Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_002947	1,932,640	+C	intergenic (‑107/+43)	rluA ← / ← minE	bifunctional tRNA pseudouridine(32) synthase TrmQ/ribosomal large subunit pseudouridine synthase RluA/cell division topological specificity factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,932,638	1	.	C	97.4%	126.3 / ‑3.3	39	intergenic (‑105/+45)	rluA/minE	bifunctional tRNA pseudouridine(32) synthase TrmQ/ribosomal large subunit pseudouridine synthase RluA/cell division topological specificity factor
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base C (19/19);  total (19/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.38e-01

TGGCGGCGTCTTCGAAGAGGATCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCC‑CTTCGCGGGCAAGCCCGCTCCTACAAAGGATAT‑GCGTCCCCTGTAGGAGCGGGCTTG‑C‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATATT  >  NC_002947/1932491‑1932780                                                                                                                                                       |                                                                                                                                                tGGCGGCGTCTTCGAAGAGGATCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCC‑CTTCGCGGGCAAGCCCGCTCCTACAAAGGATAT‑GCGTCCCCTGTAGGAGCGGGCTTG‑c                                                                                                                                                <  7:6410/149‑1 (MQ=255)   gcggcgTCTTCGAAGAGGATCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCC‑CTTCGCGGGCAAGCCCGCTCCTACAAAGGATAT‑GCGTCCCCTGTAGGAGCGGGCTTG‑c‑cc                                                                                                                                             <  6:271888/149‑2 (MQ=255)   gcggcgTCTTCGAAGAGGATCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCC‑CTTCGCGGGCAAGCCCGCTCCTACAAAGGATAT‑GCGTCCCCTGTAGGAGCGGGCTTG‑c‑c                                                                                                                                              <  2:268504/148‑1 (MQ=255)    cggcgTCTTCGAAGAGGATCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCC‑CTTCGCGGGCAAGCCCGCTCCTACAAAGGTTAT‑GCGTCCCCTGTAGGAGCGGGCTTG‑c‑ccg                                                                                                                                            <  2:166390/149‑3 (MQ=255)         tCTTCGAAGAGGATCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCC‑CTTCGCGGGCAAGCCCGCTCCTACAAAGGATAT‑GCGTCCCCTGTAGGAGCGGGCTTGCC‑CGCGAAg                                                                                                                                        <  1:318028/149‑1 (MQ=255)         tCTTCGAAGAGGATCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCC‑CTTCGCGGGCAAGCCCGCTCCTACAAAGGATAT‑GCGTCCCCTGTAGGAGCGGGCTTGCC‑CGCGAAg                                                                                                                                        <  5:98939/149‑1 (MQ=255)                      tCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCC‑CTTCGCGGGCAAGCCCCCTACAAAAAAAGAAAA‑GCGTCCCCTGTACGATCGGGCGTGCC‑CGCGAAGGGCTGCAAGGCAg                                                                                                                           >  7:372380/1‑149 (MQ=255)                         ggACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCC‑CTTCGCGGGCAAGCCCGCAACTACAAAGGATAT‑TCGTCCCCAGTAGGAGCGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGccc                                                                                                                        >  4:422327/1‑149 (MQ=38)                              ttCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCC‑CTTCGCGGGCAAGCCCGCTCCTACAAAGGATAT‑GCGTCCCCTGTAGGAGCGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAAt                                                                                                                   >  3:268178/1‑149 (MQ=255)                               tccaccgCGGCATTGCAGGTCACCCCAAAATCCCCGAAACCGCGGGGGCCGCTTGGCGGCC‑CTGCCCGGGCACCCCCGCTCCAACAAAGTATAT‑GCGCCCCCTGTCGGCGCGGGCTGGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAAtt                                                                                                                  <  6:10336/143‑1 (MQ=255)                                 caCAGCGGAATGGCAGGTCGCACTAAAATCCCAGTAACCGCGGGGGCCGCTTTGCGGCC‑CTGCGCGGGCACGCCCGCTCCTACAAAGGAAAT‑GCGTCCCCTGTAGGCGCGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGt                                                                                                                <  1:373951/148‑1 (MQ=37)                                   cAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCC‑CTTCGCGGGCAAGCCCGCTCCTACAAAGGATAT‑GCGTCCCCTGTAGGAGCGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTc                                                                                                               <  4:268178/148‑1 (MQ=255)                                       ggCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCC‑CTTCGCGGGCAAGCCCGCTCCTACAAAGGATAT‑GCGTCCCCTGTAGGAGCGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTcagatt                                                                                                          >  7:55529/1‑144 (MQ=255)                                       ggCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCC‑CTTCGCGGGCAAGCCCACTCCTACAAAGGATAT‑GCGTCCCCTGTAGGAGCGGGCTTGCC‑CGCGAAGGGCTGCAAGGCa                                                                                                                            <  8:88652/131‑1 (MQ=255)                                       ggCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCC‑CTTCGCGGGCAAGCCCACTCCTACAAAGGATAT‑GCGTCCCCTGTAGGAGCGGGCTTGCC‑CGCGAAGGGCTGCAAGGCa                                                                                                                            >  7:88652/1‑131 (MQ=255)                                       gccATTGCAGGTCTCACCAAAATTCCAGTAAACGCTGGGGCCGCTTTGCGGCC‑CTTCGCGGGCAAGCCGGCTCAAACAACGTATTT‑GCGGCCCCTGTCGGAGCGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGt                                                                                                                <  8:55529/141‑1 (MQ=21)                                         cATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCC‑CTTCGCGGGCAAGCCCGCTCCTACAAAGGATAT‑GCGTCCCCTGTAGGAGCGGGCTTG‑CGCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTAcg                                                                                                        <  6:438376/149‑1 (MQ=255)                                                 gTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCC‑CTTCGCGGGCAAGCCCGCTCCTACAAAGGATAT‑GCGTCCCCTGTAGGAGCGGGGTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAg                                                                                                <  7:2517/149‑1 (MQ=255)                                                 gTCTCACGAAAATAGCAGTAAACGCGGGGGCCGCTTTGCGGCC‑CTTCGCGGGCAAGCCCGCTCCTACAAAGGAAAT‑GCGTCCCCTGTCGGAGCGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAg                                                                                                <  2:375151/149‑1 (MQ=38)                                                      aCGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCC‑CTTCGCGGGCAAGCCCGCTCCTACAAAGGATAT‑GCGTCCCCGGTAGGAGCGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATc                                                                                           >  5:254232/1‑149 (MQ=255)                                                        gAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCGCTTCGCGGGCAAGCCCGCTCCTACAAAGGATAT‑GCGTCCCCTGTAGGAGCGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATcc                                                                                          >  1:71667/1‑149 (MQ=255)                                                          aaaTAGCAGTAAACGCTGGGGCCGCTTTGCGGCC‑CTTCGCGGGCAAGCCCGCTCCCACAAAGGATAT‑GCGTCCCCTGTAGGAGCGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCgg                                                                                        <  8:3055/148‑1 (MQ=255)                                                                   tAAACGCTGGGGCCGCTTTGCGGCC‑CTTCGCGGGCAAGCCCGCTCCTACAAAGGATAT‑GCGTCCCCTGTAGGAGCGGGCTTGCC‑CGCGCAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATg                                                                              >  7:174332/1‑149 (MQ=255)                                                                             ggCCGCTTTGCGGCC‑CTTCGCGGGCAAGCCCGCTCCTACAAAGGATAT‑GCGTCCCCTGTAGGAGCGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAgg                                                                                    >  5:346139/1‑133 (MQ=255)                                                                             ggCCGCTTTGCGGCC‑CTTCGCGGGCAAGCCCGCTCCTACAAAGGATAT‑GCGTCCCCTGTAGGAGCGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAgg                                                                                    <  6:346139/133‑1 (MQ=255)                                                                              gCCGCTTTGCGGCC‑CTTCGCGGGCAAGCCCGCTCCTACAAAGGATAT‑TCGTCCCCTGTAAGAGCGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTTTCGACTACGCGGATCATCCAACCGGCACGCTGATCTTAAACTc                                                                      >  8:189330/1‑146 (MQ=25)                                                                                           ccgtgcgcgGGCAAGCCCGCTCCTACAAAGGATAT‑GCGTCCCCTGTAGCCGCGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCt                                                       <  8:174332/144‑1 (MQ=39)                                                                                             cTTCGCGGGCAAGCCCGCTCCTACAAAGGATAT‑GCGTCCCCTGTAGGAGCGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGc                                                     >  1:349001/1‑149 (MQ=255)                                                                                                       caccccGCTCCT‑CAAACGTTAAGGCGTCCCCTGTCGGTGGGGGTTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTc                                           <  8:372380/146‑1 (MQ=255)                                                                                                       aaGCCCGCTCCTACAAAGGATAT‑GCGTCCCCTGTAGGAGCGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGAt                                                                                                   <  1:122872/93‑1 (MQ=255)                                                                                                       aaGCCCGCTCCTACAAAGGATAT‑GCGTCCCCTGTAGGAGCGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGAt                                                                                                   >  2:122872/1‑93 (MQ=255)                                                                                                       aaGCCCGCTCCTACAAAGGATAT‑GCGTCCCCTGTAGGAGCGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTc                                           >  1:212262/1‑149 (MQ=255)                                                                                                       aaGCCCGCTCCTACAAAGGATAT‑GCGTCCCCTGTAGGAGCGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTc                                           <  2:71667/149‑1 (MQ=255)                                                                                                             gcgccTACAAAGTTTAT‑GCGTCCCCTGTAGGAGGGGTCTGGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTc                                     <  6:32975/146‑1 (MQ=255)                                                                                                                            at‑GCGTCCCCTGTAGGAGCGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACatcatc                      >  3:419050/1‑149 (MQ=255)                                                                                                                               gCGTCCCCTGTAGGAGCGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGt                    >  6:416436/1‑149 (MQ=255)                                                                                                                                cGTCCCCTGTAGGAGCGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGc                                                     >  3:344239/1‑115 (MQ=255)                                                                                                                                cGTCCCCTGTAGGAGCGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGc                                                     <  4:344239/115‑1 (MQ=255)                                                                                                                                  tCCCCTGTAGGAGCGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGc                 <  4:419050/149‑1 (MQ=255)                                                                                                                                                gggCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCGCAAATTGTCGACTACGCGGATCAGCGATCAGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACatat   >  1:46943/1‑149 (MQ=255)                                                                                                                                                 ggCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATAtt  >  8:118736/1‑149 (MQ=255)                                                                                                                                                 ggCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATAtt  <  3:45819/149‑1 (MQ=255)                                                                                                                                                 ggCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATAtt  >  4:293198/1‑149 (MQ=255)                                                                                                                                                       |                                                                                                                                                TGGCGGCGTCTTCGAAGAGGATCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCC‑CTTCGCGGGCAAGCCCGCTCCTACAAAGGATAT‑GCGTCCCCTGTAGGAGCGGGCTTG‑C‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATATT  >  NC_002947/1932491‑1932780

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: ‑