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	94.7%	118.5 / 0.2	38	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 . (2/0);  new base C (18/18);  total (20/18)
Fisher's exact test for biased strand distribution p-value = 4.88e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGGCGGCGTCTTCGAAGAGGATCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGC‑TTG‑CC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATA  >  NC_002947/1932491‑1932778                                                                                                                                                      |                                                                                                                                              tGGCGGCGTCTTCGAAGAGGATCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGC‑TTG‑c                                                                                                                                              <  4:211070/149‑1 (MQ=255)       cgTCTTCGCAGAGGATCTGGACCTTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTACACGCTGGGGCCGCTTTGCGGCCCTTCGCCGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGC‑TTG‑cccgcga                                                                                                                                        <  8:272019/149‑6 (MQ=39)         tCTTCGAAGAGGATCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGC‑TTGCCC‑GCGAAg                                                                                                                                      <  5:87372/149‑1 (MQ=255)               aaGAGGATCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTACCCTGTAGGAGCGGGC‑TTGCCC‑GCGAAGGGCTg                                                                                                                                 >  3:204396/1‑148 (MQ=255)                    gATCTGGACATTAGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCTCGGGCAAGCCCGCTCCTACAAAGGATTTTCGTCCCCTGTAGGAGCGCGC‑TTGCCC‑GCGAAGGGCTGCAAgg                                                                                                                            >  5:134161/1‑148 (MQ=255)                               tCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGC‑TTGCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAAtt                                                                                                                >  8:307603/1‑149 (MQ=255)                                      cGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGC‑TTGCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGAc                                                                                                          >  5:174902/1‑148 (MQ=255)                                      cGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCAGGC‑TTGCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGAc                                                                                                          >  5:338298/1‑148 (MQ=255)                                      cGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAACCCCCTCCAACAAAAGATAATCGACCCCAGTAGGACCGGGCTTTC‑CC‑GCCAAGGGCAGCAAAGCAGCCCCAAATTGtagcc                                                                                                          >  2:128308/1‑144 (MQ=255)                                          aTTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCAGGC‑TTGCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTAcgc                                                                                                     <  6:338298/149‑1 (MQ=255)                                                gttctaACTAAAAAAGCAGTAAACGGTGGGGCCGGTTTGCGGCCGTTCGCGGGCAACCCCGCTCCTATAATGTAAATCCGTCCCCTTTATGAGCGGGC‑TTGCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCa                                                                                               <  6:134161/147‑1 (MQ=25)                                                  tctcACGAAAATAGCAGTAAACGGTGGGGCCGCTTTGCGGCCGTGCGCGGGCATGCCGGCTCCTACAAAGTATAGGCGTCCCCTGTAGTAGCGGGC‑TTGCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAg                                                                                              <  1:128308/148‑1 (MQ=38)                                                  tctcACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGC‑TTGCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGc                                                                                             >  1:6142/1‑149 (MQ=255)                                                      aCGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGC‑TTGCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATc                                                                                         >  2:237998/1‑149 (MQ=255)                                                      aCGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGC‑TTGCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATc                                                                                         >  2:98525/1‑149 (MQ=255)                                                       ctaaaaTAGCATTAAAGGGTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGTATTTGCGTCCCCTGTCGTAGGGGGC‑TTGCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATcc                                                                                        <  4:204396/147‑1 (MQ=25)                                                          aaaTAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGC‑TTGCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGc                                                                                     <  6:174902/149‑1 (MQ=255)                                                          aaaTAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGC‑TTG‑CCAGCGAAGGGCTGCAAGGCAGCCCCAAATTGTAGACTACGCGGATCAGCGATCCGGc                                                                                     >  4:276090/1‑149 (MQ=255)                                                            aTAGCATTAAAGGCTGGGGCCGCTTTGCGGCGCTTGGGGGGCAAGCCCGCTCCTACAAAGGTTATGCGTCCCCTGTAGGATCGTGG‑TTGCCC‑GCGAAGGGCTGCAAGGCATCCCGAAATTGTCGACTACGCGGATCAGCGATCCGGCAg                                                                                   <  2:33700/149‑1 (MQ=255)                                                             tAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGTGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGTAGCGGGC‑TTGCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAgg                                                                                  <  6:141896/149‑1 (MQ=255)                                                               gCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGC‑TTGCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGt                                                                                <  7:98396/149‑1 (MQ=255)                                                                  gTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGC‑TTGCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGAt                                                                             >  6:121764/1‑149 (MQ=255)                                                                            gggCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGC‑TTGCCC‑GCGACGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTcc                                                                   >  5:71991/1‑149 (MQ=255)                                                                            gggCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGC‑TTGCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTc                                                                    <  1:237998/148‑1 (MQ=255)                                                                              gCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGC‑TTGCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTAcgcg                                                                                                    >  8:261601/1‑114 (MQ=255)                                                                              gCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGC‑TTGCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTAcgcg                                                                                                    <  7:261601/114‑1 (MQ=255)                                                                                cgttttGGGGCCCTTCGCGGGCACGCCCGCTCAAAAAAAGTATATGCGCCCCCTGTCGCCGCGGGC‑TTGCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGaa                                                               <  3:51833/146‑1 (MQ=255)                                                                                           ccTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGC‑TTGCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTg                                                    <  5:121764/149‑1 (MQ=255)                                                                                                   ggCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGC‑TTGCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGtt                                            >  3:233794/1‑149 (MQ=255)                                                                                                         cccGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGC‑TTGCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTCCCCTGGTTTTCCAg                                      <  7:307603/149‑1 (MQ=255)                                                                                                           cGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGC‑TTGCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTc                                         <  4:2269/144‑1 (MQ=255)                                                                                                           cGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGC‑TTGCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAgat                                    >  3:2269/1‑147 (MQ=255)                                                                                                                     aaGGATATGCGTCCCCTGTAGGAGCGGGC‑TTGCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTAAGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGca                           >  6:19056/1‑148 (MQ=255)                                                                                                                            tGCGTCCCCTGTAGGAGCGGGC‑TTGCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACatcatc                    <  1:113043/148‑1 (MQ=255)                                                                                                                                       ttggAGCGGGC‑TTGCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGt         <  4:239347/146‑1 (MQ=255)                                                                                                                                       tAGGAGCGGGC‑TTGCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCTGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATg          <  5:19056/147‑1 (MQ=255)                                                                                                                                         ggAGCGGGC‑TTGCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTca      >  1:202173/1‑149 (MQ=255)                                                                                                                                         ggAGCGGGC‑TTGCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTca      >  5:302422/1‑149 (MQ=255)                                                                                                                                            gCGGGC‑TTGCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTcaca    >  6:131973/1‑148 (MQ=255)                                                                                                                                             cGGGC‑TTGCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACata  >  2:43464/1‑149 (MQ=255)                                                                                                                                                      |                                                                                                                                              TGGCGGCGTCTTCGAAGAGGATCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGC‑TTG‑CC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATA  >  NC_002947/1932491‑1932778

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: ‑