Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 1,932,638:1 +C 100% intergenic (‑105/+45) 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_0029471,932,6381.C92.5% 123.9 / 4.0 40intergenic (‑105/+45)rluA/minEbifunctional tRNA pseudouridine(32) synthase TrmQ/ribosomal large subunit pseudouridine synthase RluA/cell division topological specificity factor
Reads supporting (aligned to +/- strand):  ref base . (1/2);  new base C (20/17);  total (21/19)
Fisher's exact test for biased strand distribution p-value = 5.96e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.20e-01
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GGCGTCTTCGAAGAGGATCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTT‑G‑CC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATATTT  >  NC_002947/1932495‑1932781
                                                                                                                                                 |                                                                                                                                                
ggcgTCTTCGAAGAGGATCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTT‑G‑cccgc                                                                                                                                             >  3:248210/1‑146 (MQ=255)
      ttCTAAGAGGATCTGGACATTCGACCCGGGCATTGCCGGTGTCAGGAAAAAACCATTAACCGCTGGGGCCGCTTTGCGGCCCTTGGCGGGCACGCCCGCTCCTACAAAGGATTTGCGCCCCCTGTAGGAGGGGGCTT‑GCCC‑GCGAAggg                                                                                                                                       <  4:295545/149‑1 (MQ=255)
      ttCGAAGAGGATCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTT‑GCCC‑GCGAAggg                                                                                                                                       >  4:47679/1‑149 (MQ=255)
        cGAAGAGGATCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTT‑GCCC‑GCGAAggg                                                                                                                                       <  1:61400/147‑1 (MQ=255)
         gAAGAGGATCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTT‑GCCC‑GCGAAGGGCTg                                                                                                                                    >  2:13746/1‑149 (MQ=255)
              ggATCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTT‑GCCC‑GCGAAGGGCTGCAAgg                                                                                                                               <  2:263137/149‑1 (MQ=255)
                             aCAGCGGCATTGCAGGACCCCCTAAAATCGCAGTAACCCCTGGGCCCGCTTTGGGCCCGTTCGCGGGCACCCCCGCTCCAACAAAGCATATCCGCCCCCTTTCGGCGGGGGCTT‑GCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTc                                                                                                                <  4:327039/149‑1 (MQ=255)
                                  ggCTTTGCAGGTCTCACGAAAATAGCAGTAAACGGTGGGGCCGCTTTGGGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGGGGGCTT‑GCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTc                                                                                                                <  4:79471/144‑1 (MQ=37)
                                  ggCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTT‑GCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTc                                                                                                                >  3:79471/1‑144 (MQ=255)
                                                 aCGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGCGCGGGCTT‑GCCC‑GCGAGGGGCTGCAAGGCAGCCCCAAATTGTCGCCTACGCGGGTCAgggctg                                                                                            >  8:373791/1‑144 (MQ=37)
                                                 aCGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTT‑GCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATc                                                                                            <  6:132314/149‑1 (MQ=255)
                                                 aCGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTT‑GCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATc                                                                                            >  6:198211/1‑149 (MQ=255)
                                                       aTAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTT‑GCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAg                                                                                      <  6:188809/149‑1 (MQ=255)
                                                                 aCGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTT‑GCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTc                                                                            <  5:198211/149‑1 (MQ=255)
                                                                 aCGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTT‑G‑CCTGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTc                                                                            <  5:19134/149‑1 (MQ=255)
                                                                          ccGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTT‑GCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGa                                                                   <  3:342917/149‑1 (MQ=255)
                                                                            gCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTT‑GCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGCCTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAAt                                                                 >  2:54066/1‑149 (MQ=255)
                                                                               ttGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTT‑GCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATc                                                                >  5:365585/1‑147 (MQ=255)
                                                                                 gCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTT‑GCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGagc                                                            >  2:315861/1‑149 (MQ=255)
                                                                                    gCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTACCCTGTAGGAGCGGGCTT‑GCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATACGGCAGGGTGATGTTCAGCTCCAGAATCGatcc                                                           >  4:312427/1‑144 (MQ=38)
                                                                                          cgcgGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTT‑GCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGccc                                                    <  1:13746/148‑1 (MQ=255)
                                                                                           gcgGGCACGCCCGCTCCTACAAAGGATATGCTGCCCCGGTAGGCGCGGGCTT‑GCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCt                                                   <  4:248210/148‑1 (MQ=255)
                                                                                           gcgGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTT‑GCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTg                                                  >  5:152403/1‑149 (MQ=255)
                                                                                                           cTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTT‑GCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGTTCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGat                                   <  1:315861/148‑1 (MQ=255)
                                                                                                            tACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTT‑GCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGatat                                 >  7:224872/1‑149 (MQ=255)
                                                                                                             aCAAAGGATATGCGTCCCCTGTAGGAGCGGGCTT‑GCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGat                                   <  8:72677/146‑1 (MQ=255)
                                                                                                             aCAAAGGATATGCGTCCCCTGTAGGAGCGGGCTT‑GCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGat                                   >  7:72677/1‑146 (MQ=255)
                                                                                                              cAAAGGATATGCGTCCCCTGTAGGAGCGGGCTT‑GCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATg                                >  8:250570/1‑148 (MQ=255)
                                                                                                               aaaGGATATGCGTCCCCTGTAGGAGCGGGCTT‑GCCC‑GCGAAGGGCAGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATCTTAAGCTCCAGAATCGAGCAGCTGCCCTCGTTTTCCAGCTCGATATGc                               >  6:332216/1‑148 (MQ=39)
                                                                                                                     tatGCGTCCCCTGTAGGAGCGGGCTT‑GCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCAcatcat                        >  6:206252/1‑149 (MQ=255)
                                                                                                                        gCGTCCCCTGTAGGAGCGGGCTTAC‑CC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGtt                                               <  8:224213/123‑1 (MQ=255)
                                                                                                                        gCGTCCCCTGTAGGAGCGGGCTTAC‑CC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGtt                                               >  7:224213/1‑123 (MQ=255)
                                                                                                                        gCGTCCCCTGTAGGAGCGGGCTT‑GCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGt                     >  4:247082/1‑149 (MQ=255)
                                                                                                                        gCGTCCCCTGTAGGAGCGGGCTT‑GCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGt                     >  6:8755/1‑149 (MQ=255)
                                                                                                                         cGTCCCCTGTAGGAGCGGGCTT‑GCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGtt                    >  6:240553/1‑149 (MQ=255)
                                                                                                                         cGTCCCCTGTAGGAGCGGGCTT‑GCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGGTTTCCAGCTCGATATGCACATCATCGtt                    >  6:246002/1‑149 (MQ=255)
                                                                                                                          gTCCCCTGTAGGAGCGGGCTT‑GCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTg                   <  5:206252/149‑1 (MQ=255)
                                                                                                                             cccTGTAGGAGCGGGCTT‑GCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGCTCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCg                <  7:250570/149‑1 (MQ=255)
                                                                                                                                    gtaGCGGTCTT‑GCCC‑GCGAAGGGCTTCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTc          <  3:47679/146‑1 (MQ=255)
                                                                                                                                      aGCGGGCTT‑GCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTcaca       <  6:2318/149‑1 (MQ=255)
                                                                                                                                           gCTT‑GCCC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATAttt  >  7:210531/1‑149 (MQ=255)
                                                                                                                                                 |                                                                                                                                                
GGCGTCTTCGAAGAGGATCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTT‑G‑CC‑GCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATATTT  >  NC_002947/1932495‑1932781

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: ‑