:188790/149‑1 (MQ=255)                tctGGACCTGCTGGGTGGGGTGTCGAAGAAAGAAAACAAAGAGTGGGAAAAGCTGTTGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTCAATATCGCATTCGCCGGc                                                                                                                                   >  3:295712/1‑149 (MQ=255)                  tGGACCTGCTGGGTGGGGTGTCGAAGAAAGAAAACAAAGAGTGGGAAAAGCTGTTGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTCAATTTc                                                                                                                                               <  2:306092/135‑1 (MQ=255)                    gACCTGCTGGGTGGGGTGTCGAAGAAAGAAAACAAAGAGTGGGAAAAGCTGTTGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCGGCGAATGCGATATTGAATTTACCATTGCATTCGCGGGCAc                                                                                                                                 <  4:339464/147‑1 (MQ=25)                    gACCTGCTGGGTGGGGTGTCGAAGAAAGAAAACAAAGAGTGGGAAAAGCTGTTGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCGGCGAATGCGATATTGAATTTACCATTGCATTCGCGGGCACGc                                                                                                                               <  5:111261/149‑1 (MQ=25)                                                        ctggggtaaacGCTGTTGGCTTCCATCGCCTGATTCCGCTTTCCACCAACCCTGTGGCCGC‑GGGCGGGCCCGCTAAGGAAATGGTAAATTCAATATCCCATGCCCCGCCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCgg                                                                                           <  2:190359/142‑1 (MQ=255)                                                               aaaaGCTGTTGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAggg                                                                                    <  7:117956/149‑1 (MQ=255)                                                                     tGTTGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGGGTGGCCCCGCATTGAATGGGTAATTTAATATAGGATTAGCCGGGCCGCCCCCGCCCCCAGGGCCACAAAGCCCCAAAAAAACGGGGGAgggggggga                                                                              >  6:2478/1‑146 (MQ=255)                                                                       ttGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTCAATATCGCATTCGCCGGCAc                                                                                                                                 <  7:337167/96‑1 (MQ=255)                                                                       ttGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTCAATATCGCATTCGCCGGCAc                                                                                                                                 >  8:337167/1‑96 (MQ=255)                                                                       ttGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTAAATATCGCATTCGCCGGCACGCCCGCGCCCCCAGGCGCACTAAGCCCCAAAAAACCGGGGTAGGGCGGGAAGt                                                                            >  8:90693/1‑149 (MQ=255)                                                                         ggCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGGCCCCGAATTGAAATGTTAATTGAATATAGCATTGGCCCGCCCGCCCCCACCCCCAGGCCCACGAAGCCCCAAAAAACCCGGGGTGGGCGGTTAGTgg                                                                          >  4:97725/1‑148 (MQ=255)                                                                         ggCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGt                                                                            <  3:97725/147‑1 (MQ=255)                                                                          gCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATTGTAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGa                                                                          <  4:295712/148‑1 (MQ=255)                                                                           cTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGAtt                                                                        <  8:76677/149‑1 (MQ=255)                                                                            ttCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTTCCCGCGCATGCAATGGTAAATTAAATATAGCATTCGCCGGCACGCCCCCTCCCACAGGCCCACTAAGCCCCAAAAAACCGGGGGAGGGCGGTAAGTGATTg                                                                       >  5:121937/1‑149 (MQ=255)                                                                               cATCGCCTCATACAGTTTTGCACCTAACCTGGGGGAGC‑GGGGGTGCCCGCCAATGAAATTGAAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGtt                                                                     <  2:340985/148‑1 (MQ=255)                                                                                 tCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATACAATGGTAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATc                                                                  <  1:73433/149‑1 (MQ=255)                                                                                                     ccTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTAAATATAGCATTAGCCGGCACGCCCGCTGCCCCAGGCCAACTAAGCCCCAAAAAACCCGGGTAGGGCGGTAAGTGATTGTTTTCTGTGTAAAAATTTTTGAatt                                              >  6:185734/1‑148 (MQ=255)                                                                                                        aaCCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAAATGTAAATTCAATTAAGCATTCGCCGGCCCGCCCGCTGCCACAGGGCAACTAAGCCCCAAAAAAACGGGGTAGGGGGGTAAGTGATTGTTATATGTGAAAAAATTTTTGAATtttt                                           >  6:359389/1‑149 (MQ=255)                                                                                                           cAGTGGGAGCGGGGCGTGCCCCCGAATGCAATGGTAAATTAAAAATAGCAATACCCGGCCCCCCCCCACCCCCAGGCCAACTAAGCCCCAAAAAACCGGGGGAGGGCGGTTATTGATTGTTTTAAGTGTAAAAAttttt                                                   >  4:289364/1‑139 (MQ=255)                                                                                                           cAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATCTGTGAAAAAAttttt                                                   <  3:289364/138‑1 (MQ=255)                                                                                                              tGGGCGC‑GGGCGTGCCCGCTAATGCAATTGTAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATCTGTGAAAAAATTTTTGAATATTTTTGaaa                                     <  3:201640/149‑1 (MQ=255)                                                                                                                              cggcgAATGCGATATTGAATTTACCATTGCATTCGCGGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATCTGTGAAAAAATTTTTGAATATTTTTGAAAATTAGTTTGACAGcc                      >  1:85190/3‑149 (MQ=25)                                                                                                                              cggcgAATGCGATATTGAATTTACCATTGCATTCGCGGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATCTGTGAAAAAATTTTTGAATATTTTTGAAAATTAGTTTGACAGcc                      >  4:42326/3‑149 (MQ=25)                                                                                                                               cgcgAATGCAATGGTAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGt                                                                                >  3:186059/1‑90 (MQ=255)                                                                                                                               cgcgAATGCAATGGTAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGt                                                                                <  4:186059/90‑1 (MQ=255)                                                                                                                                        aaTGGTAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATCTGTGAAAAAATTTTTGAATATTTTTGAAAATTAGTTTGACAGCCCTGCAATcc             >  4:182389/1‑148 (MQ=255)                                                                                                                                          tGGTAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATCTGTGAAAAAATTTTTGAATATTTTTGAAAATTAGTTTGACAGCCCTGCAATCCGaa          >  2:98530/1‑149 (MQ=255)                                                                                                                                            gTAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATCTGTGAAAAAATTTTTGAATATTTTTGAAAATTAGTTTGACAGCCCTGCAATCCGAAc         <  6:121937/148‑1 (MQ=255)                                                                                                                                            gTAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATCTGTGAAAAAATTTTTGAATATTTTTGAAAATTAGTTTGACAGCCCTGCAATCCGAACt        >  7:112370/1‑149 (MQ=255)                                                                                                                                             tAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATCTGTGAAAAAATTTTTGATTTTTTTTGAAAATTAGTTTGACAGACCTGCAATCCGAACt        >  8:244006/1‑148 (MQ=255)                                                                                                                                               aaTTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATCTGTGAAAAAATTTTTGAATATTTTTGAAAATTAGTTTGACAGCCCTGCAATCCGAACTTaa     <  5:2478/149‑1 (MQ=255)                                                                                                                                                  tCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATCTGTGAAAAAATTTTTGAATATTTTTGAAAATTAGTTTGACAGCCCTGCAATCCGAACTTAatat  >  2:294719/1‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                                    CCGCCTGCGCCAGGCTCTGGACCTGCTGGGTGGGGTGTCGAAGAAAGAAAACAAAGAGTGGGAAAAGCTGTTGGCTTCCATCGCCTGATTCAGCTTTGCACCTAACCAGTGGGAGC‑GGGCGTGCCCGCGAATGCAATGGTAAATTCAATATCGCATTCGCCGGCACGCCCGCTCCCACAGGCCAACTAAGCCCCAAAAAACCGGGGTAGGGCGGTAAGTGATTGTTATCTGTGAAAAAATTTTTGAATATTTTTGAAAATTAGTTTGACAGCCCTGCAATCCGAACTTAATAT  >  NC_002947/2241166‑2241458

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: ‑